0.025583
0.000000
0.000000
0.000000
0.023797
0.000000
0.000000
0.000000
0.010970
0.00000
0.00000
0.00000
Hunter, J.C.
Gurbani, D.
Lim, S.M.
Westover, K.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
39.088
42.022
91.159
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
Mg 2
24.305
MAGNESIUM ION
non-polymer
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
C14 H22 N6 O12 P2
528.305
5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
non-polymer
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
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
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
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
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
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
C
N
191
N
O
N
192
N
H
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
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
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
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
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
MG
N
251
N
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
Y
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
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
N
N
275
S
C
N
276
N
C
N
277
N
O
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
O
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
O
N
297
N
O
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
R
C
N
310
N
O
N
311
N
C
N
312
N
O
N
313
N
H
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
N
N
323
S
C
N
324
N
C
N
325
N
O
N
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
C
N
333
N
O
N
334
N
O
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
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
N
N
347
S
C
N
348
N
C
N
349
N
O
N
350
N
C
N
351
N
C
N
352
N
C
N
353
N
O
N
354
N
H
N
355
N
H
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
N
C
N
367
N
O
N
368
N
P
N
369
N
P
N
370
N
C
N
371
N
N
N
372
N
O
Y
373
N
C
N
374
N
N
N
375
N
O
Y
376
N
C
Y
377
N
N
N
378
N
O
Y
379
N
C
Y
380
N
N
N
381
N
O
N
382
R
C
N
383
N
N
N
384
N
O
N
385
R
C
N
386
N
O
N
387
S
C
N
388
N
O
N
389
R
C
N
390
N
O
N
391
N
C
N
392
N
O
N
393
N
C
N
394
N
O
N
395
N
C
N
396
N
O
N
397
N
C
N
398
N
C
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
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
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
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
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
doub
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
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
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
doub
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
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
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
doub
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
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
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
sing
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
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
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
sing
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
doub
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
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
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
doub
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
doub
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
sing
N
311
N
sing
N
312
N
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
N
322
N
sing
Y
323
N
doub
N
324
N
sing
Y
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
sing
N
336
N
doub
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
Y
352
N
sing
Y
353
N
doub
Y
354
N
doub
N
355
N
sing
N
356
N
doub
Y
357
N
sing
N
358
N
sing
Y
359
N
sing
N
360
N
sing
N
361
N
doub
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
sing
N
370
N
doub
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
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
111
8895
8900
10.1073/pnas.1404639111
24889603
In situ selectivity profiling and crystal structure of SML-8-73-1, an active site inhibitor of oncogenic K-Ras G12C.
2014
10.2210/pdb4nmm/pdb
pdb_00004nmm
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
CCD
2013-06-12
ADSC QUANTUM 315
ROSENBAUM-ROCK HIGH-RESOLUTION DOUBLE-CRYSTAL MONOCHROMATOR
SINGLE WAVELENGTH
M
x-ray
1
0.97921
1.0
19-ID
APS
0.97921
SYNCHROTRON
APS BEAMLINE 19-ID
19374.902
GTPase KRas
3.6.5.2
UNP residues 1-169
G12C
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
528.305
5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
1
syn
non-polymer
18.015
water
125
nat
water
K-Ras 2, Ki-Ras, c-K-ras, c-Ki-ras, GTPase KRas, N-terminally processed
no
no
GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFL
CVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTL
VREIRKHKEK
GMTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFL
CVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTL
VREIRKHKEK
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
human
sample
KRAS, KRAS2, RASK2
9606
Homo sapiens
469008
Escherichia coli
BL21
plasmid
pJexpress401
1
1.93
36.34
4.0
0.2M MMT pH4.0, 28% PEG 6,000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_conn_type
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2014-06-04
1
1
2014-07-09
1
2
2023-09-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.conn_type_id
_struct_conn.id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn_type.id
_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 a GDP-bound G12C Oncogenic Mutant of Human GTPase KRas
Crystal Structure of GDP-bound Human KRas
RCSB
Y
RCSB
2013-11-15
REL
REL
MG
MAGNESIUM ION
Y9Z
5'-O-[(S)-{[(S)-[2-(acetylamino)ethoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
HOH
water
THE UNREACTED INHIBITOR IS 5'-O-[(S)-{[(S)-{2-[(CHLOROCARBONYL)AMINO]ETHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE, THE CHLORO-ACETLY GROUP REACTS WITH CYS A12 RESIDUE ON THE PROTEIN TO FORM A THIO-ETHER LINKAGE BETWEEN C13 ATOM OF Y9Z AND SG ATOM of CYS A12 WITH THE CHLORINE ACTING AS A LEAVING GROUP. LIGAND Y9Z REPRESENT THE REACTED/BOUND FORM OF THE INHIBITOR.
THE SEQUENCE MATCHES UNIPROT ENTRY P01116, ISOFORM 2B WITH IDENTIFIER P01116-2
4EPV
PDB ENTRY 4EPV
PDB
experimental model
MG
201
2
MG
MG
201
A
Y9Z
202
3
Y9Z
Y9Z
202
A
HOH
301
4
HOH
HOH
301
A
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
304
4
HOH
HOH
304
A
HOH
305
4
HOH
HOH
305
A
HOH
306
4
HOH
HOH
306
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
309
4
HOH
HOH
309
A
HOH
310
4
HOH
HOH
310
A
HOH
311
4
HOH
HOH
311
A
HOH
312
4
HOH
HOH
312
A
HOH
313
4
HOH
HOH
313
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
319
4
HOH
HOH
319
A
HOH
320
4
HOH
HOH
320
A
HOH
321
4
HOH
HOH
321
A
HOH
322
4
HOH
HOH
322
A
HOH
323
4
HOH
HOH
323
A
HOH
324
4
HOH
HOH
324
A
HOH
325
4
HOH
HOH
325
A
HOH
326
4
HOH
HOH
326
A
HOH
327
4
HOH
HOH
327
A
HOH
328
4
HOH
HOH
328
A
HOH
329
4
HOH
HOH
329
A
HOH
330
4
HOH
HOH
330
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
336
4
HOH
HOH
336
A
HOH
337
4
HOH
HOH
337
A
HOH
338
4
HOH
HOH
338
A
HOH
339
4
HOH
HOH
339
A
HOH
340
4
HOH
HOH
340
A
HOH
341
4
HOH
HOH
341
A
HOH
342
4
HOH
HOH
342
A
HOH
343
4
HOH
HOH
343
A
HOH
344
4
HOH
HOH
344
A
HOH
345
4
HOH
HOH
345
A
HOH
346
4
HOH
HOH
346
A
HOH
347
4
HOH
HOH
347
A
HOH
348
4
HOH
HOH
348
A
HOH
349
4
HOH
HOH
349
A
HOH
350
4
HOH
HOH
350
A
HOH
351
4
HOH
HOH
351
A
HOH
352
4
HOH
HOH
352
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
356
4
HOH
HOH
356
A
HOH
357
4
HOH
HOH
357
A
HOH
358
4
HOH
HOH
358
A
HOH
359
4
HOH
HOH
359
A
HOH
360
4
HOH
HOH
360
A
HOH
361
4
HOH
HOH
361
A
HOH
362
4
HOH
HOH
362
A
HOH
363
4
HOH
HOH
363
A
HOH
364
4
HOH
HOH
364
A
HOH
365
4
HOH
HOH
365
A
HOH
366
4
HOH
HOH
366
A
HOH
367
4
HOH
HOH
367
A
HOH
368
4
HOH
HOH
368
A
HOH
369
4
HOH
HOH
369
A
HOH
370
4
HOH
HOH
370
A
HOH
371
4
HOH
HOH
371
A
HOH
372
4
HOH
HOH
372
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
375
4
HOH
HOH
375
A
HOH
376
4
HOH
HOH
376
A
HOH
377
4
HOH
HOH
377
A
HOH
378
4
HOH
HOH
378
A
HOH
379
4
HOH
HOH
379
A
HOH
380
4
HOH
HOH
380
A
HOH
381
4
HOH
HOH
381
A
HOH
382
4
HOH
HOH
382
A
HOH
383
4
HOH
HOH
383
A
HOH
384
4
HOH
HOH
384
A
HOH
385
4
HOH
HOH
385
A
HOH
386
4
HOH
HOH
386
A
HOH
387
4
HOH
HOH
387
A
HOH
388
4
HOH
HOH
388
A
HOH
389
4
HOH
HOH
389
A
HOH
390
4
HOH
HOH
390
A
HOH
391
4
HOH
HOH
391
A
HOH
392
4
HOH
HOH
392
A
HOH
393
4
HOH
HOH
393
A
HOH
394
4
HOH
HOH
394
A
HOH
395
4
HOH
HOH
395
A
HOH
396
4
HOH
HOH
396
A
HOH
397
4
HOH
HOH
397
A
HOH
398
4
HOH
HOH
398
A
HOH
399
4
HOH
HOH
399
A
HOH
400
4
HOH
HOH
400
A
HOH
401
4
HOH
HOH
401
A
HOH
402
4
HOH
HOH
402
A
HOH
403
4
HOH
HOH
403
A
HOH
404
4
HOH
HOH
404
A
HOH
405
4
HOH
HOH
405
A
HOH
406
4
HOH
HOH
406
A
HOH
407
4
HOH
HOH
407
A
HOH
408
4
HOH
HOH
408
A
HOH
409
4
HOH
HOH
409
A
HOH
410
4
HOH
HOH
410
A
HOH
411
4
HOH
HOH
411
A
HOH
412
4
HOH
HOH
412
A
HOH
413
4
HOH
HOH
413
A
HOH
414
4
HOH
HOH
414
A
HOH
415
4
HOH
HOH
415
A
HOH
416
4
HOH
HOH
416
A
HOH
417
4
HOH
HOH
417
A
HOH
418
4
HOH
HOH
418
A
HOH
419
4
HOH
HOH
419
A
HOH
420
4
HOH
HOH
420
A
HOH
421
4
HOH
HOH
421
A
HOH
422
4
HOH
HOH
422
A
HOH
423
4
HOH
HOH
423
A
HOH
424
4
HOH
HOH
424
A
HOH
425
4
HOH
HOH
425
A
GLY
0
n
1
GLY
0
A
MET
1
n
2
MET
1
A
THR
2
n
3
THR
2
A
GLU
3
n
4
GLU
3
A
TYR
4
n
5
TYR
4
A
LYS
5
n
6
LYS
5
A
LEU
6
n
7
LEU
6
A
VAL
7
n
8
VAL
7
A
VAL
8
n
9
VAL
8
A
VAL
9
n
10
VAL
9
A
GLY
10
n
11
GLY
10
A
ALA
11
n
12
ALA
11
A
CYS
12
n
13
CYS
12
A
GLY
13
n
14
GLY
13
A
VAL
14
n
15
VAL
14
A
GLY
15
n
16
GLY
15
A
LYS
16
n
17
LYS
16
A
SER
17
n
18
SER
17
A
ALA
18
n
19
ALA
18
A
LEU
19
n
20
LEU
19
A
THR
20
n
21
THR
20
A
ILE
21
n
22
ILE
21
A
GLN
22
n
23
GLN
22
A
LEU
23
n
24
LEU
23
A
ILE
24
n
25
ILE
24
A
GLN
25
n
26
GLN
25
A
ASN
26
n
27
ASN
26
A
HIS
27
n
28
HIS
27
A
PHE
28
n
29
PHE
28
A
VAL
29
n
30
VAL
29
A
ASP
30
n
31
ASP
30
A
GLU
31
n
32
GLU
31
A
TYR
32
n
33
TYR
32
A
ASP
33
n
34
ASP
33
A
PRO
34
n
35
PRO
34
A
THR
35
n
36
THR
35
A
ILE
36
n
37
ILE
36
A
GLU
37
n
38
GLU
37
A
ASP
38
n
39
ASP
38
A
SER
39
n
40
SER
39
A
TYR
40
n
41
TYR
40
A
ARG
41
n
42
ARG
41
A
LYS
42
n
43
LYS
42
A
GLN
43
n
44
GLN
43
A
VAL
44
n
45
VAL
44
A
VAL
45
n
46
VAL
45
A
ILE
46
n
47
ILE
46
A
ASP
47
n
48
ASP
47
A
GLY
48
n
49
GLY
48
A
GLU
49
n
50
GLU
49
A
THR
50
n
51
THR
50
A
CYS
51
n
52
CYS
51
A
LEU
52
n
53
LEU
52
A
LEU
53
n
54
LEU
53
A
ASP
54
n
55
ASP
54
A
ILE
55
n
56
ILE
55
A
LEU
56
n
57
LEU
56
A
ASP
57
n
58
ASP
57
A
THR
58
n
59
THR
58
A
ALA
59
n
60
ALA
59
A
GLY
60
n
61
GLY
60
A
GLN
61
n
62
GLN
61
A
GLU
62
n
63
GLU
62
A
GLU
63
n
64
GLU
63
A
TYR
64
n
65
TYR
64
A
SER
65
n
66
SER
65
A
ALA
66
n
67
ALA
66
A
MET
67
n
68
MET
67
A
ARG
68
n
69
ARG
68
A
ASP
69
n
70
ASP
69
A
GLN
70
n
71
GLN
70
A
TYR
71
n
72
TYR
71
A
MET
72
n
73
MET
72
A
ARG
73
n
74
ARG
73
A
THR
74
n
75
THR
74
A
GLY
75
n
76
GLY
75
A
GLU
76
n
77
GLU
76
A
GLY
77
n
78
GLY
77
A
PHE
78
n
79
PHE
78
A
LEU
79
n
80
LEU
79
A
CYS
80
n
81
CYS
80
A
VAL
81
n
82
VAL
81
A
PHE
82
n
83
PHE
82
A
ALA
83
n
84
ALA
83
A
ILE
84
n
85
ILE
84
A
ASN
85
n
86
ASN
85
A
ASN
86
n
87
ASN
86
A
THR
87
n
88
THR
87
A
LYS
88
n
89
LYS
88
A
SER
89
n
90
SER
89
A
PHE
90
n
91
PHE
90
A
GLU
91
n
92
GLU
91
A
ASP
92
n
93
ASP
92
A
ILE
93
n
94
ILE
93
A
HIS
94
n
95
HIS
94
A
HIS
95
n
96
HIS
95
A
TYR
96
n
97
TYR
96
A
ARG
97
n
98
ARG
97
A
GLU
98
n
99
GLU
98
A
GLN
99
n
100
GLN
99
A
ILE
100
n
101
ILE
100
A
LYS
101
n
102
LYS
101
A
ARG
102
n
103
ARG
102
A
VAL
103
n
104
VAL
103
A
LYS
104
n
105
LYS
104
A
ASP
105
n
106
ASP
105
A
SER
106
n
107
SER
106
A
GLU
107
n
108
GLU
107
A
ASP
108
n
109
ASP
108
A
VAL
109
n
110
VAL
109
A
PRO
110
n
111
PRO
110
A
MET
111
n
112
MET
111
A
VAL
112
n
113
VAL
112
A
LEU
113
n
114
LEU
113
A
VAL
114
n
115
VAL
114
A
GLY
115
n
116
GLY
115
A
ASN
116
n
117
ASN
116
A
LYS
117
n
118
LYS
117
A
CYS
118
n
119
CYS
118
A
ASP
119
n
120
ASP
119
A
LEU
120
n
121
LEU
120
A
PRO
121
n
122
PRO
121
A
SER
122
n
123
SER
122
A
ARG
123
n
124
ARG
123
A
THR
124
n
125
THR
124
A
VAL
125
n
126
VAL
125
A
ASP
126
n
127
ASP
126
A
THR
127
n
128
THR
127
A
LYS
128
n
129
LYS
128
A
GLN
129
n
130
GLN
129
A
ALA
130
n
131
ALA
130
A
GLN
131
n
132
GLN
131
A
ASP
132
n
133
ASP
132
A
LEU
133
n
134
LEU
133
A
ALA
134
n
135
ALA
134
A
ARG
135
n
136
ARG
135
A
SER
136
n
137
SER
136
A
TYR
137
n
138
TYR
137
A
GLY
138
n
139
GLY
138
A
ILE
139
n
140
ILE
139
A
PRO
140
n
141
PRO
140
A
PHE
141
n
142
PHE
141
A
ILE
142
n
143
ILE
142
A
GLU
143
n
144
GLU
143
A
THR
144
n
145
THR
144
A
SER
145
n
146
SER
145
A
ALA
146
n
147
ALA
146
A
LYS
147
n
148
LYS
147
A
THR
148
n
149
THR
148
A
ARG
149
n
150
ARG
149
A
GLN
150
n
151
GLN
150
A
GLY
151
n
152
GLY
151
A
VAL
152
n
153
VAL
152
A
ASP
153
n
154
ASP
153
A
ASP
154
n
155
ASP
154
A
ALA
155
n
156
ALA
155
A
PHE
156
n
157
PHE
156
A
TYR
157
n
158
TYR
157
A
THR
158
n
159
THR
158
A
LEU
159
n
160
LEU
159
A
VAL
160
n
161
VAL
160
A
ARG
161
n
162
ARG
161
A
GLU
162
n
163
GLU
162
A
ILE
163
n
164
ILE
163
A
ARG
164
n
165
ARG
164
A
LYS
165
n
166
LYS
165
A
HIS
166
n
167
HIS
166
A
LYS
167
n
168
LYS
167
A
GLU
168
n
169
GLU
168
A
LYS
169
n
170
LYS
169
A
author_and_software_defined_assembly
PISA
1
monomeric
A
SER
17
A
OG
SER
18
1_555
A
MG
201
B
MG
MG
1_555
A
Y9Z
202
C
O8
Y9Z
1_555
94.6
A
SER
17
A
OG
SER
18
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
306
D
O
HOH
1_555
78.4
A
Y9Z
202
C
O8
Y9Z
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
306
D
O
HOH
1_555
85.7
A
SER
17
A
OG
SER
18
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
424
D
O
HOH
1_555
91.9
A
Y9Z
202
C
O8
Y9Z
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
424
D
O
HOH
1_555
171.7
A
HOH
306
D
O
HOH
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
424
D
O
HOH
1_555
90.5
A
SER
17
A
OG
SER
18
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
425
D
O
HOH
1_555
94.4
A
Y9Z
202
C
O8
Y9Z
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
425
D
O
HOH
1_555
105.1
A
HOH
306
D
O
HOH
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
425
D
O
HOH
1_555
167.6
A
HOH
424
D
O
HOH
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
425
D
O
HOH
1_555
79.5
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
TYR
40
A
N
TYR
41
A
O
ILE
55
A
O
ILE
56
A
O
LEU
56
A
O
LEU
57
A
N
LEU
6
A
N
LEU
7
A
N
VAL
9
A
N
VAL
10
A
O
VAL
81
A
O
VAL
82
A
N
PHE
82
A
N
PHE
83
A
O
ASN
116
A
O
ASN
117
A
N
LEU
113
A
N
LEU
114
A
O
ILE
142
A
O
ILE
143
1
3.08
0.50
120.30
123.38
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
123
123
123
N
1
A
LYS
117
71.10
30.58
1
A
ARG
149
74.32
-1.97
25.81
-2.46000
0.00000
0.00000
3.17000
0.00000
-0.71000
0.957
0.931
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.237
0.184
0.186
1.89
45.58
615
12363
11695
5.000
4.717
0.133
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.185
0.166
0.80
0.80
1.20
PDB ENTRY 4EPV
MAXIMUM LIKELIHOOD
MASK
1.89
45.58
125
1517
35
0
1357
0.015
0.019
1419
0.007
0.020
1332
1.364
1.992
1921
0.768
3.001
3072
5.011
5.000
171
36.225
24.493
69
12.006
15.000
255
20.314
15.000
10
0.075
0.200
213
0.008
0.020
1589
0.004
0.020
318
2.152
2.293
683
2.108
2.289
680
2.963
3.430
851
2.974
3.432
851
3.257
2.770
736
3.259
2.771
734
5.140
4.005
1068
6.816
20.084
1703
6.723
19.749
1658
0.2600
0.3060
1.94
28
598
20
67.75
23.29
1.890
50.000
4NMM
12363
2.000
0.12600
1
14.4690
5.800
99.8
0.88300
1.90
1.93
2.036
1
5.10
100.0
data collection
HKL-3000
phasing
PHASER
refinement
REFMAC
5.8.0049
data reduction
HKL-3000
data scaling
HKL-3000
Crystal Structure of a G12C Oncogenic Variant of Human KRas Bound to a Novel GDP Competitive Covalent Inhibitor
1
N
N
2
N
N
3
N
N
4
N
N
A
GLY
15
A
GLY
16
HELX_P
A
ASN
26
A
ASN
27
1
1
12
A
TYR
64
A
TYR
65
HELX_P
A
GLY
75
A
GLY
76
1
2
12
A
ASN
86
A
ASN
87
HELX_P
A
ASP
105
A
ASP
106
1
3
20
A
ASP
126
A
ASP
127
HELX_P
A
GLY
138
A
GLY
139
1
4
13
A
GLY
151
A
GLY
152
HELX_P
A
GLU
168
A
GLU
169
1
5
18
covale
1.804
none
B
A
CYS
12
A
SG
CYS
13
1_555
A
Y9Z
202
C
C13
Y9Z
1_555
metalc
2.178
A
SER
17
A
OG
SER
18
1_555
A
MG
201
B
MG
MG
1_555
metalc
1.859
A
MG
201
B
MG
MG
1_555
A
Y9Z
202
C
O8
Y9Z
1_555
metalc
2.370
A
MG
201
B
MG
MG
1_555
A
HOH
306
D
O
HOH
1_555
metalc
2.254
A
MG
201
B
MG
MG
1_555
A
HOH
424
D
O
HOH
1_555
metalc
2.340
A
MG
201
B
MG
MG
1_555
A
HOH
425
D
O
HOH
1_555
HYDROLASE/HYDROLASE INHIBITOR
Small GTPase, GDP bound, oncogenic mutation, covalent inhibitor, HYDROLASE-HYDROLASE INHIBITOR complex
RASK_HUMAN
UNP
1
1
P01116
MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLC
VFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLV
REIRQYRLK
1
169
4NMM
1
169
P01116
A
1
2
170
1
expression tag
GLY
0
4NMM
A
P01116
UNP
1
1
GLY
engineered mutation
CYS
12
4NMM
A
P01116
UNP
12
13
6
anti-parallel
parallel
parallel
parallel
parallel
A
ASP
38
A
ASP
39
A
ILE
46
A
ILE
47
A
GLU
49
A
GLU
50
A
ASP
57
A
ASP
58
A
GLU
3
A
GLU
4
A
VAL
9
A
VAL
10
A
GLY
77
A
GLY
78
A
ALA
83
A
ALA
84
A
MET
111
A
MET
112
A
ASN
116
A
ASN
117
A
PHE
141
A
PHE
142
A
GLU
143
A
GLU
144
BINDING SITE FOR RESIDUE MG A 201
A
MG
201
Software
6
BINDING SITE FOR RESIDUE Y9Z A 202
A
Y9Z
202
Software
26
A
SER
17
A
SER
18
6
1_555
A
TYR
32
A
TYR
33
6
1_555
A
Y9Z
202
C
Y9Z
6
1_555
A
HOH
306
D
HOH
6
1_555
A
HOH
424
D
HOH
6
1_555
A
HOH
425
D
HOH
6
1_555
A
CYS
12
A
CYS
13
26
1_555
A
GLY
13
A
GLY
14
26
1_555
A
VAL
14
A
VAL
15
26
1_555
A
GLY
15
A
GLY
16
26
1_555
A
LYS
16
A
LYS
17
26
1_555
A
SER
17
A
SER
18
26
1_555
A
ALA
18
A
ALA
19
26
1_555
A
PHE
28
A
PHE
29
26
1_555
A
VAL
29
A
VAL
30
26
1_555
A
ASP
30
A
ASP
31
26
1_555
A
TYR
32
A
TYR
33
26
1_555
A
PRO
34
A
PRO
35
26
1_555
A
ALA
59
A
ALA
60
26
1_555
A
ASN
116
A
ASN
117
26
1_555
A
LYS
117
A
LYS
118
26
1_555
A
ASP
119
A
ASP
120
26
1_555
A
LEU
120
A
LEU
121
26
1_555
A
SER
145
A
SER
146
26
1_555
A
ALA
146
A
ALA
147
26
1_555
A
LYS
147
A
LYS
148
26
1_555
A
MG
201
B
MG
26
1_555
A
HOH
306
D
HOH
26
1_555
A
HOH
336
D
HOH
26
1_555
A
HOH
375
D
HOH
26
1_555
A
HOH
411
D
HOH
26
1_555
A
HOH
425
D
HOH
26
1_555
19
P 21 21 21