0.017854
0.010308
0.000000
-0.000000
0.020616
0.000000
0.000000
-0.000000
0.008689
0.000000
0.000000
0.000000
Fansa, E.K.
Martin-Gago, P.
Waldmann, H.
Wittinghofer, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
56.010
56.010
115.090
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
C30 H39 Cl N6 O4 S2
647.251
~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide
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
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
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
Y
88
N
C
Y
89
N
C
Y
90
N
C
Y
91
N
N
Y
92
N
N
N
93
N
C
N
94
N
N
Y
95
N
C
N
96
N
C
N
97
N
N
N
98
N
C
N
99
N
C
N
100
N
C
N
101
N
C
N
102
N
N
N
103
N
C
N
104
N
C
N
105
N
S
N
106
N
O
N
107
N
O
Y
108
N
C
Y
109
N
C
Y
110
N
C
Y
111
N
C
Y
112
N
C
Y
113
N
C
N
114
N
S
N
115
N
O
N
116
N
O
N
117
N
N
N
118
N
C
N
119
N
C
N
120
N
C
N
121
N
C
N
122
N
C
N
123
N
C
Y
124
N
C
Y
125
N
C
Y
126
N
C
Y
127
N
C
N
128
N
CL
Y
129
N
C
Y
130
N
C
N
131
N
H
N
132
N
H
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
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
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
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
C
N
177
N
O
N
178
N
N
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
N
N
191
S
C
N
192
N
C
N
193
N
O
N
194
N
C
N
195
N
C
N
196
N
C
N
197
N
O
N
198
N
O
N
199
N
O
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
N
N
210
N
C
N
211
N
C
N
212
N
O
N
213
N
O
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
N
C
Y
224
N
C
Y
225
N
N
Y
226
N
C
Y
227
N
C
Y
228
N
N
N
229
N
O
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
O
N
241
N
H
N
242
N
H
N
243
N
N
N
244
S
C
N
245
N
C
N
246
N
O
N
247
S
C
N
248
N
C
N
249
N
C
N
250
N
C
N
251
N
O
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
N
N
266
S
C
N
267
N
C
N
268
N
O
N
269
N
C
N
270
N
C
N
271
N
C
N
272
N
C
N
273
N
O
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
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
C
N
295
N
N
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
S
N
319
N
C
N
320
N
O
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
Y
337
N
C
Y
338
N
C
Y
339
N
C
Y
340
N
C
Y
341
N
C
Y
342
N
C
N
343
N
O
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
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
N
N
356
S
C
N
357
N
C
N
358
N
O
N
359
N
C
N
360
N
C
N
361
N
C
N
362
N
O
N
363
N
H
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
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
O
N
378
N
O
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
R
C
N
391
N
O
N
392
N
C
N
393
N
O
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
H
N
401
N
H
N
402
N
H
N
403
N
N
N
404
S
C
N
405
N
C
N
406
N
O
N
407
N
C
Y
408
N
C
Y
409
N
C
Y
410
N
C
Y
411
N
N
Y
412
N
C
Y
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
N
417
N
O
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
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
N
N
431
S
C
N
432
N
C
N
433
N
O
N
434
N
C
Y
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
N
441
N
O
N
442
N
O
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
N
N
455
S
C
N
456
N
C
N
457
N
O
N
458
N
C
N
459
N
C
N
460
N
C
N
461
N
O
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
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
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
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
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
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
Y
84
N
doub
Y
85
N
sing
Y
86
N
sing
N
87
N
doub
Y
88
N
doub
N
89
N
doub
Y
90
N
doub
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
Y
95
N
sing
N
96
N
sing
N
97
N
sing
Y
98
N
doub
Y
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
Y
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
Y
108
N
doub
N
109
N
sing
Y
110
N
doub
N
111
N
sing
N
112
N
sing
Y
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
sing
Y
120
N
doub
Y
121
N
sing
N
122
N
doub
N
123
N
doub
N
124
N
sing
N
125
N
sing
Y
126
N
sing
Y
127
N
doub
Y
128
N
doub
Y
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
sing
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
sing
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
sing
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
sing
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
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
doub
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
doub
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
sing
N
211
N
sing
N
212
N
doub
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
doub
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
Y
226
N
sing
Y
227
N
doub
Y
228
N
doub
N
229
N
sing
Y
230
N
sing
N
231
N
sing
Y
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
doub
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
sing
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
doub
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
sing
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
doub
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
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
doub
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
sing
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
doub
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
Y
334
N
doub
Y
335
N
sing
Y
336
N
sing
N
337
N
sing
Y
338
N
doub
N
339
N
sing
Y
340
N
doub
N
341
N
sing
Y
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
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
doub
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
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
doub
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
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
doub
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
Y
403
N
doub
Y
404
N
sing
Y
405
N
sing
N
406
N
sing
Y
407
N
doub
Y
408
N
sing
Y
409
N
sing
N
410
N
sing
Y
411
N
sing
Y
412
N
doub
N
413
N
sing
Y
414
N
doub
N
415
N
sing
Y
416
N
sing
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
doub
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
Y
431
N
doub
Y
432
N
sing
Y
433
N
sing
N
434
N
sing
Y
435
N
doub
N
436
N
sing
Y
437
N
doub
N
438
N
sing
Y
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
doub
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
GE
Angew. Chem. Int. Ed. Engl.
ACIEAY
0179
1521-3773
56
2423
2428
10.1002/anie.201610957
28106325
A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2.
2017
10.2210/pdb5ml3/pdb
pdb_00005ml3
100
1
PIXEL
2014-12-04
DECTRIS PILATUS3 6M
SINGLE WAVELENGTH
M
x-ray
1
0.978
1.0
X10SA
SLS
0.978
SYNCHROTRON
SLS BEAMLINE X10SA
17309.793
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
1
man
polymer
647.251
~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide
1
syn
non-polymer
18.015
water
180
nat
water
GMP-PDE delta,Protein p17
no
no
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY
FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY
FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
B
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
Human
sample
1
149
PDE6D, PDED
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
3.02
59.28
VAPOR DIFFUSION
0.2 M NaOAc, 0.1 M Na3Cit, pH 5.5, 10 % PEG 4000
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_audit_support
pdbx_initial_refinement_model
repository
Initial release
Database references
Author supporting evidence
Data collection
Database references
Refinement description
1
0
2017-02-01
1
1
2017-02-22
1
2
2024-01-17
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_audit_support.funding_organization
Germany
SFB
SFB 642
Germany
European Research Council
ERC Grant 268782
N
PDBE
Y
PDBE
2016-12-06
REL
REL
DL3
~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide
HOH
water
3T5G
PDB
experimental model
DRG
1
2
DL3
DL3
201
B
HOH
178
3
HOH
HOH
301
B
HOH
53
3
HOH
HOH
302
B
HOH
56
3
HOH
HOH
303
B
HOH
97
3
HOH
HOH
304
B
HOH
71
3
HOH
HOH
305
B
HOH
179
3
HOH
HOH
306
B
HOH
127
3
HOH
HOH
307
B
HOH
7
3
HOH
HOH
308
B
HOH
148
3
HOH
HOH
309
B
HOH
152
3
HOH
HOH
310
B
HOH
112
3
HOH
HOH
311
B
HOH
205
3
HOH
HOH
312
B
HOH
186
3
HOH
HOH
313
B
HOH
3
3
HOH
HOH
314
B
HOH
23
3
HOH
HOH
315
B
HOH
55
3
HOH
HOH
316
B
HOH
183
3
HOH
HOH
317
B
HOH
116
3
HOH
HOH
318
B
HOH
48
3
HOH
HOH
319
B
HOH
120
3
HOH
HOH
320
B
HOH
164
3
HOH
HOH
321
B
HOH
51
3
HOH
HOH
322
B
HOH
26
3
HOH
HOH
323
B
HOH
102
3
HOH
HOH
324
B
HOH
59
3
HOH
HOH
325
B
HOH
10
3
HOH
HOH
326
B
HOH
44
3
HOH
HOH
327
B
HOH
16
3
HOH
HOH
328
B
HOH
46
3
HOH
HOH
329
B
HOH
190
3
HOH
HOH
330
B
HOH
91
3
HOH
HOH
331
B
HOH
49
3
HOH
HOH
332
B
HOH
90
3
HOH
HOH
333
B
HOH
68
3
HOH
HOH
334
B
HOH
98
3
HOH
HOH
335
B
HOH
153
3
HOH
HOH
336
B
HOH
158
3
HOH
HOH
337
B
HOH
82
3
HOH
HOH
338
B
HOH
195
3
HOH
HOH
339
B
HOH
162
3
HOH
HOH
340
B
HOH
151
3
HOH
HOH
341
B
HOH
95
3
HOH
HOH
342
B
HOH
54
3
HOH
HOH
343
B
HOH
63
3
HOH
HOH
344
B
HOH
38
3
HOH
HOH
345
B
HOH
24
3
HOH
HOH
346
B
HOH
145
3
HOH
HOH
347
B
HOH
88
3
HOH
HOH
348
B
HOH
14
3
HOH
HOH
349
B
HOH
5
3
HOH
HOH
350
B
HOH
36
3
HOH
HOH
351
B
HOH
108
3
HOH
HOH
352
B
HOH
103
3
HOH
HOH
353
B
HOH
61
3
HOH
HOH
354
B
HOH
12
3
HOH
HOH
355
B
HOH
94
3
HOH
HOH
356
B
HOH
57
3
HOH
HOH
357
B
HOH
64
3
HOH
HOH
358
B
HOH
81
3
HOH
HOH
359
B
HOH
172
3
HOH
HOH
360
B
HOH
60
3
HOH
HOH
361
B
HOH
133
3
HOH
HOH
362
B
HOH
197
3
HOH
HOH
363
B
HOH
198
3
HOH
HOH
364
B
HOH
22
3
HOH
HOH
365
B
HOH
117
3
HOH
HOH
366
B
HOH
170
3
HOH
HOH
367
B
HOH
66
3
HOH
HOH
368
B
HOH
87
3
HOH
HOH
369
B
HOH
92
3
HOH
HOH
370
B
HOH
2
3
HOH
HOH
371
B
HOH
33
3
HOH
HOH
372
B
HOH
118
3
HOH
HOH
373
B
HOH
70
3
HOH
HOH
374
B
HOH
30
3
HOH
HOH
375
B
HOH
21
3
HOH
HOH
376
B
HOH
37
3
HOH
HOH
377
B
HOH
113
3
HOH
HOH
378
B
HOH
176
3
HOH
HOH
379
B
HOH
200
3
HOH
HOH
380
B
HOH
19
3
HOH
HOH
381
B
HOH
35
3
HOH
HOH
382
B
HOH
20
3
HOH
HOH
383
B
HOH
9
3
HOH
HOH
384
B
HOH
34
3
HOH
HOH
385
B
HOH
58
3
HOH
HOH
386
B
HOH
74
3
HOH
HOH
387
B
HOH
41
3
HOH
HOH
388
B
HOH
111
3
HOH
HOH
389
B
HOH
157
3
HOH
HOH
390
B
HOH
173
3
HOH
HOH
391
B
HOH
40
3
HOH
HOH
392
B
HOH
155
3
HOH
HOH
393
B
HOH
75
3
HOH
HOH
394
B
HOH
160
3
HOH
HOH
395
B
HOH
80
3
HOH
HOH
396
B
HOH
39
3
HOH
HOH
397
B
HOH
86
3
HOH
HOH
398
B
HOH
13
3
HOH
HOH
399
B
HOH
6
3
HOH
HOH
400
B
HOH
201
3
HOH
HOH
401
B
HOH
119
3
HOH
HOH
402
B
HOH
193
3
HOH
HOH
403
B
HOH
184
3
HOH
HOH
404
B
HOH
101
3
HOH
HOH
405
B
HOH
156
3
HOH
HOH
406
B
HOH
121
3
HOH
HOH
407
B
HOH
72
3
HOH
HOH
408
B
HOH
65
3
HOH
HOH
409
B
HOH
4
3
HOH
HOH
410
B
HOH
202
3
HOH
HOH
411
B
HOH
50
3
HOH
HOH
412
B
HOH
47
3
HOH
HOH
413
B
HOH
154
3
HOH
HOH
414
B
HOH
67
3
HOH
HOH
415
B
HOH
31
3
HOH
HOH
416
B
HOH
29
3
HOH
HOH
417
B
HOH
8
3
HOH
HOH
418
B
HOH
165
3
HOH
HOH
419
B
HOH
123
3
HOH
HOH
420
B
HOH
126
3
HOH
HOH
421
B
HOH
15
3
HOH
HOH
422
B
HOH
18
3
HOH
HOH
423
B
HOH
177
3
HOH
HOH
424
B
HOH
159
3
HOH
HOH
425
B
HOH
27
3
HOH
HOH
426
B
HOH
122
3
HOH
HOH
427
B
HOH
42
3
HOH
HOH
428
B
HOH
196
3
HOH
HOH
429
B
HOH
181
3
HOH
HOH
430
B
HOH
45
3
HOH
HOH
431
B
HOH
96
3
HOH
HOH
432
B
HOH
52
3
HOH
HOH
433
B
HOH
77
3
HOH
HOH
434
B
HOH
43
3
HOH
HOH
435
B
HOH
130
3
HOH
HOH
436
B
HOH
182
3
HOH
HOH
437
B
HOH
25
3
HOH
HOH
438
B
HOH
93
3
HOH
HOH
439
B
HOH
125
3
HOH
HOH
440
B
HOH
62
3
HOH
HOH
441
B
HOH
11
3
HOH
HOH
442
B
HOH
114
3
HOH
HOH
443
B
HOH
137
3
HOH
HOH
444
B
HOH
79
3
HOH
HOH
445
B
HOH
199
3
HOH
HOH
446
B
HOH
194
3
HOH
HOH
447
B
HOH
163
3
HOH
HOH
448
B
HOH
28
3
HOH
HOH
449
B
HOH
124
3
HOH
HOH
450
B
HOH
185
3
HOH
HOH
451
B
HOH
89
3
HOH
HOH
452
B
HOH
189
3
HOH
HOH
453
B
HOH
84
3
HOH
HOH
454
B
HOH
106
3
HOH
HOH
455
B
HOH
73
3
HOH
HOH
456
B
HOH
131
3
HOH
HOH
457
B
HOH
168
3
HOH
HOH
458
B
HOH
76
3
HOH
HOH
459
B
HOH
188
3
HOH
HOH
460
B
HOH
110
3
HOH
HOH
461
B
HOH
167
3
HOH
HOH
462
B
HOH
132
3
HOH
HOH
463
B
HOH
69
3
HOH
HOH
464
B
HOH
150
3
HOH
HOH
465
B
HOH
128
3
HOH
HOH
466
B
HOH
85
3
HOH
HOH
467
B
HOH
203
3
HOH
HOH
468
B
HOH
109
3
HOH
HOH
469
B
HOH
147
3
HOH
HOH
470
B
HOH
99
3
HOH
HOH
471
B
HOH
192
3
HOH
HOH
472
B
HOH
129
3
HOH
HOH
473
B
HOH
191
3
HOH
HOH
474
B
HOH
161
3
HOH
HOH
475
B
HOH
169
3
HOH
HOH
476
B
HOH
180
3
HOH
HOH
477
B
HOH
166
3
HOH
HOH
478
B
HOH
204
3
HOH
HOH
479
B
HOH
115
3
HOH
HOH
480
B
SER
2
n
1
SER
2
B
ALA
3
n
2
ALA
3
B
LYS
4
n
3
LYS
4
B
ASP
5
n
4
ASP
5
B
GLU
6
n
5
GLU
6
B
ARG
7
n
6
ARG
7
B
ALA
8
n
7
ALA
8
B
ARG
9
n
8
ARG
9
B
GLU
10
n
9
GLU
10
B
ILE
11
n
10
ILE
11
B
LEU
12
n
11
LEU
12
B
ARG
13
n
12
ARG
13
B
GLY
14
n
13
GLY
14
B
PHE
15
n
14
PHE
15
B
LYS
16
n
15
LYS
16
B
LEU
17
n
16
LEU
17
B
ASN
18
n
17
ASN
18
B
TRP
19
n
18
TRP
19
B
MET
20
n
19
MET
20
B
ASN
21
n
20
ASN
21
B
LEU
22
n
21
LEU
22
B
ARG
23
n
22
ARG
23
B
ASP
24
n
23
ASP
24
B
ALA
25
n
24
ALA
25
B
ALA
26
n
25
GLU
26
B
THR
27
n
26
THR
27
B
GLY
28
n
27
GLY
28
B
LYS
29
n
28
LYS
29
B
ILE
30
n
29
ILE
30
B
LEU
31
n
30
LEU
31
B
TRP
32
n
31
TRP
32
B
GLN
33
n
32
GLN
33
B
GLY
34
n
33
GLY
34
B
THR
35
n
34
THR
35
B
GLU
36
n
35
GLU
36
B
ASP
37
n
36
ASP
37
B
LEU
38
n
37
LEU
38
B
SER
39
n
38
SER
39
B
VAL
40
n
39
VAL
40
B
PRO
41
n
40
PRO
41
B
GLY
42
n
41
GLY
42
B
VAL
43
n
42
VAL
43
B
GLU
44
n
43
GLU
44
B
HIS
45
n
44
HIS
45
B
GLU
46
n
45
GLU
46
B
ALA
47
n
46
ALA
47
B
ARG
48
n
47
ARG
48
B
VAL
49
n
48
VAL
49
B
PRO
50
n
49
PRO
50
B
LYS
51
n
50
LYS
51
B
LYS
52
n
51
LYS
52
B
ILE
53
n
52
ILE
53
B
LEU
54
n
53
LEU
54
B
LYS
55
n
54
LYS
55
B
CYS
56
n
55
CYS
56
B
LYS
57
n
56
LYS
57
B
ALA
58
n
57
ALA
58
B
VAL
59
n
58
VAL
59
B
SER
60
n
59
SER
60
B
ARG
61
n
60
ARG
61
B
GLU
62
n
61
GLU
62
B
LEU
63
n
62
LEU
63
B
ASN
64
n
63
ASN
64
B
PHE
65
n
64
PHE
65
B
SER
66
n
65
SER
66
B
SER
67
n
66
SER
67
B
THR
68
n
67
THR
68
B
GLU
69
n
68
GLU
69
B
GLN
70
n
69
GLN
70
B
MET
71
n
70
MET
71
B
GLU
72
n
71
GLU
72
B
LYS
73
n
72
LYS
73
B
PHE
74
n
73
PHE
74
B
ARG
75
n
74
ARG
75
B
LEU
76
n
75
LEU
76
B
GLU
77
n
76
GLU
77
B
GLN
78
n
77
GLN
78
B
LYS
79
n
78
LYS
79
B
VAL
80
n
79
VAL
80
B
TYR
81
n
80
TYR
81
B
PHE
82
n
81
PHE
82
B
LYS
83
n
82
LYS
83
B
GLY
84
n
83
GLY
84
B
GLN
85
n
84
GLN
85
B
CYS
86
n
85
CYS
86
B
LEU
87
n
86
LEU
87
B
GLU
88
n
87
GLU
88
B
GLU
89
n
88
GLU
89
B
TRP
90
n
89
TRP
90
B
PHE
91
n
90
PHE
91
B
PHE
92
n
91
PHE
92
B
GLU
93
n
92
GLU
93
B
PHE
94
n
93
PHE
94
B
GLY
95
n
94
GLY
95
B
PHE
96
n
95
PHE
96
B
VAL
97
n
96
VAL
97
B
ILE
98
n
97
ILE
98
B
PRO
99
n
98
PRO
99
B
ASN
100
n
99
ASN
100
B
SER
101
n
100
SER
101
B
THR
102
n
101
THR
102
B
ASN
103
n
102
ASN
103
B
THR
104
n
103
THR
104
B
TRP
105
n
104
TRP
105
B
GLN
106
n
105
GLN
106
B
SER
107
n
106
SER
107
B
LEU
108
n
107
LEU
108
B
ILE
109
n
108
ILE
109
B
GLU
110
n
109
GLU
110
B
ALA
111
n
110
ALA
111
B
ALA
112
n
111
ALA
112
B
PRO
113
n
112
PRO
113
B
GLU
114
n
113
GLU
114
B
SER
115
n
114
SER
115
B
GLN
116
n
115
GLN
116
B
MET
117
n
116
MET
117
B
MET
118
n
117
MET
118
B
PRO
119
n
118
PRO
119
B
ALA
120
n
119
ALA
120
B
SER
121
n
120
SER
121
B
VAL
122
n
121
VAL
122
B
LEU
123
n
122
LEU
123
B
THR
124
n
123
THR
124
B
GLY
125
n
124
GLY
125
B
ASN
126
n
125
ASN
126
B
VAL
127
n
126
VAL
127
B
ILE
128
n
127
ILE
128
B
ILE
129
n
128
ILE
129
B
GLU
130
n
129
GLU
130
B
THR
131
n
130
THR
131
B
LYS
132
n
131
LYS
132
B
PHE
133
n
132
PHE
133
B
PHE
134
n
133
PHE
134
B
ASP
135
n
134
ASP
135
B
ASP
136
n
135
ASP
136
B
ASP
137
n
136
ASP
137
B
LEU
138
n
137
LEU
138
B
LEU
139
n
138
LEU
139
B
VAL
140
n
139
VAL
140
B
SER
141
n
140
SER
141
B
THR
142
n
141
THR
142
B
SER
143
n
142
SER
143
B
ARG
144
n
143
ARG
144
B
VAL
145
n
144
VAL
145
B
ARG
146
n
145
ARG
146
B
LEU
147
n
146
LEU
147
B
PHE
148
n
147
PHE
148
B
TYR
149
n
148
TYR
149
B
VAL
150
n
149
VAL
150
B
author_and_software_defined_assembly
PISA
1
monomeric
0
0
8100
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
B
O
LEU
31
A
O
LEU
30
B
N
LEU
22
A
N
LEU
21
B
N
TRP
19
A
N
TRP
18
B
O
ASN
64
A
O
ASN
63
B
N
VAL
59
A
N
VAL
58
B
O
ILE
109
A
O
ILE
108
B
N
VAL
49
A
N
VAL
48
B
O
PHE
148
A
O
PHE
147
B
O
VAL
140
A
O
VAL
139
B
N
PHE
133
A
N
PHE
132
B
O
ILE
128
A
O
ILE
127
B
N
TYR
81
A
N
TYR
80
B
N
VAL
80
A
N
VAL
79
B
O
LEU
87
A
O
LEU
86
1
B
CG
GLU
10
A
CG
GLU
9
1
Y
1
B
CD
GLU
10
A
CD
GLU
9
1
Y
1
B
OE1
GLU
10
A
OE1
GLU
9
1
Y
1
B
OE2
GLU
10
A
OE2
GLU
9
1
Y
1
B
CG
GLU
26
A
CG
GLU
25
1
Y
1
B
CD
GLU
26
A
CD
GLU
25
1
Y
1
B
OE1
GLU
26
A
OE1
GLU
25
1
Y
1
B
OE2
GLU
26
A
OE2
GLU
25
1
Y
1
B
CG
GLU
36
A
CG
GLU
35
1
Y
1
B
CD
GLU
36
A
CD
GLU
35
1
Y
1
B
OE1
GLU
36
A
OE1
GLU
35
1
Y
1
B
OE2
GLU
36
A
OE2
GLU
35
1
Y
1
B
CG
GLU
72
A
CG
GLU
71
1
Y
1
B
CD
GLU
72
A
CD
GLU
71
1
Y
1
B
OE1
GLU
72
A
OE1
GLU
71
1
Y
1
B
OE2
GLU
72
A
OE2
GLU
71
1
Y
1
B
CG
GLN
106
A
CG
GLN
105
1
Y
1
B
CD
GLN
106
A
CD
GLN
105
1
Y
1
B
OE1
GLN
106
A
OE1
GLN
105
1
Y
1
B
NE2
GLN
106
A
NE2
GLN
105
1
Y
1
B
CG
GLU
114
A
CG
GLU
113
1
Y
1
B
CD
GLU
114
A
CD
GLU
113
1
Y
1
B
OE1
GLU
114
A
OE1
GLU
113
1
Y
1
B
OE2
GLU
114
A
OE2
GLU
113
1
Y
1
B
B
C
N
ARG
VAL
144
145
1.16
1
-16.95
2.20
117.20
100.25
B
B
B
CA
C
N
PHE
PHE
PHE
133
133
134
Y
1
15.04
1.60
122.70
137.74
B
B
B
O
C
N
PHE
PHE
PHE
133
133
134
Y
1
B
B
C
N
ARG
VAL
144
145
-0.180
0.023
1.336
1.156
Y
1
B
GLU
114
-97.74
41.85
1
B
ASP
136
59.74
-114.79
61.310
20.7880
10.340
0.3600
0.3600
-0.0000
0.3600
-0.0000
-1.1800
0.9650
0.9570
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
0.2034
0.1891
0.1898
1.4000
44.7000
2098
39854
5.0000
99.9600
0.9080
0.0360
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.0560
0.0560
0.8000
0.8000
1.2000
3T5G
1.4000
44.7000
180
1416
21.73
33.46
43
0
1193
149
0.011
0.020
1320
0.003
0.020
1276
1.665
1.985
1792
0.998
3.013
2934
6.039
5.000
159
39.260
22.951
61
11.861
15.000
235
16.345
15.000
12
0.127
0.200
195
0.006
0.020
1460
0.001
0.020
328
0.2830
0.0000
0.2670
1.4360
153
2902
3055
20
99.9700
1.4
44.700
5ML3
39854
0.075
1
16.5
9.6
100
0.64
1.4
1.5
3.4
1
9.4
100
data scaling
XSCALE
refinement
REFMAC
5.7.0032
data extraction
PDB_EXTRACT
3.22
data reduction
XDS
phasing
MOLREP
N
The crystal structure of PDE6D in complex to Deltasonamide1
1
N
N
2
N
N
3
N
N
B
SER
2
A
SER
1
HELX_P
B
GLY
14
A
GLY
13
1
AA1
13
B
LYS
52
A
LYS
51
HELX_P
B
CYS
56
A
CYS
55
5
AA2
5
B
PRO
119
A
PRO
118
HELX_P
B
THR
124
A
THR
123
1
AA3
6
LIPID BINDING PROTEIN
Prenyl binding protein, farnesylated KRas, plasma membrane, Arl2, Lipid binding protein
B
PRO
113
A
PRO
112
1
B
GLU
114
A
GLU
113
-27.43
PDE6D_HUMAN
UNP
1
2
O43924
SAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKVY
FKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
2
150
5ML3
2
150
O43924
B
1
1
149
4
5
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
B
ILE
30
A
ILE
29
B
GLY
34
A
GLY
33
B
PHE
15
A
PHE
14
B
ASP
24
A
ASP
23
B
ALA
58
A
ALA
57
B
SER
67
A
SER
66
B
SER
101
A
SER
100
B
GLU
110
A
GLU
109
B
GLU
44
A
GLU
43
B
PRO
50
A
PRO
49
B
LEU
138
A
LEU
137
B
VAL
150
A
VAL
149
B
VAL
127
A
VAL
126
B
ASP
135
A
ASP
134
B
MET
71
A
MET
70
B
PHE
82
A
PHE
81
B
GLN
85
A
GLN
84
B
VAL
97
A
VAL
96
binding site for residue DL3 B 201
B
DL3
201
Software
23
B
LEU
17
A
LEU
16
23
1_555
B
MET
20
A
MET
19
23
1_555
B
LEU
22
A
LEU
21
23
1_555
B
TRP
32
A
TRP
31
23
1_555
B
VAL
49
A
VAL
48
23
1_555
B
ILE
53
A
ILE
52
23
1_555
B
LEU
54
A
LEU
53
23
1_555
B
CYS
56
A
CYS
55
23
1_555
B
LYS
57
A
LYS
56
23
1_555
B
VAL
59
A
VAL
58
23
1_555
B
ARG
61
A
ARG
60
23
1_555
B
GLN
78
A
GLN
77
23
1_555
B
GLU
88
A
GLU
87
23
1_555
B
TRP
90
A
TRP
89
23
1_555
B
ILE
109
A
ILE
108
23
1_555
B
MET
117
A
MET
116
23
1_555
B
THR
131
A
THR
130
23
1_555
B
PHE
133
A
PHE
132
23
1_555
B
LEU
147
A
LEU
146
23
1_555
B
TYR
149
A
TYR
148
23
1_555
B
HOH
341
C
HOH
23
1_555
B
HOH
399
C
HOH
23
1_555
B
HOH
430
C
HOH
23
1_555
154
P 32 2 1