0.017960
0.010369
0.000000
0.000000
0.020738
0.000000
0.000000
0.000000
0.008580
0.00000
0.00000
0.00000
Gunther, Z.
Papke, B.
Ismail, S.
Vartak, N.
Chandra, A.
Hoffmann, M.
Hahn, S.
Triola, G.
Wittinghofer, A.
Bastiaens, P.
Waldmann, H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
55.680
55.680
116.550
C38 H32 N4 O
560.687
1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
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
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
Y
1
N
C
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
C
Y
8
N
N
Y
9
N
C
Y
10
N
C
Y
11
N
C
Y
12
N
C
Y
13
N
C
Y
14
N
C
Y
15
N
N
Y
16
N
C
Y
17
N
C
Y
18
N
C
Y
19
N
C
Y
20
N
C
Y
21
N
C
Y
22
N
C
N
23
N
O
N
24
N
C
N
25
R
C
N
26
N
C
N
27
N
C
N
28
N
C
Y
29
N
N
Y
30
N
C
Y
31
N
C
Y
32
N
C
Y
33
N
C
Y
34
N
C
Y
35
N
C
Y
36
N
N
Y
37
N
C
Y
38
N
C
Y
39
N
C
Y
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
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
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
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
N
N
77
S
C
N
78
N
C
N
79
N
O
N
80
N
C
N
81
N
O
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
S
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
C
N
95
N
C
N
96
N
N
N
97
N
C
N
98
N
N
N
99
N
N
N
100
N
O
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
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
H
N
116
N
N
N
117
S
C
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
C
N
122
N
O
N
123
N
N
N
124
N
O
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
N
N
134
S
C
N
135
N
C
N
136
N
O
N
137
N
C
N
138
N
C
N
139
N
O
N
140
N
O
N
141
N
O
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
N
N
150
R
C
N
151
N
C
N
152
N
O
N
153
N
C
N
154
N
S
N
155
N
O
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
N
N
164
S
C
N
165
N
C
N
166
N
O
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
N
171
N
N
N
172
N
O
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
O
N
191
N
O
N
192
N
O
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
N
N
203
N
C
N
204
N
C
N
205
N
O
N
206
N
O
N
207
N
H
N
208
N
H
N
209
N
H
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
N
C
Y
217
N
C
Y
218
N
N
Y
219
N
C
Y
220
N
C
Y
221
N
N
N
222
N
O
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
O
N
234
N
H
N
235
N
H
N
236
N
N
N
237
S
C
N
238
N
C
N
239
N
O
N
240
S
C
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
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
H
N
258
N
N
N
259
S
C
N
260
N
C
N
261
N
O
N
262
N
C
N
263
N
C
N
264
N
C
N
265
N
C
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
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
C
N
288
N
N
N
289
N
O
N
290
N
H
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
H
N
303
N
H
N
304
N
H
N
305
N
N
N
306
S
C
N
307
N
C
N
308
N
O
N
309
N
C
N
310
N
C
N
311
N
S
N
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
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
Y
335
N
C
N
336
N
O
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
O
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
O
N
371
N
O
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
N
N
380
S
C
N
381
N
C
N
382
N
O
N
383
R
C
N
384
N
O
N
385
N
C
N
386
N
O
N
387
N
H
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
N
N
397
S
C
N
398
N
C
N
399
N
O
N
400
N
C
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
N
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
C
Y
409
N
C
N
410
N
O
N
411
N
H
N
412
N
H
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
N
N
424
S
C
N
425
N
C
N
426
N
O
N
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
C
Y
431
N
C
Y
432
N
C
Y
433
N
C
N
434
N
O
N
435
N
O
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
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
N
N
448
S
C
N
449
N
C
N
450
N
O
N
451
N
C
N
452
N
C
N
453
N
C
N
454
N
O
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
Y
1
N
doub
Y
2
N
sing
Y
3
N
sing
Y
4
N
sing
Y
5
N
doub
Y
6
N
doub
Y
7
N
doub
Y
8
N
sing
Y
9
N
sing
N
10
N
sing
Y
11
N
sing
Y
12
N
doub
Y
13
N
sing
Y
14
N
doub
Y
15
N
doub
Y
16
N
sing
Y
17
N
sing
Y
18
N
doub
Y
19
N
sing
Y
20
N
sing
Y
21
N
doub
N
22
N
sing
N
23
N
sing
Y
24
N
doub
Y
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
doub
N
31
N
sing
N
32
N
sing
Y
33
N
sing
Y
34
N
sing
Y
35
N
doub
Y
36
N
sing
Y
37
N
sing
Y
38
N
doub
Y
39
N
sing
Y
40
N
doub
Y
41
N
doub
Y
42
N
sing
Y
43
N
sing
N
44
N
sing
Y
45
N
doub
Y
46
N
doub
Y
47
N
sing
Y
48
N
doub
Y
49
N
sing
N
50
N
sing
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
sing
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
sing
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
sing
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
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
doub
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
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
doub
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
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
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
doub
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
doub
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
sing
N
188
N
sing
N
189
N
doub
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
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
doub
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
doub
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
Y
221
N
sing
Y
222
N
doub
Y
223
N
doub
N
224
N
sing
Y
225
N
sing
N
226
N
sing
Y
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
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
doub
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
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
doub
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
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
doub
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
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
doub
N
306
N
sing
N
307
N
sing
N
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
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
doub
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
Y
329
N
doub
Y
330
N
sing
Y
331
N
sing
N
332
N
sing
Y
333
N
doub
N
334
N
sing
Y
335
N
doub
N
336
N
sing
Y
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
doub
N
348
N
sing
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
N
369
N
sing
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
doub
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
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
sing
N
393
N
doub
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
Y
398
N
doub
Y
399
N
sing
Y
400
N
sing
N
401
N
sing
Y
402
N
doub
Y
403
N
sing
Y
404
N
sing
N
405
N
sing
Y
406
N
sing
Y
407
N
doub
N
408
N
sing
Y
409
N
doub
N
410
N
sing
Y
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
doub
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
Y
426
N
doub
Y
427
N
sing
Y
428
N
sing
N
429
N
sing
Y
430
N
doub
N
431
N
sing
Y
432
N
doub
N
433
N
sing
Y
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
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
doub
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
N
456
N
sing
UK
Nature
NATUAS
0006
0028-0836
497
638
642
10.1038/nature12205
23698361
Small molecule inhibition of the KRAS PDEd interaction impairs oncogenic KRAS signalling
2013
10.2210/pdb4jvb/pdb
pdb_00004jvb
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
PIXEL
2011-08-12
DECTRIS PILATUS 6M
SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
1
1.0
X10SA
SLS
1
SYNCHROTRON
SLS BEAMLINE X10SA
17585.121
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
1
man
polymer
560.687
1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
1
syn
non-polymer
18.015
water
156
nat
water
GMP-PDE delta, Protein p17
no
no
GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ
KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
GSMSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQ
KVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
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
n
n
n
human
sample
PDE6D, PDED
9606
Homo sapiens
562
Escherichia coli
1
2.97
58.53
VAPOR DIFFUSION, SITTING DROP
4.6
100mM Sodium Acetate, 2.0M NaCl, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2013-05-22
1
1
2013-06-05
1
2
2023-09-20
_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
RCSB
Y
RCSB
2013-03-25
REL
REL
1M0
1-benzyl-2-(4-{[(2R)-2-(2-phenyl-1H-benzimidazol-1-yl)pent-4-en-1-yl]oxy}phenyl)-1H-benzimidazole
HOH
water
3T5G
PDB
experimental model
1M0
1
2
1M0
1M0
201
B
HOH
301
3
HOH
HOH
301
B
HOH
302
3
HOH
HOH
302
B
HOH
303
3
HOH
HOH
303
B
HOH
304
3
HOH
HOH
304
B
HOH
305
3
HOH
HOH
305
B
HOH
306
3
HOH
HOH
306
B
HOH
307
3
HOH
HOH
307
B
HOH
308
3
HOH
HOH
308
B
HOH
309
3
HOH
HOH
309
B
HOH
310
3
HOH
HOH
310
B
HOH
311
3
HOH
HOH
311
B
HOH
312
3
HOH
HOH
312
B
HOH
313
3
HOH
HOH
313
B
HOH
314
3
HOH
HOH
314
B
HOH
315
3
HOH
HOH
315
B
HOH
316
3
HOH
HOH
316
B
HOH
317
3
HOH
HOH
317
B
HOH
318
3
HOH
HOH
318
B
HOH
319
3
HOH
HOH
319
B
HOH
320
3
HOH
HOH
320
B
HOH
321
3
HOH
HOH
321
B
HOH
322
3
HOH
HOH
322
B
HOH
323
3
HOH
HOH
323
B
HOH
324
3
HOH
HOH
324
B
HOH
325
3
HOH
HOH
325
B
HOH
327
3
HOH
HOH
326
B
HOH
328
3
HOH
HOH
327
B
HOH
329
3
HOH
HOH
328
B
HOH
331
3
HOH
HOH
329
B
HOH
332
3
HOH
HOH
330
B
HOH
333
3
HOH
HOH
331
B
HOH
334
3
HOH
HOH
332
B
HOH
335
3
HOH
HOH
333
B
HOH
336
3
HOH
HOH
334
B
HOH
337
3
HOH
HOH
335
B
HOH
338
3
HOH
HOH
336
B
HOH
339
3
HOH
HOH
337
B
HOH
340
3
HOH
HOH
338
B
HOH
341
3
HOH
HOH
339
B
HOH
342
3
HOH
HOH
340
B
HOH
343
3
HOH
HOH
341
B
HOH
344
3
HOH
HOH
342
B
HOH
345
3
HOH
HOH
343
B
HOH
346
3
HOH
HOH
344
B
HOH
347
3
HOH
HOH
345
B
HOH
348
3
HOH
HOH
346
B
HOH
349
3
HOH
HOH
347
B
HOH
350
3
HOH
HOH
348
B
HOH
351
3
HOH
HOH
349
B
HOH
352
3
HOH
HOH
350
B
HOH
353
3
HOH
HOH
351
B
HOH
354
3
HOH
HOH
352
B
HOH
355
3
HOH
HOH
353
B
HOH
356
3
HOH
HOH
354
B
HOH
357
3
HOH
HOH
355
B
HOH
358
3
HOH
HOH
356
B
HOH
359
3
HOH
HOH
357
B
HOH
360
3
HOH
HOH
358
B
HOH
361
3
HOH
HOH
359
B
HOH
362
3
HOH
HOH
360
B
HOH
363
3
HOH
HOH
361
B
HOH
364
3
HOH
HOH
362
B
HOH
365
3
HOH
HOH
363
B
HOH
366
3
HOH
HOH
364
B
HOH
367
3
HOH
HOH
365
B
HOH
368
3
HOH
HOH
366
B
HOH
369
3
HOH
HOH
367
B
HOH
370
3
HOH
HOH
368
B
HOH
372
3
HOH
HOH
369
B
HOH
373
3
HOH
HOH
370
B
HOH
374
3
HOH
HOH
371
B
HOH
375
3
HOH
HOH
372
B
HOH
376
3
HOH
HOH
373
B
HOH
377
3
HOH
HOH
374
B
HOH
378
3
HOH
HOH
375
B
HOH
379
3
HOH
HOH
376
B
HOH
380
3
HOH
HOH
377
B
HOH
381
3
HOH
HOH
378
B
HOH
382
3
HOH
HOH
379
B
HOH
383
3
HOH
HOH
380
B
HOH
385
3
HOH
HOH
381
B
HOH
386
3
HOH
HOH
382
B
HOH
387
3
HOH
HOH
383
B
HOH
388
3
HOH
HOH
384
B
HOH
389
3
HOH
HOH
385
B
HOH
390
3
HOH
HOH
386
B
HOH
391
3
HOH
HOH
387
B
HOH
392
3
HOH
HOH
388
B
HOH
393
3
HOH
HOH
389
B
HOH
394
3
HOH
HOH
390
B
HOH
395
3
HOH
HOH
391
B
HOH
396
3
HOH
HOH
392
B
HOH
398
3
HOH
HOH
393
B
HOH
399
3
HOH
HOH
394
B
HOH
400
3
HOH
HOH
395
B
HOH
401
3
HOH
HOH
396
B
HOH
403
3
HOH
HOH
397
B
HOH
404
3
HOH
HOH
398
B
HOH
405
3
HOH
HOH
399
B
HOH
406
3
HOH
HOH
400
B
HOH
408
3
HOH
HOH
401
B
HOH
409
3
HOH
HOH
402
B
HOH
410
3
HOH
HOH
403
B
HOH
411
3
HOH
HOH
404
B
HOH
412
3
HOH
HOH
405
B
HOH
413
3
HOH
HOH
406
B
HOH
414
3
HOH
HOH
407
B
HOH
415
3
HOH
HOH
408
B
HOH
416
3
HOH
HOH
409
B
HOH
417
3
HOH
HOH
410
B
HOH
418
3
HOH
HOH
411
B
HOH
419
3
HOH
HOH
412
B
HOH
420
3
HOH
HOH
413
B
HOH
421
3
HOH
HOH
414
B
HOH
422
3
HOH
HOH
415
B
HOH
423
3
HOH
HOH
416
B
HOH
424
3
HOH
HOH
417
B
HOH
425
3
HOH
HOH
418
B
HOH
426
3
HOH
HOH
419
B
HOH
428
3
HOH
HOH
420
B
HOH
430
3
HOH
HOH
421
B
HOH
431
3
HOH
HOH
422
B
HOH
432
3
HOH
HOH
423
B
HOH
433
3
HOH
HOH
424
B
HOH
434
3
HOH
HOH
425
B
HOH
435
3
HOH
HOH
426
B
HOH
436
3
HOH
HOH
427
B
HOH
437
3
HOH
HOH
428
B
HOH
438
3
HOH
HOH
429
B
HOH
439
3
HOH
HOH
430
B
HOH
440
3
HOH
HOH
431
B
HOH
441
3
HOH
HOH
432
B
HOH
442
3
HOH
HOH
433
B
HOH
443
3
HOH
HOH
434
B
HOH
444
3
HOH
HOH
435
B
HOH
445
3
HOH
HOH
436
B
HOH
446
3
HOH
HOH
437
B
HOH
447
3
HOH
HOH
438
B
HOH
448
3
HOH
HOH
439
B
HOH
449
3
HOH
HOH
440
B
HOH
450
3
HOH
HOH
441
B
HOH
451
3
HOH
HOH
442
B
HOH
452
3
HOH
HOH
443
B
HOH
453
3
HOH
HOH
444
B
HOH
454
3
HOH
HOH
445
B
HOH
455
3
HOH
HOH
446
B
HOH
456
3
HOH
HOH
447
B
HOH
457
3
HOH
HOH
448
B
HOH
458
3
HOH
HOH
449
B
HOH
459
3
HOH
HOH
450
B
HOH
462
3
HOH
HOH
451
B
HOH
463
3
HOH
HOH
452
B
HOH
468
3
HOH
HOH
453
B
HOH
469
3
HOH
HOH
454
B
HOH
471
3
HOH
HOH
455
B
HOH
472
3
HOH
HOH
456
B
n
1
-1
B
n
2
0
B
n
3
1
B
SER
2
n
4
SER
2
B
ALA
3
n
5
ALA
3
B
LYS
4
n
6
LYS
4
B
ASP
5
n
7
ASP
5
B
GLU
6
n
8
GLU
6
B
ARG
7
n
9
ARG
7
B
ALA
8
n
10
ALA
8
B
ARG
9
n
11
ARG
9
B
GLU
10
n
12
GLU
10
B
ILE
11
n
13
ILE
11
B
LEU
12
n
14
LEU
12
B
ARG
13
n
15
ARG
13
B
GLY
14
n
16
GLY
14
B
PHE
15
n
17
PHE
15
B
LYS
16
n
18
LYS
16
B
LEU
17
n
19
LEU
17
B
ASN
18
n
20
ASN
18
B
TRP
19
n
21
TRP
19
B
MET
20
n
22
MET
20
B
ASN
21
n
23
ASN
21
B
LEU
22
n
24
LEU
22
B
ARG
23
n
25
ARG
23
B
ASP
24
n
26
ASP
24
B
ALA
25
n
27
ALA
25
B
ALA
26
n
28
GLU
26
B
ALA
27
n
29
THR
27
B
GLY
28
n
30
GLY
28
B
LYS
29
n
31
LYS
29
B
ILE
30
n
32
ILE
30
B
LEU
31
n
33
LEU
31
B
TRP
32
n
34
TRP
32
B
GLN
33
n
35
GLN
33
B
GLY
34
n
36
GLY
34
B
THR
35
n
37
THR
35
B
GLU
36
n
38
GLU
36
B
ASP
37
n
39
ASP
37
B
LEU
38
n
40
LEU
38
B
SER
39
n
41
SER
39
B
VAL
40
n
42
VAL
40
B
PRO
41
n
43
PRO
41
B
GLY
42
n
44
GLY
42
B
VAL
43
n
45
VAL
43
B
GLU
44
n
46
GLU
44
B
HIS
45
n
47
HIS
45
B
GLU
46
n
48
GLU
46
B
ALA
47
n
49
ALA
47
B
ARG
48
n
50
ARG
48
B
VAL
49
n
51
VAL
49
B
PRO
50
n
52
PRO
50
B
LYS
51
n
53
LYS
51
B
LYS
52
n
54
LYS
52
B
ILE
53
n
55
ILE
53
B
LEU
54
n
56
LEU
54
B
LYS
55
n
57
LYS
55
B
CYS
56
n
58
CYS
56
B
LYS
57
n
59
LYS
57
B
ALA
58
n
60
ALA
58
B
VAL
59
n
61
VAL
59
B
SER
60
n
62
SER
60
B
ARG
61
n
63
ARG
61
B
GLU
62
n
64
GLU
62
B
LEU
63
n
65
LEU
63
B
ASN
64
n
66
ASN
64
B
PHE
65
n
67
PHE
65
B
SER
66
n
68
SER
66
B
SER
67
n
69
SER
67
B
THR
68
n
70
THR
68
B
GLU
69
n
71
GLU
69
B
GLN
70
n
72
GLN
70
B
MET
71
n
73
MET
71
B
GLU
72
n
74
GLU
72
B
LYS
73
n
75
LYS
73
B
PHE
74
n
76
PHE
74
B
ARG
75
n
77
ARG
75
B
LEU
76
n
78
LEU
76
B
GLU
77
n
79
GLU
77
B
GLN
78
n
80
GLN
78
B
LYS
79
n
81
LYS
79
B
VAL
80
n
82
VAL
80
B
TYR
81
n
83
TYR
81
B
PHE
82
n
84
PHE
82
B
LYS
83
n
85
LYS
83
B
GLY
84
n
86
GLY
84
B
GLN
85
n
87
GLN
85
B
CYS
86
n
88
CYS
86
B
LEU
87
n
89
LEU
87
B
GLU
88
n
90
GLU
88
B
GLU
89
n
91
GLU
89
B
TRP
90
n
92
TRP
90
B
PHE
91
n
93
PHE
91
B
PHE
92
n
94
PHE
92
B
GLU
93
n
95
GLU
93
B
PHE
94
n
96
PHE
94
B
GLY
95
n
97
GLY
95
B
PHE
96
n
98
PHE
96
B
VAL
97
n
99
VAL
97
B
ILE
98
n
100
ILE
98
B
PRO
99
n
101
PRO
99
B
ASN
100
n
102
ASN
100
B
SER
101
n
103
SER
101
B
THR
102
n
104
THR
102
B
ASN
103
n
105
ASN
103
B
THR
104
n
106
THR
104
B
TRP
105
n
107
TRP
105
B
GLN
106
n
108
GLN
106
B
SER
107
n
109
SER
107
B
LEU
108
n
110
LEU
108
B
ILE
109
n
111
ILE
109
B
GLU
110
n
112
GLU
110
B
ALA
111
n
113
ALA
111
B
ALA
112
n
114
ALA
112
B
n
115
113
B
n
116
114
B
n
117
115
B
GLN
116
n
118
GLN
116
B
MET
117
n
119
MET
117
B
MET
118
n
120
MET
118
B
PRO
119
n
121
PRO
119
B
ALA
120
n
122
ALA
120
B
SER
121
n
123
SER
121
B
VAL
122
n
124
VAL
122
B
LEU
123
n
125
LEU
123
B
THR
124
n
126
THR
124
B
GLY
125
n
127
GLY
125
B
ASN
126
n
128
ASN
126
B
VAL
127
n
129
VAL
127
B
ILE
128
n
130
ILE
128
B
ILE
129
n
131
ILE
129
B
GLU
130
n
132
GLU
130
B
THR
131
n
133
THR
131
B
LYS
132
n
134
LYS
132
B
PHE
133
n
135
PHE
133
B
PHE
134
n
136
PHE
134
B
ASP
135
n
137
ASP
135
B
ASP
136
n
138
ASP
136
B
ASP
137
n
139
ASP
137
B
LEU
138
n
140
LEU
138
B
LEU
139
n
141
LEU
139
B
VAL
140
n
142
VAL
140
B
SER
141
n
143
SER
141
B
THR
142
n
144
THR
142
B
SER
143
n
145
SER
143
B
ARG
144
n
146
ARG
144
B
VAL
145
n
147
VAL
145
B
ARG
146
n
148
ARG
146
B
LEU
147
n
149
LEU
147
B
PHE
148
n
150
PHE
148
B
TYR
149
n
151
TYR
149
B
VAL
150
n
152
VAL
150
B
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
B
O
LEU
31
A
O
LEU
33
B
N
LEU
22
A
N
LEU
24
B
N
ASN
18
A
N
ASN
20
B
O
ASN
64
A
O
ASN
66
B
N
VAL
59
A
N
VAL
61
B
O
ILE
109
A
O
ILE
111
B
N
VAL
49
A
N
VAL
51
B
O
PHE
148
A
O
PHE
150
B
O
VAL
140
A
O
VAL
142
B
N
PHE
133
A
N
PHE
135
B
O
LYS
132
A
O
LYS
134
B
N
GLU
77
A
N
GLU
79
B
N
MET
71
A
N
MET
73
B
O
VAL
97
A
O
VAL
99
1
B
CG
GLU
26
A
CG
GLU
28
1
Y
1
B
CD
GLU
26
A
CD
GLU
28
1
Y
1
B
OE1
GLU
26
A
OE1
GLU
28
1
Y
1
B
OE2
GLU
26
A
OE2
GLU
28
1
Y
1
B
OG1
THR
27
A
OG1
THR
29
1
Y
1
B
CG2
THR
27
A
CG2
THR
29
1
Y
1
B
GLY
-1
A
GLY
1
1
Y
1
B
SER
0
A
SER
2
1
Y
1
B
MET
1
A
MET
3
1
Y
1
B
PRO
113
A
PRO
115
1
Y
1
B
GLU
114
A
GLU
116
1
Y
1
B
SER
115
A
SER
117
1
Y
1
B
B
O
O
GLY
HOH
28
430
2.18
1
3.11
0.50
120.30
123.41
B
B
B
NE
CZ
NH1
ARG
ARG
ARG
9
9
9
N
1
-3.14
0.50
120.30
117.16
B
B
B
NE
CZ
NH2
ARG
ARG
ARG
9
9
9
N
1
B
B
CG
CD
GLU
GLU
10
10
0.103
0.015
1.515
1.618
N
1
B
ASP
136
61.03
-114.44
31.822
1.11
0.55
0.00
1.11
0.00
-1.66
0.965
0.937
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.23588
0.18771
0.19011
1.75
27.84
1089
20677
20677
5.0
99.75
2.328
0.075
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.102
0.109
0.80
0.80
1.20
3T5g
MAXIMUM LIKELIHOOD
MASK
1.75
27.84
156
1388
43
0
1189
0.026
0.022
1279
2.483
1.995
1726
6.962
5.000
148
39.310
23.934
61
15.982
15.000
228
20.153
15.000
9
0.183
0.200
181
0.012
0.020
967
0.319
0.293
1.795
79
1368
20
99.59
1.75
27.842
4JVB
21768
21768
-3
-3
1
99.8
1.75
1.8
1
99.5
data collection
PRO
DC
phasing
MOLREP
refinement
REFMAC
5.6.0093
data reduction
XDS
data scaling
XSCALE
Crystal structure of PDE6D in complex with the inhibitor rac-2
1
N
N
2
N
N
3
N
N
Monomer
B
SER
2
A
SER
4
HELX_P
B
GLY
14
A
GLY
16
1
1
13
B
LYS
52
A
LYS
54
HELX_P
B
CYS
56
A
CYS
58
5
2
5
B
PRO
119
A
PRO
121
HELX_P
B
THR
124
A
THR
126
1
3
6
Protein binding/inhibitor
Immunoglobulin-like beta-sandwich, GDI-like solubilizing factor, prenyl binding, Protein binding-inhibitor complex
PDE6D_HUMAN
UNP
1
1
O43924
MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVSRELNFSSTEQMEKFRLEQKV
YFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPASVLTGNVIIETKFFDDDLLVSTSRVRLFYV
1
150
4JVB
1
150
O43924
B
1
3
152
1
expression tag
GLY
-1
4JVB
B
O43924
UNP
1
1
expression tag
SER
0
4JVB
B
O43924
UNP
2
4
5
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
B
ILE
30
A
ILE
32
B
GLY
34
A
GLY
36
B
PHE
15
A
PHE
17
B
ASP
24
A
ASP
26
B
ALA
58
A
ALA
60
B
SER
67
A
SER
69
B
SER
101
A
SER
103
B
GLU
110
A
GLU
112
B
GLU
44
A
GLU
46
B
PRO
50
A
PRO
52
B
LEU
138
A
LEU
140
B
VAL
150
A
VAL
152
B
VAL
127
A
VAL
129
B
ASP
135
A
ASP
137
B
MET
71
A
MET
73
B
PHE
82
A
PHE
84
B
GLN
85
A
GLN
87
B
VAL
97
A
VAL
99
BINDING SITE FOR RESIDUE 1M0 B 201
B
1M0
201
Software
15
B
LEU
17
A
LEU
19
15
1_555
B
LEU
22
A
LEU
24
15
1_555
B
TRP
32
A
TRP
34
15
1_555
B
ALA
47
A
ALA
49
15
1_555
B
VAL
49
A
VAL
51
15
1_555
B
ILE
53
A
ILE
55
15
1_555
B
ARG
61
A
ARG
63
15
1_555
B
GLN
78
A
GLN
80
15
1_555
B
GLU
88
A
GLU
90
15
1_555
B
ILE
109
A
ILE
111
15
1_555
B
ALA
111
A
ALA
113
15
1_555
B
MET
117
A
MET
119
15
1_555
B
ILE
129
A
ILE
131
15
1_555
B
LEU
147
A
LEU
149
15
1_555
B
TYR
149
A
TYR
151
15
1_555
154
P 32 2 1