0.009816
0.005667
0.000000
0.000000
0.011334
0.000000
0.000000
0.000000
0.005911
0.000000
0.000000
0.000000
Sickmier, E.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.000
90.000
120.000
101.875
101.875
169.165
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
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C19 H25 N3 O
311.421
3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
non-polymer
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
US
J.Med.Chem.
JMCMAR
0151
0022-2623
54
5836
5857
10.1021/jm200544q
21707077
From Fragment Screening to In Vivo Efficacy: Optimization of a Series of 2-Aminoquinolines as Potent Inhibitors of Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1).
2011
1
2008-02-27
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
5.0.2
ALS
1
SYNCHROTRON
ALS BEAMLINE 5.0.2
45822.445
Beta-secretase 1
3.4.23.46
UNP residues 43-453
R14K, R15K
1
man
polymer
126.904
IODIDE ION
3
syn
non-polymer
92.094
GLYCEROL
2
syn
non-polymer
311.421
3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
1
syn
non-polymer
18.015
water
54
nat
water
Aspartyl protease 2, ASP2, Asp 2, Beta-site amyloid precursor protein cleaving enzyme 1, Beta-site APP cleaving enzyme 1, Memapsin-2, Membrane-associated aspartic protease 2
no
no
LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYR
DLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLV
KQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYN
YDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITIL
PQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMED
CGYNIPQTDES
LPRETDEEPEEPGKKGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYR
DLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLV
KQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYN
YDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITIL
PQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMED
CGYNIPQTDES
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
n
n
n
n
n
n
n
n
n
human
sample
BACE1, BACE, KIAA1149
9606
Homo sapiens
562
Escherichia coli
1
2.77
55.52
VAPOR DIFFUSION, HANGING DROP
6.6
20% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate (pH 6.6) and 200mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
repository
Initial release
1
0
2011-08-31
RCSB
Y
RCSB
2011-05-03
REL
REL
IOD
IODIDE ION
GOL
GLYCEROL
RTM
3-(2-aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
HOH
water
IOD
1502
2
IOD
IOD
1502
A
IOD
1503
2
IOD
IOD
1503
A
IOD
1505
2
IOD
IOD
1505
A
GOL
1
3
GOL
GOL
393
A
GOL
2
3
GOL
GOL
394
A
RTM
1
4
RTM
RTM
395
A
HOH
1
5
HOH
HOH
396
A
HOH
2
5
HOH
HOH
397
A
HOH
3
5
HOH
HOH
398
A
HOH
4
5
HOH
HOH
399
A
HOH
5
5
HOH
HOH
400
A
HOH
6
5
HOH
HOH
401
A
HOH
7
5
HOH
HOH
402
A
HOH
8
5
HOH
HOH
403
A
HOH
10
5
HOH
HOH
404
A
HOH
11
5
HOH
HOH
405
A
HOH
12
5
HOH
HOH
406
A
HOH
14
5
HOH
HOH
407
A
HOH
15
5
HOH
HOH
408
A
HOH
16
5
HOH
HOH
409
A
HOH
17
5
HOH
HOH
410
A
HOH
18
5
HOH
HOH
411
A
HOH
19
5
HOH
HOH
412
A
HOH
20
5
HOH
HOH
413
A
HOH
21
5
HOH
HOH
414
A
HOH
22
5
HOH
HOH
415
A
HOH
23
5
HOH
HOH
416
A
HOH
24
5
HOH
HOH
417
A
HOH
25
5
HOH
HOH
418
A
HOH
26
5
HOH
HOH
419
A
HOH
27
5
HOH
HOH
420
A
HOH
28
5
HOH
HOH
421
A
HOH
29
5
HOH
HOH
422
A
HOH
30
5
HOH
HOH
423
A
HOH
31
5
HOH
HOH
424
A
HOH
32
5
HOH
HOH
425
A
HOH
33
5
HOH
HOH
426
A
HOH
34
5
HOH
HOH
427
A
HOH
35
5
HOH
HOH
428
A
HOH
36
5
HOH
HOH
429
A
HOH
37
5
HOH
HOH
430
A
HOH
38
5
HOH
HOH
431
A
HOH
39
5
HOH
HOH
432
A
HOH
40
5
HOH
HOH
433
A
HOH
41
5
HOH
HOH
434
A
HOH
42
5
HOH
HOH
435
A
HOH
43
5
HOH
HOH
436
A
HOH
44
5
HOH
HOH
437
A
HOH
45
5
HOH
HOH
438
A
HOH
47
5
HOH
HOH
439
A
HOH
48
5
HOH
HOH
440
A
HOH
49
5
HOH
HOH
441
A
HOH
50
5
HOH
HOH
442
A
HOH
51
5
HOH
HOH
443
A
HOH
52
5
HOH
HOH
444
A
HOH
53
5
HOH
HOH
445
A
HOH
54
5
HOH
HOH
446
A
HOH
55
5
HOH
HOH
447
A
HOH
56
5
HOH
HOH
448
A
HOH
57
5
HOH
HOH
449
A
n
1
-18
A
n
2
-17
A
n
3
-16
A
n
4
-15
A
n
5
-14
A
n
6
-13
A
n
7
-12
A
n
8
-11
A
n
9
-10
A
n
10
-9
A
n
11
-8
A
n
12
-7
A
n
13
-6
A
n
14
-5
A
n
15
-4
A
n
16
-3
A
n
17
-2
A
PHE
-1
n
18
PHE
-1
A
VAL
0
n
19
VAL
0
A
GLU
1
n
20
GLU
1
A
MET
2
n
21
MET
2
A
VAL
3
n
22
VAL
3
A
ASP
4
n
23
ASP
4
A
ASN
5
n
24
ASN
5
A
LEU
6
n
25
LEU
6
A
ARG
7
n
26
ARG
7
A
GLY
8
n
27
GLY
8
A
LYS
9
n
28
LYS
9
A
SER
10
n
29
SER
10
A
GLY
11
n
30
GLY
11
A
GLN
12
n
31
GLN
12
A
GLY
13
n
32
GLY
13
A
TYR
14
n
33
TYR
14
A
TYR
15
n
34
TYR
15
A
VAL
16
n
35
VAL
16
A
GLU
17
n
36
GLU
17
A
MET
18
n
37
MET
18
A
THR
19
n
38
THR
19
A
VAL
20
n
39
VAL
20
A
GLY
21
n
40
GLY
21
A
SER
22
n
41
SER
22
A
PRO
23
n
42
PRO
23
A
PRO
24
n
43
PRO
24
A
GLN
25
n
44
GLN
25
A
THR
26
n
45
THR
26
A
LEU
27
n
46
LEU
27
A
ASN
28
n
47
ASN
28
A
ILE
29
n
48
ILE
29
A
LEU
30
n
49
LEU
30
A
VAL
31
n
50
VAL
31
A
ASP
32
n
51
ASP
32
A
THR
33
n
52
THR
33
A
GLY
34
n
53
GLY
34
A
SER
35
n
54
SER
35
A
SER
36
n
55
SER
36
A
ASN
37
n
56
ASN
37
A
PHE
38
n
57
PHE
38
A
ALA
39
n
58
ALA
39
A
VAL
40
n
59
VAL
40
A
GLY
41
n
60
GLY
41
A
ALA
42
n
61
ALA
42
A
ALA
43
n
62
ALA
43
A
PRO
44
n
63
PRO
44
A
HIS
45
n
64
HIS
45
A
PRO
46
n
65
PRO
46
A
PHE
47
n
66
PHE
47
A
LEU
48
n
67
LEU
48
A
HIS
49
n
68
HIS
49
A
ARG
50
n
69
ARG
50
A
TYR
51
n
70
TYR
51
A
TYR
52
n
71
TYR
52
A
GLN
53
n
72
GLN
53
A
ARG
54
n
73
ARG
54
A
GLN
55
n
74
GLN
55
A
LEU
56
n
75
LEU
56
A
SER
57
n
76
SER
57
A
SER
58
n
77
SER
58
A
THR
59
n
78
THR
59
A
TYR
60
n
79
TYR
60
A
ARG
61
n
80
ARG
61
A
ASP
62
n
81
ASP
62
A
LEU
63
n
82
LEU
63
A
ARG
64
n
83
ARG
64
A
LYS
65
n
84
LYS
65
A
GLY
66
n
85
GLY
66
A
VAL
67
n
86
VAL
67
A
TYR
68
n
87
TYR
68
A
VAL
69
n
88
VAL
69
A
PRO
70
n
89
PRO
70
A
TYR
71
n
90
TYR
71
A
THR
72
n
91
THR
72
A
GLN
73
n
92
GLN
73
A
GLY
74
n
93
GLY
74
A
LYS
75
n
94
LYS
75
A
TRP
76
n
95
TRP
76
A
GLU
77
n
96
GLU
77
A
GLY
78
n
97
GLY
78
A
GLU
79
n
98
GLU
79
A
LEU
80
n
99
LEU
80
A
GLY
81
n
100
GLY
81
A
THR
82
n
101
THR
82
A
ASP
83
n
102
ASP
83
A
LEU
84
n
103
LEU
84
A
VAL
85
n
104
VAL
85
A
SER
86
n
105
SER
86
A
ILE
87
n
106
ILE
87
A
PRO
88
n
107
PRO
88
A
HIS
89
n
108
HIS
89
A
GLY
90
n
109
GLY
90
A
PRO
91
n
110
PRO
91
A
ASN
92
n
111
ASN
92
A
VAL
93
n
112
VAL
93
A
THR
94
n
113
THR
94
A
VAL
95
n
114
VAL
95
A
ARG
96
n
115
ARG
96
A
ALA
97
n
116
ALA
97
A
ASN
98
n
117
ASN
98
A
ILE
99
n
118
ILE
99
A
ALA
100
n
119
ALA
100
A
ALA
101
n
120
ALA
101
A
ILE
102
n
121
ILE
102
A
THR
103
n
122
THR
103
A
GLU
104
n
123
GLU
104
A
SER
105
n
124
SER
105
A
ASP
106
n
125
ASP
106
A
LYS
107
n
126
LYS
107
A
PHE
108
n
127
PHE
108
A
PHE
109
n
128
PHE
109
A
ILE
110
n
129
ILE
110
A
ASN
111
n
130
ASN
111
A
GLY
112
n
131
GLY
112
A
SER
113
n
132
SER
113
A
ASN
114
n
133
ASN
114
A
TRP
115
n
134
TRP
115
A
GLU
116
n
135
GLU
116
A
GLY
117
n
136
GLY
117
A
ILE
118
n
137
ILE
118
A
LEU
119
n
138
LEU
119
A
GLY
120
n
139
GLY
120
A
LEU
121
n
140
LEU
121
A
ALA
122
n
141
ALA
122
A
TYR
123
n
142
TYR
123
A
ALA
124
n
143
ALA
124
A
GLU
125
n
144
GLU
125
A
ILE
126
n
145
ILE
126
A
ALA
127
n
146
ALA
127
A
ARG
128
n
147
ARG
128
A
PRO
129
n
148
PRO
129
A
ASP
130
n
149
ASP
130
A
ASP
131
n
150
ASP
131
A
SER
132
n
151
SER
132
A
LEU
133
n
152
LEU
133
A
GLU
134
n
153
GLU
134
A
PRO
135
n
154
PRO
135
A
PHE
136
n
155
PHE
136
A
PHE
137
n
156
PHE
137
A
ASP
138
n
157
ASP
138
A
SER
139
n
158
SER
139
A
LEU
140
n
159
LEU
140
A
VAL
141
n
160
VAL
141
A
LYS
142
n
161
LYS
142
A
GLN
143
n
162
GLN
143
A
THR
144
n
163
THR
144
A
HIS
145
n
164
HIS
145
A
VAL
146
n
165
VAL
146
A
PRO
147
n
166
PRO
147
A
ASN
148
n
167
ASN
148
A
LEU
149
n
168
LEU
149
A
PHE
150
n
169
PHE
150
A
SER
151
n
170
SER
151
A
LEU
152
n
171
LEU
152
A
GLN
153
n
172
GLN
153
A
LEU
154
n
173
LEU
154
A
CYS
155
n
174
CYS
155
A
GLY
156
n
175
GLY
156
A
n
176
157
A
n
177
158
A
n
178
159
A
n
179
160
A
n
180
161
A
n
181
162
A
n
182
163
A
n
183
164
A
n
184
165
A
n
185
166
A
n
186
167
A
ALA
168
n
187
ALA
168
A
SER
169
n
188
SER
169
A
VAL
170
n
189
VAL
170
A
GLY
171
n
190
GLY
171
A
GLY
172
n
191
GLY
172
A
SER
173
n
192
SER
173
A
MET
174
n
193
MET
174
A
ILE
175
n
194
ILE
175
A
ILE
176
n
195
ILE
176
A
GLY
177
n
196
GLY
177
A
GLY
178
n
197
GLY
178
A
ILE
179
n
198
ILE
179
A
ASP
180
n
199
ASP
180
A
HIS
181
n
200
HIS
181
A
SER
182
n
201
SER
182
A
LEU
183
n
202
LEU
183
A
TYR
184
n
203
TYR
184
A
THR
185
n
204
THR
185
A
GLY
186
n
205
GLY
186
A
SER
187
n
206
SER
187
A
LEU
188
n
207
LEU
188
A
TRP
189
n
208
TRP
189
A
TYR
190
n
209
TYR
190
A
THR
191
n
210
THR
191
A
PRO
192
n
211
PRO
192
A
ILE
193
n
212
ILE
193
A
ARG
194
n
213
ARG
194
A
ARG
195
n
214
ARG
195
A
GLU
196
n
215
GLU
196
A
TRP
197
n
216
TRP
197
A
TYR
198
n
217
TYR
198
A
TYR
199
n
218
TYR
199
A
GLU
200
n
219
GLU
200
A
VAL
201
n
220
VAL
201
A
ILE
202
n
221
ILE
202
A
ILE
203
n
222
ILE
203
A
VAL
204
n
223
VAL
204
A
ARG
205
n
224
ARG
205
A
VAL
206
n
225
VAL
206
A
GLU
207
n
226
GLU
207
A
ILE
208
n
227
ILE
208
A
ASN
209
n
228
ASN
209
A
GLY
210
n
229
GLY
210
A
GLN
211
n
230
GLN
211
A
ASP
212
n
231
ASP
212
A
LEU
213
n
232
LEU
213
A
LYS
214
n
233
LYS
214
A
MET
215
n
234
MET
215
A
ASP
216
n
235
ASP
216
A
CYS
217
n
236
CYS
217
A
LYS
218
n
237
LYS
218
A
GLU
219
n
238
GLU
219
A
TYR
220
n
239
TYR
220
A
ASN
221
n
240
ASN
221
A
TYR
222
n
241
TYR
222
A
ASP
223
n
242
ASP
223
A
LYS
224
n
243
LYS
224
A
SER
225
n
244
SER
225
A
ILE
226
n
245
ILE
226
A
VAL
227
n
246
VAL
227
A
ASP
228
n
247
ASP
228
A
SER
229
n
248
SER
229
A
GLY
230
n
249
GLY
230
A
THR
231
n
250
THR
231
A
THR
232
n
251
THR
232
A
ASN
233
n
252
ASN
233
A
LEU
234
n
253
LEU
234
A
ARG
235
n
254
ARG
235
A
LEU
236
n
255
LEU
236
A
PRO
237
n
256
PRO
237
A
LYS
238
n
257
LYS
238
A
LYS
239
n
258
LYS
239
A
VAL
240
n
259
VAL
240
A
PHE
241
n
260
PHE
241
A
GLU
242
n
261
GLU
242
A
ALA
243
n
262
ALA
243
A
ALA
244
n
263
ALA
244
A
VAL
245
n
264
VAL
245
A
LYS
246
n
265
LYS
246
A
SER
247
n
266
SER
247
A
ILE
248
n
267
ILE
248
A
LYS
249
n
268
LYS
249
A
ALA
250
n
269
ALA
250
A
ALA
251
n
270
ALA
251
A
SER
252
n
271
SER
252
A
SER
253
n
272
SER
253
A
THR
254
n
273
THR
254
A
GLU
255
n
274
GLU
255
A
LYS
256
n
275
LYS
256
A
PHE
257
n
276
PHE
257
A
PRO
258
n
277
PRO
258
A
ASP
259
n
278
ASP
259
A
GLY
260
n
279
GLY
260
A
PHE
261
n
280
PHE
261
A
TRP
262
n
281
TRP
262
A
LEU
263
n
282
LEU
263
A
GLY
264
n
283
GLY
264
A
GLU
265
n
284
GLU
265
A
GLN
266
n
285
GLN
266
A
LEU
267
n
286
LEU
267
A
VAL
268
n
287
VAL
268
A
CYS
269
n
288
CYS
269
A
TRP
270
n
289
TRP
270
A
GLN
271
n
290
GLN
271
A
ALA
272
n
291
ALA
272
A
GLY
273
n
292
GLY
273
A
THR
274
n
293
THR
274
A
THR
275
n
294
THR
275
A
PRO
276
n
295
PRO
276
A
TRP
277
n
296
TRP
277
A
ASN
278
n
297
ASN
278
A
ILE
279
n
298
ILE
279
A
PHE
280
n
299
PHE
280
A
PRO
281
n
300
PRO
281
A
VAL
282
n
301
VAL
282
A
ILE
283
n
302
ILE
283
A
SER
284
n
303
SER
284
A
LEU
285
n
304
LEU
285
A
TYR
286
n
305
TYR
286
A
LEU
287
n
306
LEU
287
A
MET
288
n
307
MET
288
A
GLY
289
n
308
GLY
289
A
GLU
290
n
309
GLU
290
A
VAL
291
n
310
VAL
291
A
THR
292
n
311
THR
292
A
ASN
293
n
312
ASN
293
A
GLN
294
n
313
GLN
294
A
SER
295
n
314
SER
295
A
PHE
296
n
315
PHE
296
A
ARG
297
n
316
ARG
297
A
ILE
298
n
317
ILE
298
A
THR
299
n
318
THR
299
A
ILE
300
n
319
ILE
300
A
LEU
301
n
320
LEU
301
A
PRO
302
n
321
PRO
302
A
GLN
303
n
322
GLN
303
A
GLN
304
n
323
GLN
304
A
TYR
305
n
324
TYR
305
A
LEU
306
n
325
LEU
306
A
ARG
307
n
326
ARG
307
A
PRO
308
n
327
PRO
308
A
VAL
309
n
328
VAL
309
A
GLU
310
n
329
GLU
310
A
n
330
311
A
n
331
312
A
n
332
313
A
n
333
314
A
n
334
315
A
n
335
316
A
n
336
317
A
ASP
318
n
337
ASP
318
A
CYS
319
n
338
CYS
319
A
TYR
320
n
339
TYR
320
A
LYS
321
n
340
LYS
321
A
PHE
322
n
341
PHE
322
A
ALA
323
n
342
ALA
323
A
ILE
324
n
343
ILE
324
A
SER
325
n
344
SER
325
A
GLN
326
n
345
GLN
326
A
SER
327
n
346
SER
327
A
SER
328
n
347
SER
328
A
THR
329
n
348
THR
329
A
GLY
330
n
349
GLY
330
A
THR
331
n
350
THR
331
A
VAL
332
n
351
VAL
332
A
MET
333
n
352
MET
333
A
GLY
334
n
353
GLY
334
A
ALA
335
n
354
ALA
335
A
VAL
336
n
355
VAL
336
A
ILE
337
n
356
ILE
337
A
MET
338
n
357
MET
338
A
GLU
339
n
358
GLU
339
A
GLY
340
n
359
GLY
340
A
PHE
341
n
360
PHE
341
A
TYR
342
n
361
TYR
342
A
VAL
343
n
362
VAL
343
A
VAL
344
n
363
VAL
344
A
PHE
345
n
364
PHE
345
A
ASP
346
n
365
ASP
346
A
ARG
347
n
366
ARG
347
A
ALA
348
n
367
ALA
348
A
ARG
349
n
368
ARG
349
A
LYS
350
n
369
LYS
350
A
ARG
351
n
370
ARG
351
A
ILE
352
n
371
ILE
352
A
GLY
353
n
372
GLY
353
A
PHE
354
n
373
PHE
354
A
ALA
355
n
374
ALA
355
A
VAL
356
n
375
VAL
356
A
SER
357
n
376
SER
357
A
ALA
358
n
377
ALA
358
A
CYS
359
n
378
CYS
359
A
HIS
360
n
379
HIS
360
A
VAL
361
n
380
VAL
361
A
HIS
362
n
381
HIS
362
A
ASP
363
n
382
ASP
363
A
GLU
364
n
383
GLU
364
A
PHE
365
n
384
PHE
365
A
ARG
366
n
385
ARG
366
A
THR
367
n
386
THR
367
A
ALA
368
n
387
ALA
368
A
ALA
369
n
388
ALA
369
A
VAL
370
n
389
VAL
370
A
GLU
371
n
390
GLU
371
A
GLY
372
n
391
GLY
372
A
PRO
373
n
392
PRO
373
A
PHE
374
n
393
PHE
374
A
VAL
375
n
394
VAL
375
A
THR
376
n
395
THR
376
A
LEU
377
n
396
LEU
377
A
ASP
378
n
397
ASP
378
A
MET
379
n
398
MET
379
A
GLU
380
n
399
GLU
380
A
ASP
381
n
400
ASP
381
A
CYS
382
n
401
CYS
382
A
GLY
383
n
402
GLY
383
A
TYR
384
n
403
TYR
384
A
ASN
385
n
404
ASN
385
A
n
405
386
A
n
406
387
A
n
407
388
A
n
408
389
A
n
409
390
A
n
410
391
A
n
411
392
A
author_and_software_defined_assembly
PISA
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
VAL
69
A
N
VAL
88
A
O
TRP
76
A
O
TRP
95
A
O
SER
86
A
O
SER
105
A
N
THR
19
A
N
THR
38
A
O
TYR
15
A
O
TYR
34
A
N
ARG
7
A
N
ARG
26
A
N
LEU
6
A
N
LEU
25
A
O
GLY
172
A
O
GLY
191
A
O
SER
173
A
O
SER
192
A
N
GLN
153
A
N
GLN
172
A
N
PHE
150
A
N
PHE
169
A
O
PHE
345
A
O
PHE
364
A
N
VAL
344
A
N
VAL
363
A
O
GLY
353
A
O
GLY
372
A
O
ILE
352
A
O
ILE
371
A
N
THR
191
A
N
THR
210
A
N
VAL
69
A
N
VAL
88
A
O
TRP
76
A
O
TRP
95
A
N
VAL
85
A
N
VAL
104
A
O
VAL
95
A
O
VAL
114
A
O
ILE
102
A
O
ILE
121
A
N
VAL
40
A
N
VAL
59
A
N
ALA
39
A
N
ALA
58
A
O
ILE
118
A
O
ILE
137
A
O
LEU
119
A
O
LEU
138
A
N
LEU
30
A
N
LEU
49
A
O
LEU
27
A
O
LEU
46
A
N
MET
18
A
N
MET
37
A
O
TYR
15
A
O
TYR
34
A
N
ARG
7
A
N
ARG
26
A
N
LEU
6
A
N
LEU
25
A
O
GLY
172
A
O
GLY
191
A
O
SER
173
A
O
SER
192
A
N
GLN
153
A
N
GLN
172
A
N
PHE
150
A
N
PHE
169
A
O
PHE
345
A
O
PHE
364
A
N
VAL
344
A
N
VAL
363
A
O
GLY
353
A
O
GLY
372
A
O
ILE
352
A
O
ILE
371
A
N
THR
191
A
N
THR
210
A
N
ARG
205
A
N
ARG
224
A
O
TYR
286
A
O
TYR
305
A
N
LEU
285
A
N
LEU
304
A
O
ILE
298
A
O
ILE
317
A
N
ARG
297
A
N
ARG
316
A
O
GLU
371
A
O
GLU
390
A
N
ILE
226
A
N
ILE
245
A
O
MET
333
A
O
MET
352
A
O
VAL
332
A
O
VAL
351
A
N
ARG
235
A
N
ARG
254
A
N
LEU
236
A
N
LEU
255
A
O
SER
325
A
O
SER
344
A
N
VAL
268
A
N
VAL
287
A
O
TYR
320
A
O
TYR
339
A
O
LYS
321
A
O
LYS
340
A
N
ARG
307
A
N
ARG
326
1
A
LEU
-18
A
LEU
1
1
Y
1
A
PRO
-17
A
PRO
2
1
Y
1
A
ARG
-16
A
ARG
3
1
Y
1
A
GLU
-15
A
GLU
4
1
Y
1
A
THR
-14
A
THR
5
1
Y
1
A
ASP
-13
A
ASP
6
1
Y
1
A
GLU
-12
A
GLU
7
1
Y
1
A
GLU
-11
A
GLU
8
1
Y
1
A
PRO
-10
A
PRO
9
1
Y
1
A
GLU
-9
A
GLU
10
1
Y
1
A
GLU
-8
A
GLU
11
1
Y
1
A
PRO
-7
A
PRO
12
1
Y
1
A
GLY
-6
A
GLY
13
1
Y
1
A
LYS
-5
A
LYS
14
1
Y
1
A
LYS
-4
A
LYS
15
1
Y
1
A
GLY
-3
A
GLY
16
1
Y
1
A
SER
-2
A
SER
17
1
Y
1
A
ALA
157
A
ALA
176
1
Y
1
A
GLY
158
A
GLY
177
1
Y
1
A
PHE
159
A
PHE
178
1
Y
1
A
PRO
160
A
PRO
179
1
Y
1
A
LEU
161
A
LEU
180
1
Y
1
A
ASN
162
A
ASN
181
1
Y
1
A
GLN
163
A
GLN
182
1
Y
1
A
SER
164
A
SER
183
1
Y
1
A
GLU
165
A
GLU
184
1
Y
1
A
VAL
166
A
VAL
185
1
Y
1
A
LEU
167
A
LEU
186
1
Y
1
A
ASP
311
A
ASP
330
1
Y
1
A
VAL
312
A
VAL
331
1
Y
1
A
ALA
313
A
ALA
332
1
Y
1
A
THR
314
A
THR
333
1
Y
1
A
SER
315
A
SER
334
1
Y
1
A
GLN
316
A
GLN
335
1
Y
1
A
ASP
317
A
ASP
336
1
Y
1
A
ILE
386
A
ILE
405
1
Y
1
A
PRO
387
A
PRO
406
1
Y
1
A
GLN
388
A
GLN
407
1
Y
1
A
THR
389
A
THR
408
1
Y
1
A
ASP
390
A
ASP
409
1
Y
1
A
GLU
391
A
GLU
410
1
Y
1
A
SER
392
A
SER
411
1
Y
1
A
TRP
197
-134.31
-79.12
1
A
ARG
205
-176.33
140.40
1
A
ASN
209
63.91
63.57
1
A
GLU
255
172.17
153.68
1
A
ALA
272
-59.50
10.62
1
A
TRP
277
72.19
-53.16
1
A
ASP
363
-76.25
-164.15
104.550
54.7680
17.790
1.4500
0.7300
0.0000
1.4500
0.0000
-2.1800
0.9290
0.8960
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
0.2884
0.2212
0.2246
2.7600
20.0000
680
13653
5.0000
98.0500
0.2884
0.2169
1.000
0.500
0.7863
14.5630
0.3000
1.1049
0.3921
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.3920
0.8000
0.8000
1.4000
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.7600
20.0000
54
3002
38
0
2910
0.013
0.022
3022
1.455
1.955
4103
7.047
5.000
366
35.714
23.723
137
18.435
15.000
477
16.039
15.000
17
0.090
0.200
442
0.006
0.021
2308
0.751
1.500
1828
1.399
2.000
2956
1.667
3.000
1194
2.851
4.500
1147
0.3270
0.2780
2.8300
38
888
926
20
93.9100
2.750
20.000
3RTM
13736
0.082
1.060
1
12.500
7.600
98.500
0.387
2.750
2.850
1308
0.989
1
5.700
97.500
0.313
2.850
2.960
1354
1.100
1
7.300
99.500
0.232
2.960
3.100
1345
1.097
1
8.000
99.600
0.184
3.100
3.260
1362
1.081
1
8.000
99.300
0.140
3.260
3.460
1352
1.058
1
8.100
99.000
0.097
3.460
3.730
1371
1.018
1
8.000
99.100
0.080
3.730
4.100
1371
1.038
1
7.900
98.700
0.067
4.100
4.690
1388
1.075
1
7.800
98.300
0.057
4.690
5.880
1394
1.102
1
7.500
97.900
0.056
5.880
20.000
1491
1.027
1
7.500
96.500
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
program
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
data collection
HKL-2000
data reduction
HKL-2000
phasing
PHASER
Beta-secretase 1 (E.C.3.4.23.46)
Structure of Bace-1 (Beta-Secretase) in Complex with 3-(2-Aminoquinolin-3-yl)-N-cyclohexyl-N-methylpropanamide
1
N
N
2
N
N
2
N
N
2
N
N
3
N
N
3
N
N
4
N
N
5
N
N
A
PHE
-1
A
PHE
18
HELX_P
A
VAL
3
A
VAL
22
5
1
5
A
GLN
53
A
GLN
72
HELX_P
A
SER
57
A
SER
76
5
2
5
A
TYR
123
A
TYR
142
HELX_P
A
ALA
127
A
ALA
146
5
3
5
A
PRO
135
A
PRO
154
HELX_P
A
THR
144
A
THR
163
1
4
10
A
ASP
180
A
ASP
199
HELX_P
A
SER
182
A
SER
201
5
5
3
A
ASP
216
A
ASP
235
HELX_P
A
TYR
220
A
TYR
239
5
6
5
A
LYS
238
A
LYS
257
HELX_P
A
SER
252
A
SER
271
1
7
15
A
PRO
258
A
PRO
277
HELX_P
A
LEU
263
A
LEU
282
1
8
6
A
LEU
301
A
LEU
320
HELX_P
A
TYR
305
A
TYR
324
1
9
5
A
GLY
334
A
GLY
353
HELX_P
A
GLU
339
A
GLU
358
1
10
6
A
ARG
347
A
ARG
366
HELX_P
A
ARG
349
A
ARG
368
5
11
3
A
ASP
378
A
ASP
397
HELX_P
A
GLY
383
A
GLY
402
5
12
6
disulf
2.075
A
CYS
155
A
SG
CYS
174
1_555
A
CYS
359
A
SG
CYS
378
1_555
disulf
2.040
A
CYS
217
A
SG
CYS
236
1_555
A
CYS
382
A
SG
CYS
401
1_555
disulf
2.060
A
CYS
269
A
SG
CYS
288
1_555
A
CYS
319
A
SG
CYS
338
1_555
Hydrolase/Hydrolase Inhibitor
ASPARTYL PROTEASE, Hydrolase-Hydrolase Inhibitor complex
A
SER
22
A
SER
41
1
A
PRO
23
A
PRO
42
-9.24
A
ARG
128
A
ARG
147
1
A
PRO
129
A
PRO
148
4.00
A
TYR
222
A
TYR
241
1
A
ASP
223
A
ASP
242
-2.74
A
GLY
372
A
GLY
391
1
A
PRO
373
A
PRO
392
-0.66
BACE1_HUMAN
UNP
1
43
P56817
LPRETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYR
DLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLV
KQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYN
YDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITIL
PQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMED
CGYNIPQTDES
43
453
3RTM
-18
392
P56817
A
1
1
411
1
ARG
ENGINEERED MUTATION
LYS
-5
3RTM
A
P56817
UNP
56
14
1
ARG
ENGINEERED MUTATION
LYS
-4
3RTM
A
P56817
UNP
57
15
9
13
4
4
3
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
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
ARG
61
A
ARG
80
A
TYR
71
A
TYR
90
A
GLY
74
A
GLY
93
A
SER
86
A
SER
105
A
TYR
14
A
TYR
33
A
VAL
20
A
VAL
39
A
LEU
6
A
LEU
25
A
LYS
9
A
LYS
28
A
SER
169
A
SER
188
A
ILE
176
A
ILE
195
A
PHE
150
A
PHE
169
A
LEU
154
A
LEU
173
A
PHE
341
A
PHE
360
A
ASP
346
A
ASP
365
A
ARG
351
A
ARG
370
A
SER
357
A
SER
376
A
TYR
184
A
TYR
203
A
PRO
192
A
PRO
211
A
ARG
61
A
ARG
80
A
TYR
71
A
TYR
90
A
GLY
74
A
GLY
93
A
SER
86
A
SER
105
A
VAL
95
A
VAL
114
A
ASP
106
A
ASP
125
A
PHE
38
A
PHE
57
A
GLY
41
A
GLY
60
A
GLY
117
A
GLY
136
A
GLY
120
A
GLY
139
A
GLN
25
A
GLN
44
A
ASP
32
A
ASP
51
A
TYR
14
A
TYR
33
A
VAL
20
A
VAL
39
A
LEU
6
A
LEU
25
A
LYS
9
A
LYS
28
A
SER
169
A
SER
188
A
ILE
176
A
ILE
195
A
PHE
150
A
PHE
169
A
LEU
154
A
LEU
173
A
PHE
341
A
PHE
360
A
ASP
346
A
ASP
365
A
ARG
351
A
ARG
370
A
SER
357
A
SER
376
A
TYR
184
A
TYR
203
A
PRO
192
A
PRO
211
A
ILE
203
A
ILE
222
A
ILE
208
A
ILE
227
A
ILE
283
A
ILE
302
A
MET
288
A
MET
307
A
GLN
294
A
GLN
313
A
ILE
300
A
ILE
319
A
ALA
369
A
ALA
388
A
VAL
375
A
VAL
394
A
SER
225
A
SER
244
A
VAL
227
A
VAL
246
A
THR
331
A
THR
350
A
MET
333
A
MET
352
A
LEU
234
A
LEU
253
A
PRO
237
A
PRO
256
A
ILE
324
A
ILE
343
A
SER
327
A
SER
346
A
VAL
268
A
VAL
287
A
CYS
269
A
CYS
288
A
CYS
319
A
CYS
338
A
PHE
322
A
PHE
341
A
LEU
306
A
LEU
325
A
PRO
308
A
PRO
327
BINDING SITE FOR RESIDUE IOD A 1502
Software
1
BINDING SITE FOR RESIDUE IOD A 1503
Software
1
BINDING SITE FOR RESIDUE IOD A 1505
Software
1
BINDING SITE FOR RESIDUE GOL A 393
Software
3
BINDING SITE FOR RESIDUE GOL A 394
Software
7
BINDING SITE FOR RESIDUE RTM A 395
Software
6
A
SER
105
A
SER
124
1
1_555
A
LYS
107
A
LYS
126
1
1_555
A
ARG
349
A
ARG
368
1
1_555
A
ARG
50
A
ARG
69
3
1_555
A
TYR
51
A
TYR
70
3
1_555
A
GLN
53
A
GLN
72
3
1_555
A
LYS
9
A
LYS
28
7
1_555
A
GLY
11
A
GLY
30
7
1_555
A
GLY
13
A
GLY
32
7
1_555
A
VAL
170
A
VAL
189
7
1_555
A
THR
232
A
THR
251
7
1_555
A
ARG
307
A
ARG
326
7
1_555
A
GLU
339
A
GLU
358
7
1_555
A
ASP
32
A
ASP
51
6
1_555
A
SER
35
A
SER
54
6
1_555
A
ILE
118
A
ILE
137
6
1_555
A
ASP
228
A
ASP
247
6
1_555
A
GLY
230
A
GLY
249
6
1_555
A
THR
231
A
THR
250
6
1_555
178
P 61 2 2