0.009871
0.005699
0.000000
0.000000
0.011398
0.000000
0.000000
0.000000
0.005870
0.00000
0.00000
0.00000
Patel, S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
101.303
101.303
170.355
C18 H18 N4 O
306.362
N~3~-[3-(5-METHOXYPYRIDIN-3-YL)BENZYL]PYRIDINE-2,3-DIAMINE
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C2 H6 O S
78.133
DIMETHYL SULFOXIDE
non-polymer
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
I -1
126.904
IODIDE ION
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
C
N
2
N
O
Y
3
N
C
Y
4
N
C
Y
5
N
N
Y
6
N
C
Y
7
N
C
Y
8
N
C
Y
9
N
C
Y
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
N
14
N
C
N
15
N
N
Y
16
N
C
Y
17
N
C
Y
18
N
C
Y
19
N
C
Y
20
N
N
Y
21
N
C
N
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
N
N
43
S
C
N
44
N
C
N
45
N
O
N
46
N
C
N
47
N
O
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
N
N
56
S
C
N
57
N
C
N
58
N
O
N
59
N
C
N
60
N
C
N
61
N
C
N
62
N
N
N
63
N
C
N
64
N
N
N
65
N
N
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
N
N
83
S
C
N
84
N
C
N
85
N
O
N
86
N
C
N
87
N
C
N
88
N
O
N
89
N
N
N
90
N
O
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
N
N
100
S
C
N
101
N
C
N
102
N
O
N
103
N
C
N
104
N
C
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
N
N
116
R
C
N
117
N
C
N
118
N
O
N
119
N
C
N
120
N
S
N
121
N
O
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
S
N
130
N
O
N
131
N
C
N
132
N
C
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
N
N
140
S
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
C
N
145
N
C
N
146
N
O
N
147
N
N
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
N
N
160
S
C
N
161
N
C
N
162
N
O
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
N
N
179
N
C
N
180
N
C
N
181
N
O
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
Y
193
N
C
Y
194
N
N
Y
195
N
C
Y
196
N
C
Y
197
N
N
N
198
N
O
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
O
N
210
N
H
N
211
N
H
N
212
N
N
N
213
S
C
N
214
N
C
N
215
N
O
N
216
S
C
N
217
N
C
N
218
N
C
N
219
N
C
N
220
N
O
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
I
N
235
N
N
N
236
S
C
N
237
N
C
N
238
N
O
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
C
N
243
N
O
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
N
N
258
S
C
N
259
N
C
N
260
N
O
N
261
N
C
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
N
N
266
N
O
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
N
N
283
S
C
N
284
N
C
N
285
N
O
N
286
N
C
N
287
N
C
N
288
N
S
N
289
N
C
N
290
N
O
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
N
N
303
S
C
N
304
N
C
N
305
N
O
N
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
311
N
C
Y
312
N
C
N
313
N
O
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
N
330
N
C
N
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
N
C
N
347
N
O
N
348
N
O
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
R
C
N
361
N
O
N
362
N
C
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
N
N
374
S
C
N
375
N
C
N
376
N
O
N
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
Y
381
N
N
Y
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
N
387
N
O
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
N
411
N
O
N
412
N
O
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
N
N
425
S
C
N
426
N
C
N
427
N
O
N
428
N
C
N
429
N
C
N
430
N
C
N
431
N
O
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
Y
6
N
doub
Y
7
N
sing
Y
8
N
sing
N
9
N
sing
Y
10
N
doub
Y
11
N
sing
N
12
N
sing
Y
13
N
doub
Y
14
N
sing
N
15
N
sing
Y
16
N
doub
Y
17
N
sing
Y
18
N
doub
N
19
N
sing
Y
20
N
sing
N
21
N
sing
Y
22
N
doub
N
23
N
sing
Y
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
Y
31
N
sing
Y
32
N
doub
Y
33
N
sing
N
34
N
sing
Y
35
N
doub
N
36
N
sing
Y
37
N
sing
N
38
N
sing
Y
39
N
doub
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
doub
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
doub
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
doub
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
doub
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
doub
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
doub
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
doub
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
Y
192
N
sing
Y
193
N
doub
Y
194
N
doub
N
195
N
sing
Y
196
N
sing
N
197
N
sing
Y
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
doub
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
doub
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
doub
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
doub
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
Y
300
N
doub
Y
301
N
sing
Y
302
N
sing
N
303
N
sing
Y
304
N
doub
N
305
N
sing
Y
306
N
doub
N
307
N
sing
Y
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
doub
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
doub
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
doub
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
Y
369
N
doub
Y
370
N
sing
Y
371
N
sing
N
372
N
sing
Y
373
N
doub
Y
374
N
sing
Y
375
N
sing
N
376
N
sing
Y
377
N
sing
Y
378
N
doub
N
379
N
sing
Y
380
N
doub
N
381
N
sing
Y
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
Y
397
N
doub
Y
398
N
sing
Y
399
N
sing
N
400
N
sing
Y
401
N
doub
N
402
N
sing
Y
403
N
doub
N
404
N
sing
Y
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
doub
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
US
J.Med.Chem.
JMCMAR
0151
0022-2623
50
1124
1132
10.1021/jm061197u
17315857
Application of fragment screening by X-ray crystallography to the discovery of aminopyridines as inhibitors of beta-secretase.
2007
10.2210/pdb2ohs/pdb
pdb_00002ohs
CHIRALITY ERRORS AT RESIDUE A 106
100
1
CCD
2004-02-23
MAR CCD 165 mm
SINGLE WAVELENGTH
M
x-ray
1
0.93100
1.0
ID14-3
ESRF
0.93100
SYNCHROTRON
ESRF BEAMLINE ID14-3
44841.395
Beta-secretase 1
3.4.23.46
protease domain
R56K, R57K
1
man
polymer
126.904
IODIDE ION
2
syn
non-polymer
78.133
DIMETHYL SULFOXIDE
1
syn
non-polymer
306.362
N~3~-[3-(5-METHOXYPYRIDIN-3-YL)BENZYL]PYRIDINE-2,3-DIAMINE
1
syn
non-polymer
18.015
water
209
nat
water
Beta-site APP cleaving enzyme 1, Beta-site amyloid precursor protein cleaving enzyme 1, Membrane-associated aspartic protease 2, Memapsin-2, Aspartyl protease 2, Asp 2, ASP2
no
no
RETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDL
RKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQ
THVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYD
KSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCG
YN
RETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDL
RKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQ
THVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYD
KSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCG
YN
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
Homo
Escherichia
Escherichia coli
sample
BACE1, BACE
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
BL21(DE3)
plasmid
pET
1
2.81
56.26
VAPOR DIFFUSION, HANGING DROP
6.6
20-22.5% (w/v) PEG 5000 monomethylether (MME), 200 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
software
database_2
struct_ref_seq_dif
struct_site
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Database references
Derived calculations
Data collection
Refinement description
1
0
2007-03-13
1
1
2008-05-01
1
2
2011-07-13
1
3
2017-10-18
1
4
2021-10-20
1
5
2023-08-30
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal structure of beta secretase complexed with compound 5
Crystal structure of beta secretase complexed with 1-amino-isoquinoline
Crystal structure of beta secretase complexed with 2-aminoquinoline
Crystal structure of beta secretase complexed with 2,3-diaminopyridine
Crystal structure of beta secretase complexed with compound 4
Crystal structure of beta secretase complexed with compound 3
Crystal structure of beta secretase complexed with compound 4
Crystal structure of beta secretase complexed with compound 6a
Crystal structure of beta secretase complexed with compound 7
Crystal structure of beta secretase complexed with compound 8b
HETEROGEN
THERE IS AN EXTRA ATOM H21 IN MOLECULE 9IP. AUTHOR STATES
THAT THE MOLECULE 9IP IS PROTONATED (CHARGED) UNDER THE
PH CONDITIONS OF THE EXPERIMENT, AND THIS PROTONATION
STATE IS CRITICAL TO THE BINDING MODE OBSERVED.
RCSB
Y
RCSB
2007-01-10
REL
REL
IOD
IODIDE ION
DMS
DIMETHYL SULFOXIDE
9IP
N~3~-[3-(5-METHOXYPYRIDIN-3-YL)BENZYL]PYRIDINE-2,3-DIAMINE
HOH
water
1W50
PDB entry 1W50
PDB
experimental model
IOD
301
2
IOD
IOD
386
A
IOD
302
2
IOD
IOD
387
A
DMS
303
3
DMS
DMS
388
A
9IP
1
4
9IP
9IP
389
A
HOH
2
5
HOH
HOH
390
A
HOH
3
5
HOH
HOH
391
A
HOH
4
5
HOH
HOH
392
A
HOH
5
5
HOH
HOH
393
A
HOH
6
5
HOH
HOH
394
A
HOH
7
5
HOH
HOH
395
A
HOH
8
5
HOH
HOH
396
A
HOH
9
5
HOH
HOH
397
A
HOH
10
5
HOH
HOH
398
A
HOH
11
5
HOH
HOH
399
A
HOH
12
5
HOH
HOH
400
A
HOH
13
5
HOH
HOH
401
A
HOH
14
5
HOH
HOH
402
A
HOH
15
5
HOH
HOH
403
A
HOH
16
5
HOH
HOH
404
A
HOH
17
5
HOH
HOH
405
A
HOH
18
5
HOH
HOH
406
A
HOH
19
5
HOH
HOH
407
A
HOH
20
5
HOH
HOH
408
A
HOH
21
5
HOH
HOH
409
A
HOH
22
5
HOH
HOH
410
A
HOH
23
5
HOH
HOH
411
A
HOH
24
5
HOH
HOH
412
A
HOH
25
5
HOH
HOH
413
A
HOH
26
5
HOH
HOH
414
A
HOH
27
5
HOH
HOH
415
A
HOH
28
5
HOH
HOH
416
A
HOH
29
5
HOH
HOH
417
A
HOH
30
5
HOH
HOH
418
A
HOH
31
5
HOH
HOH
419
A
HOH
32
5
HOH
HOH
420
A
HOH
33
5
HOH
HOH
421
A
HOH
34
5
HOH
HOH
422
A
HOH
36
5
HOH
HOH
423
A
HOH
37
5
HOH
HOH
424
A
HOH
38
5
HOH
HOH
425
A
HOH
39
5
HOH
HOH
426
A
HOH
40
5
HOH
HOH
427
A
HOH
43
5
HOH
HOH
428
A
HOH
44
5
HOH
HOH
429
A
HOH
45
5
HOH
HOH
430
A
HOH
47
5
HOH
HOH
431
A
HOH
48
5
HOH
HOH
432
A
HOH
49
5
HOH
HOH
433
A
HOH
50
5
HOH
HOH
434
A
HOH
51
5
HOH
HOH
435
A
HOH
52
5
HOH
HOH
436
A
HOH
55
5
HOH
HOH
437
A
HOH
56
5
HOH
HOH
438
A
HOH
57
5
HOH
HOH
439
A
HOH
58
5
HOH
HOH
440
A
HOH
59
5
HOH
HOH
441
A
HOH
60
5
HOH
HOH
442
A
HOH
61
5
HOH
HOH
443
A
HOH
62
5
HOH
HOH
444
A
HOH
63
5
HOH
HOH
445
A
HOH
65
5
HOH
HOH
446
A
HOH
66
5
HOH
HOH
447
A
HOH
69
5
HOH
HOH
448
A
HOH
71
5
HOH
HOH
449
A
HOH
73
5
HOH
HOH
450
A
HOH
74
5
HOH
HOH
451
A
HOH
75
5
HOH
HOH
452
A
HOH
76
5
HOH
HOH
453
A
HOH
77
5
HOH
HOH
454
A
HOH
80
5
HOH
HOH
455
A
HOH
81
5
HOH
HOH
456
A
HOH
82
5
HOH
HOH
457
A
HOH
83
5
HOH
HOH
458
A
HOH
84
5
HOH
HOH
459
A
HOH
87
5
HOH
HOH
460
A
HOH
88
5
HOH
HOH
461
A
HOH
89
5
HOH
HOH
462
A
HOH
91
5
HOH
HOH
463
A
HOH
92
5
HOH
HOH
464
A
HOH
93
5
HOH
HOH
465
A
HOH
94
5
HOH
HOH
466
A
HOH
96
5
HOH
HOH
467
A
HOH
97
5
HOH
HOH
468
A
HOH
99
5
HOH
HOH
469
A
HOH
100
5
HOH
HOH
470
A
HOH
101
5
HOH
HOH
471
A
HOH
102
5
HOH
HOH
472
A
HOH
105
5
HOH
HOH
473
A
HOH
106
5
HOH
HOH
474
A
HOH
107
5
HOH
HOH
475
A
HOH
108
5
HOH
HOH
476
A
HOH
109
5
HOH
HOH
477
A
HOH
110
5
HOH
HOH
478
A
HOH
112
5
HOH
HOH
479
A
HOH
115
5
HOH
HOH
480
A
HOH
116
5
HOH
HOH
481
A
HOH
120
5
HOH
HOH
482
A
HOH
123
5
HOH
HOH
483
A
HOH
124
5
HOH
HOH
484
A
HOH
126
5
HOH
HOH
485
A
HOH
128
5
HOH
HOH
486
A
HOH
129
5
HOH
HOH
487
A
HOH
130
5
HOH
HOH
488
A
HOH
131
5
HOH
HOH
489
A
HOH
133
5
HOH
HOH
490
A
HOH
135
5
HOH
HOH
491
A
HOH
140
5
HOH
HOH
492
A
HOH
141
5
HOH
HOH
493
A
HOH
142
5
HOH
HOH
494
A
HOH
143
5
HOH
HOH
495
A
HOH
144
5
HOH
HOH
496
A
HOH
145
5
HOH
HOH
497
A
HOH
146
5
HOH
HOH
498
A
HOH
148
5
HOH
HOH
499
A
HOH
150
5
HOH
HOH
500
A
HOH
153
5
HOH
HOH
501
A
HOH
156
5
HOH
HOH
502
A
HOH
157
5
HOH
HOH
503
A
HOH
158
5
HOH
HOH
504
A
HOH
160
5
HOH
HOH
505
A
HOH
161
5
HOH
HOH
506
A
HOH
164
5
HOH
HOH
507
A
HOH
165
5
HOH
HOH
508
A
HOH
166
5
HOH
HOH
509
A
HOH
167
5
HOH
HOH
510
A
HOH
168
5
HOH
HOH
511
A
HOH
169
5
HOH
HOH
512
A
HOH
171
5
HOH
HOH
513
A
HOH
172
5
HOH
HOH
514
A
HOH
173
5
HOH
HOH
515
A
HOH
174
5
HOH
HOH
516
A
HOH
175
5
HOH
HOH
517
A
HOH
176
5
HOH
HOH
518
A
HOH
177
5
HOH
HOH
519
A
HOH
178
5
HOH
HOH
520
A
HOH
179
5
HOH
HOH
521
A
HOH
180
5
HOH
HOH
522
A
HOH
181
5
HOH
HOH
523
A
HOH
182
5
HOH
HOH
524
A
HOH
183
5
HOH
HOH
525
A
HOH
184
5
HOH
HOH
526
A
HOH
186
5
HOH
HOH
527
A
HOH
187
5
HOH
HOH
528
A
HOH
188
5
HOH
HOH
529
A
HOH
189
5
HOH
HOH
530
A
HOH
190
5
HOH
HOH
531
A
HOH
191
5
HOH
HOH
532
A
HOH
192
5
HOH
HOH
533
A
HOH
193
5
HOH
HOH
534
A
HOH
194
5
HOH
HOH
535
A
HOH
195
5
HOH
HOH
536
A
HOH
197
5
HOH
HOH
537
A
HOH
198
5
HOH
HOH
538
A
HOH
200
5
HOH
HOH
539
A
HOH
201
5
HOH
HOH
540
A
HOH
205
5
HOH
HOH
541
A
HOH
207
5
HOH
HOH
542
A
HOH
209
5
HOH
HOH
543
A
HOH
211
5
HOH
HOH
544
A
HOH
212
5
HOH
HOH
545
A
HOH
213
5
HOH
HOH
546
A
HOH
215
5
HOH
HOH
547
A
HOH
216
5
HOH
HOH
548
A
HOH
217
5
HOH
HOH
549
A
HOH
218
5
HOH
HOH
550
A
HOH
220
5
HOH
HOH
551
A
HOH
221
5
HOH
HOH
552
A
HOH
222
5
HOH
HOH
553
A
HOH
223
5
HOH
HOH
554
A
HOH
224
5
HOH
HOH
555
A
HOH
225
5
HOH
HOH
556
A
HOH
226
5
HOH
HOH
557
A
HOH
227
5
HOH
HOH
558
A
HOH
228
5
HOH
HOH
559
A
HOH
229
5
HOH
HOH
560
A
HOH
230
5
HOH
HOH
561
A
HOH
231
5
HOH
HOH
562
A
HOH
232
5
HOH
HOH
563
A
HOH
233
5
HOH
HOH
564
A
HOH
234
5
HOH
HOH
565
A
HOH
235
5
HOH
HOH
566
A
HOH
236
5
HOH
HOH
567
A
HOH
237
5
HOH
HOH
568
A
HOH
238
5
HOH
HOH
569
A
HOH
239
5
HOH
HOH
570
A
HOH
240
5
HOH
HOH
571
A
HOH
241
5
HOH
HOH
572
A
HOH
242
5
HOH
HOH
573
A
HOH
243
5
HOH
HOH
574
A
HOH
244
5
HOH
HOH
575
A
HOH
245
5
HOH
HOH
576
A
HOH
246
5
HOH
HOH
577
A
HOH
247
5
HOH
HOH
578
A
HOH
248
5
HOH
HOH
579
A
HOH
249
5
HOH
HOH
580
A
HOH
250
5
HOH
HOH
581
A
HOH
251
5
HOH
HOH
582
A
HOH
252
5
HOH
HOH
583
A
HOH
253
5
HOH
HOH
584
A
HOH
254
5
HOH
HOH
585
A
HOH
255
5
HOH
HOH
586
A
HOH
256
5
HOH
HOH
587
A
HOH
257
5
HOH
HOH
588
A
HOH
258
5
HOH
HOH
589
A
HOH
259
5
HOH
HOH
590
A
HOH
260
5
HOH
HOH
591
A
HOH
261
5
HOH
HOH
592
A
HOH
262
5
HOH
HOH
593
A
HOH
263
5
HOH
HOH
594
A
HOH
264
5
HOH
HOH
595
A
HOH
265
5
HOH
HOH
596
A
HOH
266
5
HOH
HOH
597
A
HOH
267
5
HOH
HOH
598
A
n
1
-16
A
n
2
-15
A
n
3
-14
A
n
4
-13
A
n
5
-12
A
n
6
-11
A
n
7
-10
A
n
8
-9
A
n
9
-8
A
n
10
-7
A
n
11
-6
A
n
12
-5
A
n
13
-4
A
n
14
-3
A
n
15
-2
A
PHE
-1
n
16
PHE
-1
A
VAL
0
n
17
VAL
0
A
GLU
1
n
18
GLU
1
A
MET
2
n
19
MET
2
A
VAL
3
n
20
VAL
3
A
ASP
4
n
21
ASP
4
A
ASN
5
n
22
ASN
5
A
LEU
6
n
23
LEU
6
A
ARG
7
n
24
ARG
7
A
GLY
8
n
25
GLY
8
A
LYS
9
n
26
LYS
9
A
SER
10
n
27
SER
10
A
GLY
11
n
28
GLY
11
A
GLN
12
n
29
GLN
12
A
GLY
13
n
30
GLY
13
A
TYR
14
n
31
TYR
14
A
TYR
15
n
32
TYR
15
A
VAL
16
n
33
VAL
16
A
GLU
17
n
34
GLU
17
A
MET
18
n
35
MET
18
A
THR
19
n
36
THR
19
A
VAL
20
n
37
VAL
20
A
GLY
21
n
38
GLY
21
A
SER
22
n
39
SER
22
A
PRO
23
n
40
PRO
23
A
PRO
24
n
41
PRO
24
A
GLN
25
n
42
GLN
25
A
THR
26
n
43
THR
26
A
LEU
27
n
44
LEU
27
A
ASN
28
n
45
ASN
28
A
ILE
29
n
46
ILE
29
A
LEU
30
n
47
LEU
30
A
VAL
31
n
48
VAL
31
A
ASP
32
n
49
ASP
32
A
THR
33
n
50
THR
33
A
GLY
34
n
51
GLY
34
A
SER
35
n
52
SER
35
A
SER
36
n
53
SER
36
A
ASN
37
n
54
ASN
37
A
PHE
38
n
55
PHE
38
A
ALA
39
n
56
ALA
39
A
VAL
40
n
57
VAL
40
A
GLY
41
n
58
GLY
41
A
ALA
42
n
59
ALA
42
A
ALA
43
n
60
ALA
43
A
PRO
44
n
61
PRO
44
A
HIS
45
n
62
HIS
45
A
PRO
46
n
63
PRO
46
A
PHE
47
n
64
PHE
47
A
LEU
48
n
65
LEU
48
A
HIS
49
n
66
HIS
49
A
ARG
50
n
67
ARG
50
A
TYR
51
n
68
TYR
51
A
TYR
52
n
69
TYR
52
A
GLN
53
n
70
GLN
53
A
ARG
54
n
71
ARG
54
A
GLN
55
n
72
GLN
55
A
LEU
56
n
73
LEU
56
A
SER
57
n
74
SER
57
A
SER
58
n
75
SER
58
A
THR
59
n
76
THR
59
A
TYR
60
n
77
TYR
60
A
ARG
61
n
78
ARG
61
A
ASP
62
n
79
ASP
62
A
LEU
63
n
80
LEU
63
A
ARG
64
n
81
ARG
64
A
LYS
65
n
82
LYS
65
A
GLY
66
n
83
GLY
66
A
VAL
67
n
84
VAL
67
A
TYR
68
n
85
TYR
68
A
VAL
69
n
86
VAL
69
A
PRO
70
n
87
PRO
70
A
TYR
71
n
88
TYR
71
A
THR
72
n
89
THR
72
A
GLN
73
n
90
GLN
73
A
GLY
74
n
91
GLY
74
A
LYS
75
n
92
LYS
75
A
TRP
76
n
93
TRP
76
A
GLU
77
n
94
GLU
77
A
GLY
78
n
95
GLY
78
A
GLU
79
n
96
GLU
79
A
LEU
80
n
97
LEU
80
A
GLY
81
n
98
GLY
81
A
THR
82
n
99
THR
82
A
ASP
83
n
100
ASP
83
A
LEU
84
n
101
LEU
84
A
VAL
85
n
102
VAL
85
A
SER
86
n
103
SER
86
A
ILE
87
n
104
ILE
87
A
PRO
88
n
105
PRO
88
A
HIS
89
n
106
HIS
89
A
GLY
90
n
107
GLY
90
A
PRO
91
n
108
PRO
91
A
ASN
92
n
109
ASN
92
A
VAL
93
n
110
VAL
93
A
THR
94
n
111
THR
94
A
VAL
95
n
112
VAL
95
A
ARG
96
n
113
ARG
96
A
ALA
97
n
114
ALA
97
A
ASN
98
n
115
ASN
98
A
ILE
99
n
116
ILE
99
A
ALA
100
n
117
ALA
100
A
ALA
101
n
118
ALA
101
A
ILE
102
n
119
ILE
102
A
THR
103
n
120
THR
103
A
GLU
104
n
121
GLU
104
A
SER
105
n
122
SER
105
A
ASP
106
n
123
ASP
106
A
LYS
107
n
124
LYS
107
A
PHE
108
n
125
PHE
108
A
PHE
109
n
126
PHE
109
A
ILE
110
n
127
ILE
110
A
ASN
111
n
128
ASN
111
A
GLY
112
n
129
GLY
112
A
SER
113
n
130
SER
113
A
ASN
114
n
131
ASN
114
A
TRP
115
n
132
TRP
115
A
GLU
116
n
133
GLU
116
A
GLY
117
n
134
GLY
117
A
ILE
118
n
135
ILE
118
A
LEU
119
n
136
LEU
119
A
GLY
120
n
137
GLY
120
A
LEU
121
n
138
LEU
121
A
ALA
122
n
139
ALA
122
A
TYR
123
n
140
TYR
123
A
ALA
124
n
141
ALA
124
A
GLU
125
n
142
GLU
125
A
ILE
126
n
143
ILE
126
A
ALA
127
n
144
ALA
127
A
ARG
128
n
145
ARG
128
A
PRO
129
n
146
PRO
129
A
ASP
130
n
147
ASP
130
A
ASP
131
n
148
ASP
131
A
SER
132
n
149
SER
132
A
LEU
133
n
150
LEU
133
A
GLU
134
n
151
GLU
134
A
PRO
135
n
152
PRO
135
A
PHE
136
n
153
PHE
136
A
PHE
137
n
154
PHE
137
A
ASP
138
n
155
ASP
138
A
SER
139
n
156
SER
139
A
LEU
140
n
157
LEU
140
A
VAL
141
n
158
VAL
141
A
LYS
142
n
159
LYS
142
A
GLN
143
n
160
GLN
143
A
THR
144
n
161
THR
144
A
HIS
145
n
162
HIS
145
A
VAL
146
n
163
VAL
146
A
PRO
147
n
164
PRO
147
A
ASN
148
n
165
ASN
148
A
LEU
149
n
166
LEU
149
A
PHE
150
n
167
PHE
150
A
SER
151
n
168
SER
151
A
LEU
152
n
169
LEU
152
A
GLN
153
n
170
GLN
153
A
LEU
154
n
171
LEU
154
A
CYS
155
n
172
CYS
155
A
GLY
156
n
173
GLY
156
A
ALA
157
n
174
ALA
157
A
n
175
158
A
n
176
159
A
n
177
160
A
n
178
161
A
n
179
162
A
n
180
163
A
n
181
164
A
n
182
165
A
n
183
166
A
n
184
167
A
n
185
168
A
n
186
169
A
n
187
170
A
GLY
171
n
188
GLY
171
A
GLY
172
n
189
GLY
172
A
SER
173
n
190
SER
173
A
MET
174
n
191
MET
174
A
ILE
175
n
192
ILE
175
A
ILE
176
n
193
ILE
176
A
GLY
177
n
194
GLY
177
A
GLY
178
n
195
GLY
178
A
ILE
179
n
196
ILE
179
A
ASP
180
n
197
ASP
180
A
HIS
181
n
198
HIS
181
A
SER
182
n
199
SER
182
A
LEU
183
n
200
LEU
183
A
TYR
184
n
201
TYR
184
A
THR
185
n
202
THR
185
A
GLY
186
n
203
GLY
186
A
SER
187
n
204
SER
187
A
LEU
188
n
205
LEU
188
A
TRP
189
n
206
TRP
189
A
TYR
190
n
207
TYR
190
A
THR
191
n
208
THR
191
A
PRO
192
n
209
PRO
192
A
ILE
193
n
210
ILE
193
A
ARG
194
n
211
ARG
194
A
ARG
195
n
212
ARG
195
A
GLU
196
n
213
GLU
196
A
TRP
197
n
214
TRP
197
A
TYR
198
n
215
TYR
198
A
TYR
199
n
216
TYR
199
A
GLU
200
n
217
GLU
200
A
VAL
201
n
218
VAL
201
A
ILE
202
n
219
ILE
202
A
ILE
203
n
220
ILE
203
A
VAL
204
n
221
VAL
204
A
ARG
205
n
222
ARG
205
A
VAL
206
n
223
VAL
206
A
GLU
207
n
224
GLU
207
A
ILE
208
n
225
ILE
208
A
ASN
209
n
226
ASN
209
A
GLY
210
n
227
GLY
210
A
GLN
211
n
228
GLN
211
A
ASP
212
n
229
ASP
212
A
LEU
213
n
230
LEU
213
A
LYS
214
n
231
LYS
214
A
MET
215
n
232
MET
215
A
ASP
216
n
233
ASP
216
A
CYS
217
n
234
CYS
217
A
LYS
218
n
235
LYS
218
A
GLU
219
n
236
GLU
219
A
TYR
220
n
237
TYR
220
A
ASN
221
n
238
ASN
221
A
TYR
222
n
239
TYR
222
A
ASP
223
n
240
ASP
223
A
LYS
224
n
241
LYS
224
A
SER
225
n
242
SER
225
A
ILE
226
n
243
ILE
226
A
VAL
227
n
244
VAL
227
A
ASP
228
n
245
ASP
228
A
SER
229
n
246
SER
229
A
GLY
230
n
247
GLY
230
A
THR
231
n
248
THR
231
A
THR
232
n
249
THR
232
A
ASN
233
n
250
ASN
233
A
LEU
234
n
251
LEU
234
A
ARG
235
n
252
ARG
235
A
LEU
236
n
253
LEU
236
A
PRO
237
n
254
PRO
237
A
LYS
238
n
255
LYS
238
A
LYS
239
n
256
LYS
239
A
VAL
240
n
257
VAL
240
A
PHE
241
n
258
PHE
241
A
GLU
242
n
259
GLU
242
A
ALA
243
n
260
ALA
243
A
ALA
244
n
261
ALA
244
A
VAL
245
n
262
VAL
245
A
LYS
246
n
263
LYS
246
A
SER
247
n
264
SER
247
A
ILE
248
n
265
ILE
248
A
LYS
249
n
266
LYS
249
A
ALA
250
n
267
ALA
250
A
ALA
251
n
268
ALA
251
A
SER
252
n
269
SER
252
A
SER
253
n
270
SER
253
A
THR
254
n
271
THR
254
A
GLU
255
n
272
GLU
255
A
LYS
256
n
273
LYS
256
A
PHE
257
n
274
PHE
257
A
PRO
258
n
275
PRO
258
A
ASP
259
n
276
ASP
259
A
GLY
260
n
277
GLY
260
A
PHE
261
n
278
PHE
261
A
TRP
262
n
279
TRP
262
A
LEU
263
n
280
LEU
263
A
GLY
264
n
281
GLY
264
A
GLU
265
n
282
GLU
265
A
GLN
266
n
283
GLN
266
A
LEU
267
n
284
LEU
267
A
VAL
268
n
285
VAL
268
A
CYS
269
n
286
CYS
269
A
TRP
270
n
287
TRP
270
A
GLN
271
n
288
GLN
271
A
ALA
272
n
289
ALA
272
A
GLY
273
n
290
GLY
273
A
THR
274
n
291
THR
274
A
THR
275
n
292
THR
275
A
PRO
276
n
293
PRO
276
A
TRP
277
n
294
TRP
277
A
ASN
278
n
295
ASN
278
A
ILE
279
n
296
ILE
279
A
PHE
280
n
297
PHE
280
A
PRO
281
n
298
PRO
281
A
VAL
282
n
299
VAL
282
A
ILE
283
n
300
ILE
283
A
SER
284
n
301
SER
284
A
LEU
285
n
302
LEU
285
A
TYR
286
n
303
TYR
286
A
LEU
287
n
304
LEU
287
A
MET
288
n
305
MET
288
A
GLY
289
n
306
GLY
289
A
GLU
290
n
307
GLU
290
A
VAL
291
n
308
VAL
291
A
THR
292
n
309
THR
292
A
ASN
293
n
310
ASN
293
A
GLN
294
n
311
GLN
294
A
SER
295
n
312
SER
295
A
PHE
296
n
313
PHE
296
A
ARG
297
n
314
ARG
297
A
ILE
298
n
315
ILE
298
A
THR
299
n
316
THR
299
A
ILE
300
n
317
ILE
300
A
LEU
301
n
318
LEU
301
A
PRO
302
n
319
PRO
302
A
GLN
303
n
320
GLN
303
A
GLN
304
n
321
GLN
304
A
TYR
305
n
322
TYR
305
A
LEU
306
n
323
LEU
306
A
ARG
307
n
324
ARG
307
A
PRO
308
n
325
PRO
308
A
VAL
309
n
326
VAL
309
A
GLU
310
n
327
GLU
310
A
ASP
311
n
328
ASP
311
A
VAL
312
n
329
VAL
312
A
ALA
313
n
330
ALA
313
A
THR
314
n
331
THR
314
A
SER
315
n
332
SER
315
A
GLN
316
n
333
GLN
316
A
ASP
317
n
334
ASP
317
A
ASP
318
n
335
ASP
318
A
CYS
319
n
336
CYS
319
A
TYR
320
n
337
TYR
320
A
LYS
321
n
338
LYS
321
A
PHE
322
n
339
PHE
322
A
ALA
323
n
340
ALA
323
A
ILE
324
n
341
ILE
324
A
SER
325
n
342
SER
325
A
GLN
326
n
343
GLN
326
A
SER
327
n
344
SER
327
A
SER
328
n
345
SER
328
A
THR
329
n
346
THR
329
A
GLY
330
n
347
GLY
330
A
THR
331
n
348
THR
331
A
VAL
332
n
349
VAL
332
A
MET
333
n
350
MET
333
A
GLY
334
n
351
GLY
334
A
ALA
335
n
352
ALA
335
A
VAL
336
n
353
VAL
336
A
ILE
337
n
354
ILE
337
A
MET
338
n
355
MET
338
A
GLU
339
n
356
GLU
339
A
GLY
340
n
357
GLY
340
A
PHE
341
n
358
PHE
341
A
TYR
342
n
359
TYR
342
A
VAL
343
n
360
VAL
343
A
VAL
344
n
361
VAL
344
A
PHE
345
n
362
PHE
345
A
ASP
346
n
363
ASP
346
A
ARG
347
n
364
ARG
347
A
ALA
348
n
365
ALA
348
A
ARG
349
n
366
ARG
349
A
LYS
350
n
367
LYS
350
A
ARG
351
n
368
ARG
351
A
ILE
352
n
369
ILE
352
A
GLY
353
n
370
GLY
353
A
PHE
354
n
371
PHE
354
A
ALA
355
n
372
ALA
355
A
VAL
356
n
373
VAL
356
A
SER
357
n
374
SER
357
A
ALA
358
n
375
ALA
358
A
CYS
359
n
376
CYS
359
A
HIS
360
n
377
HIS
360
A
VAL
361
n
378
VAL
361
A
HIS
362
n
379
HIS
362
A
ASP
363
n
380
ASP
363
A
GLU
364
n
381
GLU
364
A
PHE
365
n
382
PHE
365
A
ARG
366
n
383
ARG
366
A
THR
367
n
384
THR
367
A
ALA
368
n
385
ALA
368
A
ALA
369
n
386
ALA
369
A
VAL
370
n
387
VAL
370
A
GLU
371
n
388
GLU
371
A
GLY
372
n
389
GLY
372
A
PRO
373
n
390
PRO
373
A
PHE
374
n
391
PHE
374
A
VAL
375
n
392
VAL
375
A
THR
376
n
393
THR
376
A
LEU
377
n
394
LEU
377
A
ASP
378
n
395
ASP
378
A
MET
379
n
396
MET
379
A
GLU
380
n
397
GLU
380
A
ASP
381
n
398
ASP
381
A
CYS
382
n
399
CYS
382
A
GLY
383
n
400
GLY
383
A
TYR
384
n
401
TYR
384
A
ASN
385
n
402
ASN
385
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ARG
7
A
N
ARG
24
A
O
TYR
15
A
O
TYR
32
A
N
TYR
14
A
N
TYR
31
A
O
VAL
31
A
O
VAL
48
A
N
LEU
30
A
N
LEU
47
A
O
LEU
119
A
O
LEU
136
A
O
ILE
118
A
O
ILE
135
A
N
ALA
39
A
N
ALA
56
A
N
VAL
40
A
N
VAL
57
A
O
ILE
102
A
O
ILE
119
A
O
ASP
106
A
O
ASP
123
A
N
LYS
75
A
N
LYS
92
A
O
LEU
80
A
O
LEU
97
A
N
LYS
65
A
N
LYS
82
A
N
ARG
7
A
N
ARG
24
A
O
TYR
15
A
O
TYR
32
A
N
THR
19
A
N
THR
36
A
O
SER
86
A
O
SER
103
A
O
LEU
80
A
O
LEU
97
A
N
LYS
65
A
N
LYS
82
A
O
SER
173
A
O
SER
190
A
N
GLN
153
A
N
GLN
170
A
N
PHE
150
A
N
PHE
167
A
O
PHE
345
A
O
PHE
362
A
N
TYR
342
A
N
TYR
359
A
O
ALA
355
A
O
ALA
372
A
O
ILE
352
A
O
ILE
369
A
N
THR
191
A
N
THR
208
A
N
VAL
201
A
N
VAL
218
A
O
SER
225
A
O
SER
242
A
N
ILE
226
A
N
ILE
243
A
O
MET
333
A
O
MET
350
A
O
VAL
332
A
O
VAL
349
A
N
ARG
235
A
N
ARG
252
A
N
LEU
236
A
N
LEU
253
A
O
SER
327
A
O
SER
344
A
O
GLN
211
A
O
GLN
228
A
N
ILE
208
A
N
ILE
225
A
N
ARG
205
A
N
ARG
222
A
O
TYR
286
A
O
TYR
303
A
N
ILE
283
A
N
ILE
300
A
O
ILE
300
A
O
ILE
317
A
N
ARG
297
A
N
ARG
314
A
O
GLU
371
A
O
GLU
388
A
N
TRP
270
A
N
TRP
287
A
O
ASP
318
A
O
ASP
335
A
O
LYS
321
A
O
LYS
338
A
N
ARG
307
A
N
ARG
324
1
A
HOH
554
F
HOH
1
A
ARG
-16
A
ARG
1
1
Y
1
A
GLU
-15
A
GLU
2
1
Y
1
A
THR
-14
A
THR
3
1
Y
1
A
ASP
-13
A
ASP
4
1
Y
1
A
GLU
-12
A
GLU
5
1
Y
1
A
GLU
-11
A
GLU
6
1
Y
1
A
PRO
-10
A
PRO
7
1
Y
1
A
GLU
-9
A
GLU
8
1
Y
1
A
GLU
-8
A
GLU
9
1
Y
1
A
PRO
-7
A
PRO
10
1
Y
1
A
GLY
-6
A
GLY
11
1
Y
1
A
LYS
-5
A
LYS
12
1
Y
1
A
LYS
-4
A
LYS
13
1
Y
1
A
GLY
-3
A
GLY
14
1
Y
1
A
SER
-2
A
SER
15
1
Y
1
A
GLY
158
A
GLY
175
1
Y
1
A
PHE
159
A
PHE
176
1
Y
1
A
PRO
160
A
PRO
177
1
Y
1
A
LEU
161
A
LEU
178
1
Y
1
A
ASN
162
A
ASN
179
1
Y
1
A
GLN
163
A
GLN
180
1
Y
1
A
SER
164
A
SER
181
1
Y
1
A
GLU
165
A
GLU
182
1
Y
1
A
VAL
166
A
VAL
183
1
Y
1
A
LEU
167
A
LEU
184
1
Y
1
A
ALA
168
A
ALA
185
1
Y
1
A
SER
169
A
SER
186
1
Y
1
A
VAL
170
A
VAL
187
1
Y
1
A
A
O
O
HOH
HOH
390
464
2.04
1
A
A
NE2
O
HIS
HOH
360
396
2.15
1
A
A
OE1
O
GLU
HOH
125
517
2.17
1
12.75
2.00
110.40
123.15
A
A
A
CB
CA
C
ASP
ASP
ASP
106
106
106
N
1
A
LYS
75
177.55
164.22
1
A
HIS
89
-109.11
48.57
1
A
PHE
108
-103.82
-64.80
1
A
CYS
155
-108.13
-106.33
1
A
TRP
197
-142.61
-86.36
1
A
ARG
205
-172.23
144.75
1
A
GLU
310
-78.82
-141.38
1
A
ASP
311
-51.42
103.43
1
A
VAL
312
-86.89
-107.03
1
A
THR
314
-152.67
80.14
1
A
GLN
316
-142.98
25.40
1
A
ASP
317
-109.54
-150.45
1
A
LYS
350
36.44
57.58
24.868
-0.930
-0.460
0.000
-0.930
0.000
1.390
0.943
0.897
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.251
0.182
0.185
0.185
2.450
50.650
947
18681
18681
5.100
94.890
7.784
0.176
RANDOM
1
THROUGHOUT
0.00
MOLECULAR REPLACEMENT
0.369
0.270
0.800
0.800
1.200
PDB entry 1W50
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.450
50.650
209
3205
48
0
2948
0.013
0.022
3054
0.001
0.020
2049
1.478
1.945
4151
0.988
2.991
4959
6.872
5.000
372
34.052
23.678
143
16.474
15.000
482
17.123
15.000
17
0.154
0.200
448
0.004
0.020
3421
0.001
0.020
656
0.208
0.200
599
0.205
0.200
2172
0.191
0.200
1490
0.089
0.200
1631
0.185
0.200
48
0.197
0.200
20
0.254
0.200
49
0.118
0.200
2
0.062
5.000
1856
0.022
5.000
761
0.091
6.000
3003
0.100
6.000
1198
0.127
7.500
1148
0.361
0.226
2.514
59
1148
1207
20
85.420
2.45
50.65
2OHS
18681
18681
0.0
0.118
1
95.8
refinement
Murshudov, G.N.
ccp4@dl.ac.uk
Fortran_77
http://www.ccp4.ac.uk/main.html
REFMAC
program
5.2.0019g
data extraction
PDB
sw-help@rcsb.rutgers.edu
April. 3, 2006
C++
http://pdb.rutgers.edu/software/
PDB_EXTRACT
package
2.000
data collection
ProDC
data reduction
MOSFLM
data scaling
CCP4
(SCALA)
phasing
C-SEARCH
(IN-HOUSE MR PROGRAM
X-ray crystal structure of beta secretase complexed with compound 6b
1
N
N
2
N
N
2
N
N
3
N
N
4
N
N
5
N
N
The biological assembly is a monomer
A
GLN
53
A
GLN
70
HELX_P
A
SER
57
A
SER
74
5
1
5
A
TYR
123
A
TYR
140
HELX_P
A
ALA
127
A
ALA
144
5
2
5
A
PRO
135
A
PRO
152
HELX_P
A
THR
144
A
THR
161
1
3
10
A
ASP
180
A
ASP
197
HELX_P
A
SER
182
A
SER
199
5
4
3
A
ASP
216
A
ASP
233
HELX_P
A
TYR
222
A
TYR
239
5
5
7
A
LYS
238
A
LYS
255
HELX_P
A
SER
252
A
SER
269
1
6
15
A
PRO
258
A
PRO
275
HELX_P
A
LEU
263
A
LEU
280
1
7
6
A
PRO
276
A
PRO
293
HELX_P
A
PHE
280
A
PHE
297
5
8
5
A
LEU
301
A
LEU
318
HELX_P
A
TYR
305
A
TYR
322
1
9
5
A
GLY
334
A
GLY
351
HELX_P
A
GLU
339
A
GLU
356
1
10
6
A
MET
379
A
MET
396
HELX_P
A
GLY
383
A
GLY
400
5
11
5
disulf
2.001
A
CYS
155
A
SG
CYS
172
1_555
A
CYS
359
A
SG
CYS
376
1_555
disulf
2.037
A
CYS
217
A
SG
CYS
234
1_555
A
CYS
382
A
SG
CYS
399
1_555
disulf
2.016
A
CYS
269
A
SG
CYS
286
1_555
A
CYS
319
A
SG
CYS
336
1_555
HYDROLASE
ALTERNATIVE SPLICING, ALZHEIMER'S DISEASE, ASPARTIC PROTEASE, ASPARTYL PROTEASE, BASE, BETA-SECRETASE, GLYCOPROTEIN, HYDROLASE, MEMAPSIN 2, TRANSMEMBRANE, ZYMOGEN
A
SER
22
A
SER
39
1
A
PRO
23
A
PRO
40
2.41
A
ARG
128
A
ARG
145
1
A
PRO
129
A
PRO
146
4.97
A
TYR
222
A
TYR
239
1
A
ASP
223
A
ASP
240
3.38
A
GLY
372
A
GLY
389
1
A
PRO
373
A
PRO
390
-0.21
BACE1_HUMAN
UNP
1
45
P56817
RETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDL
RKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQ
THVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYD
KSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQ
QYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCG
YN
45
446
2OHS
-16
385
P56817
A
1
1
402
1
ARG
engineered mutation
LYS
-5
2OHS
A
P56817
UNP
56
12
1
ARG
engineered mutation
LYS
-4
2OHS
A
P56817
UNP
57
13
8
4
5
5
5
3
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LEU
6
A
LEU
23
A
LYS
9
A
LYS
26
A
GLY
13
A
GLY
30
A
VAL
20
A
VAL
37
A
GLN
25
A
GLN
42
A
ASP
32
A
ASP
49
A
GLY
117
A
GLY
134
A
GLY
120
A
GLY
137
A
PHE
38
A
PHE
55
A
GLY
41
A
GLY
58
A
VAL
95
A
VAL
112
A
ASP
106
A
ASP
123
A
LYS
75
A
LYS
92
A
SER
86
A
SER
103
A
ARG
61
A
ARG
78
A
PRO
70
A
PRO
87
A
LEU
6
A
LEU
23
A
LYS
9
A
LYS
26
A
GLY
13
A
GLY
30
A
VAL
20
A
VAL
37
A
LYS
75
A
LYS
92
A
SER
86
A
SER
103
A
ARG
61
A
ARG
78
A
PRO
70
A
PRO
87
A
GLY
172
A
GLY
189
A
ILE
176
A
ILE
193
A
PHE
150
A
PHE
167
A
LEU
154
A
LEU
171
A
PHE
341
A
PHE
358
A
ASP
346
A
ASP
363
A
ARG
351
A
ARG
368
A
SER
357
A
SER
374
A
TYR
184
A
TYR
201
A
PRO
192
A
PRO
209
A
GLU
200
A
GLU
217
A
VAL
201
A
VAL
218
A
SER
225
A
SER
242
A
VAL
227
A
VAL
244
A
VAL
332
A
VAL
349
A
MET
333
A
MET
350
A
LEU
234
A
LEU
251
A
PRO
237
A
PRO
254
A
ILE
324
A
ILE
341
A
SER
327
A
SER
344
A
GLN
211
A
GLN
228
A
ASP
212
A
ASP
229
A
ILE
203
A
ILE
220
A
ILE
208
A
ILE
225
A
ILE
283
A
ILE
300
A
MET
288
A
MET
305
A
GLN
294
A
GLN
311
A
ILE
300
A
ILE
317
A
ALA
369
A
ALA
386
A
VAL
375
A
VAL
392
A
VAL
268
A
VAL
285
A
TRP
270
A
TRP
287
A
ASP
318
A
ASP
335
A
PHE
322
A
PHE
339
A
LEU
306
A
LEU
323
A
PRO
308
A
PRO
325
BINDING SITE FOR RESIDUE IOD A 386
A
IOD
386
Software
2
BINDING SITE FOR RESIDUE IOD A 387
A
IOD
387
Software
2
BINDING SITE FOR RESIDUE DMS A 388
A
DMS
388
Software
2
BINDING SITE FOR RESIDUE 9IP A 389
A
9IP
389
Software
14
A
SER
105
A
SER
122
2
1_555
A
HOH
531
F
HOH
2
1_555
A
HIS
45
A
HIS
62
2
1_555
A
LYS
107
A
LYS
124
2
1_555
A
ARG
96
A
ARG
113
2
1_555
A
ASN
98
A
ASN
115
2
1_555
A
SER
10
A
SER
27
14
1_555
A
GLY
11
A
GLY
28
14
1_555
A
GLY
13
A
GLY
30
14
1_555
A
ASP
32
A
ASP
49
14
1_555
A
GLY
34
A
GLY
51
14
1_555
A
GLN
73
A
GLN
90
14
12_555
A
LYS
107
A
LYS
124
14
12_555
A
PHE
108
A
PHE
125
14
1_555
A
ILE
118
A
ILE
135
14
1_555
A
ASP
228
A
ASP
245
14
1_555
A
SER
229
A
SER
246
14
1_555
A
GLY
230
A
GLY
247
14
1_555
A
THR
231
A
THR
248
14
1_555
A
HOH
530
F
HOH
14
1_555
178
P 61 2 2