0.027315
0.000000
0.000000
-0.000000
0.017683
0.000000
0.000000
-0.000000
0.010276
0.000000
0.000000
0.000000
Twarda-Clapa, A.
Zak, K.M.
Wrona, E.M.
Grudnik, P.
Dubin, G.
Holak, T.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
36.610
56.550
97.310
C26 H18 Cl3 N O3
498.785
(5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one
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
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
CL
Y
2
N
C
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
Y
7
N
C
N
8
N
C
N
9
N
C
N
10
N
C
N
11
N
O
N
12
N
O
N
13
R
C
N
14
N
O
N
15
N
C
Y
16
N
C
Y
17
N
C
Y
18
N
C
Y
19
N
C
Y
20
N
C
Y
21
N
C
N
22
N
CL
N
23
N
C
Y
24
N
C
Y
25
N
C
Y
26
N
N
Y
27
N
C
Y
28
N
C
Y
29
N
C
Y
30
N
C
N
31
N
CL
Y
32
N
C
Y
33
N
C
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
H
N
42
N
H
N
43
N
H
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
N
N
53
S
C
N
54
N
C
N
55
N
O
N
56
N
C
N
57
N
O
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
N
N
66
S
C
N
67
N
C
N
68
N
O
N
69
N
C
N
70
N
C
N
71
N
C
N
72
N
N
N
73
N
C
N
74
N
N
N
75
N
N
N
76
N
O
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
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
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
N
N
93
S
C
N
94
N
C
N
95
N
O
N
96
N
C
N
97
N
C
N
98
N
O
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
N
N
110
S
C
N
111
N
C
N
112
N
O
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
N
N
126
R
C
N
127
N
C
N
128
N
O
N
129
N
C
N
130
N
S
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
H
N
138
N
H
N
139
N
N
N
140
S
C
N
141
N
C
N
142
N
O
N
143
N
C
N
144
N
C
N
145
N
C
N
146
N
O
N
147
N
N
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
N
N
160
S
C
N
161
N
C
N
162
N
O
N
163
N
C
N
164
N
C
N
165
N
C
N
166
N
O
N
167
N
O
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
N
N
179
N
C
N
180
N
C
N
181
N
O
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
Y
193
N
C
Y
194
N
N
Y
195
N
C
Y
196
N
C
Y
197
N
N
N
198
N
O
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
O
N
210
N
H
N
211
N
H
N
212
N
N
N
213
S
C
N
214
N
C
N
215
N
O
N
216
S
C
N
217
N
C
N
218
N
C
N
219
N
C
N
220
N
O
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
N
N
235
S
C
N
236
N
C
N
237
N
O
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
C
N
242
N
O
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
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
N
N
257
S
C
N
258
N
C
N
259
N
O
N
260
N
C
N
261
N
C
N
262
N
C
N
263
N
C
N
264
N
N
N
265
N
O
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
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
N
N
282
S
C
N
283
N
C
N
284
N
O
N
285
N
C
N
286
N
C
N
287
N
S
N
288
N
C
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
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
Y
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
H
N
323
N
H
N
324
N
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
N
329
N
C
N
330
N
C
N
331
N
O
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
N
N
342
S
C
N
343
N
C
N
344
N
O
N
345
N
C
N
346
N
O
N
347
N
O
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
R
C
N
360
N
O
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
Y
377
N
C
Y
378
N
C
Y
379
N
C
Y
380
N
C
Y
381
N
C
Y
382
N
C
N
383
N
O
N
384
N
O
N
385
N
H
N
386
N
H
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
N
401
N
C
N
402
N
C
N
403
N
O
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
1
N
sing
Y
2
N
doub
Y
3
N
sing
N
4
N
sing
Y
5
N
sing
Y
6
N
doub
Y
7
N
sing
Y
8
N
doub
Y
9
N
sing
N
10
N
doub
Y
11
N
doub
Y
12
N
doub
Y
13
N
sing
N
14
N
sing
Y
15
N
doub
N
16
N
sing
N
17
N
sing
N
18
N
sing
Y
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
doub
N
24
N
sing
N
25
N
sing
N
26
N
sing
Y
27
N
doub
Y
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
Y
32
N
sing
Y
33
N
sing
Y
34
N
doub
Y
35
N
doub
Y
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
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
doub
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
doub
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
doub
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
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
doub
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
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
sing
N
143
N
sing
N
144
N
doub
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
doub
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
doub
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
doub
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
sing
N
180
N
sing
N
181
N
doub
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
doub
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
Y
195
N
sing
Y
196
N
doub
Y
197
N
doub
N
198
N
sing
Y
199
N
sing
N
200
N
sing
Y
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
doub
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
doub
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
doub
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
doub
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
doub
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
Y
303
N
doub
Y
304
N
sing
Y
305
N
sing
N
306
N
sing
Y
307
N
doub
N
308
N
sing
Y
309
N
doub
N
310
N
sing
Y
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
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
doub
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
sing
N
349
N
sing
N
350
N
sing
N
351
N
doub
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
sing
N
365
N
sing
N
366
N
sing
N
367
N
doub
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
Y
372
N
doub
Y
373
N
sing
Y
374
N
sing
N
375
N
sing
Y
376
N
doub
N
377
N
sing
Y
378
N
doub
N
379
N
sing
Y
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
doub
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
US
ACS Chem. Biol.
1554-8937
11
3310
3318
10.1021/acschembio.6b00596
27709883
A Unique Mdm2-Binding Mode of the 3-Pyrrolin-2-one- and 2-Furanone-Based Antagonists of the p53-Mdm2 Interaction.
2016
10.2210/pdb4zgk/pdb
pdb_00004zgk
100
1
PIXEL
2014-11-27
DECTRIS PILATUS 6M
SINGLE WAVELENGTH
M
x-ray
1
0.873
1.0
ID23-2
ESRF
0.873
SYNCHROTRON
ESRF BEAMLINE ID23-2
11528.488
E3 ubiquitin-protein ligase Mdm2
6.3.2.-
UNP residues 18-114
2
man
polymer
498.785
(5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one
2
syn
non-polymer
18.015
water
114
nat
water
Double minute 2 protein,Hdm2,Oncoprotein Mdm2,p53-binding protein Mdm2
no
no
MQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEH
RKIYTMIYRNLVVVNQQE
MQIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEH
RKIYTMIYRNLVVVNQQE
A,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
Human
sample
1
98
MDM2
9606
Homo sapiens
511693
Escherichia coli BL21
Biological sequence
1
2.21
44.38
VAPOR DIFFUSION, SITTING DROP
0.1 M HEPES pH 7.5 containing 30% PEG 1000
277.15
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_ncs_dom_lim
repository
Initial release
Database references
Data collection
Database references
Refinement description
1
0
2016-10-19
1
1
2016-12-28
1
2
2024-01-10
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ncs_dom_lim.beg_auth_comp_id
_struct_ncs_dom_lim.beg_label_asym_id
_struct_ncs_dom_lim.beg_label_comp_id
_struct_ncs_dom_lim.beg_label_seq_id
_struct_ncs_dom_lim.end_auth_comp_id
_struct_ncs_dom_lim.end_label_asym_id
_struct_ncs_dom_lim.end_label_comp_id
_struct_ncs_dom_lim.end_label_seq_id
Poland
Foundation for Polish Science
TEAM/2011-8/2
Poland
National Centre of Science
UMO-2011/01/D/NZ1/01169
4ZFI contains the same protein in complex with different small molecule group based on the same scaffold.
N
RCSB
Y
PDBE
2015-04-23
REL
REL
4NX
(5R)-3,5-bis(4-chlorobenzyl)-4-(6-chloro-1H-indol-3-yl)-5-hydroxyfuran-2(5H)-one
HOH
water
3TJ2
PDB
experimental model
p2d
2
2
4NX
4NX
201
A
p2d
1
2
4NX
4NX
201
B
HOH
135
3
HOH
HOH
301
A
HOH
7
3
HOH
HOH
302
A
HOH
34
3
HOH
HOH
303
A
HOH
163
3
HOH
HOH
304
A
HOH
148
3
HOH
HOH
305
A
HOH
12
3
HOH
HOH
306
A
HOH
84
3
HOH
HOH
307
A
HOH
11
3
HOH
HOH
308
A
HOH
138
3
HOH
HOH
309
A
HOH
173
3
HOH
HOH
310
A
HOH
213
3
HOH
HOH
311
A
HOH
125
3
HOH
HOH
312
A
HOH
243
3
HOH
HOH
313
A
HOH
53
3
HOH
HOH
314
A
HOH
52
3
HOH
HOH
315
A
HOH
86
3
HOH
HOH
316
A
HOH
13
3
HOH
HOH
317
A
HOH
1
3
HOH
HOH
318
A
HOH
101
3
HOH
HOH
319
A
HOH
55
3
HOH
HOH
320
A
HOH
65
3
HOH
HOH
321
A
HOH
35
3
HOH
HOH
322
A
HOH
130
3
HOH
HOH
323
A
HOH
97
3
HOH
HOH
324
A
HOH
56
3
HOH
HOH
325
A
HOH
131
3
HOH
HOH
326
A
HOH
6
3
HOH
HOH
327
A
HOH
221
3
HOH
HOH
328
A
HOH
43
3
HOH
HOH
329
A
HOH
60
3
HOH
HOH
330
A
HOH
140
3
HOH
HOH
331
A
HOH
96
3
HOH
HOH
332
A
HOH
57
3
HOH
HOH
333
A
HOH
244
3
HOH
HOH
334
A
HOH
66
3
HOH
HOH
335
A
HOH
133
3
HOH
HOH
336
A
HOH
158
3
HOH
HOH
337
A
HOH
233
3
HOH
HOH
338
A
HOH
188
3
HOH
HOH
339
A
HOH
83
3
HOH
HOH
340
A
HOH
8
3
HOH
HOH
341
A
HOH
129
3
HOH
HOH
342
A
HOH
63
3
HOH
HOH
343
A
HOH
237
3
HOH
HOH
344
A
HOH
9
3
HOH
HOH
345
A
HOH
225
3
HOH
HOH
346
A
HOH
134
3
HOH
HOH
347
A
HOH
47
3
HOH
HOH
301
B
HOH
74
3
HOH
HOH
302
B
HOH
209
3
HOH
HOH
303
B
HOH
190
3
HOH
HOH
304
B
HOH
73
3
HOH
HOH
305
B
HOH
18
3
HOH
HOH
306
B
HOH
145
3
HOH
HOH
307
B
HOH
164
3
HOH
HOH
308
B
HOH
99
3
HOH
HOH
309
B
HOH
245
3
HOH
HOH
310
B
HOH
127
3
HOH
HOH
311
B
HOH
136
3
HOH
HOH
312
B
HOH
242
3
HOH
HOH
313
B
HOH
54
3
HOH
HOH
314
B
HOH
2
3
HOH
HOH
315
B
HOH
189
3
HOH
HOH
316
B
HOH
28
3
HOH
HOH
317
B
HOH
25
3
HOH
HOH
318
B
HOH
155
3
HOH
HOH
319
B
HOH
104
3
HOH
HOH
320
B
HOH
202
3
HOH
HOH
321
B
HOH
22
3
HOH
HOH
322
B
HOH
106
3
HOH
HOH
323
B
HOH
150
3
HOH
HOH
324
B
HOH
17
3
HOH
HOH
325
B
HOH
77
3
HOH
HOH
326
B
HOH
152
3
HOH
HOH
327
B
HOH
71
3
HOH
HOH
328
B
HOH
123
3
HOH
HOH
329
B
HOH
206
3
HOH
HOH
330
B
HOH
160
3
HOH
HOH
331
B
HOH
27
3
HOH
HOH
332
B
HOH
20
3
HOH
HOH
333
B
HOH
23
3
HOH
HOH
334
B
HOH
70
3
HOH
HOH
335
B
HOH
230
3
HOH
HOH
336
B
HOH
228
3
HOH
HOH
337
B
HOH
143
3
HOH
HOH
338
B
HOH
102
3
HOH
HOH
339
B
HOH
26
3
HOH
HOH
340
B
HOH
166
3
HOH
HOH
341
B
HOH
137
3
HOH
HOH
342
B
HOH
208
3
HOH
HOH
343
B
HOH
193
3
HOH
HOH
344
B
HOH
62
3
HOH
HOH
345
B
HOH
21
3
HOH
HOH
346
B
HOH
15
3
HOH
HOH
347
B
HOH
75
3
HOH
HOH
348
B
HOH
3
3
HOH
HOH
349
B
HOH
157
3
HOH
HOH
350
B
HOH
205
3
HOH
HOH
351
B
HOH
38
3
HOH
HOH
352
B
HOH
235
3
HOH
HOH
353
B
HOH
210
3
HOH
HOH
354
B
HOH
240
3
HOH
HOH
355
B
HOH
222
3
HOH
HOH
356
B
HOH
227
3
HOH
HOH
357
B
HOH
24
3
HOH
HOH
358
B
HOH
192
3
HOH
HOH
359
B
HOH
61
3
HOH
HOH
360
B
HOH
203
3
HOH
HOH
361
B
HOH
121
3
HOH
HOH
362
B
HOH
191
3
HOH
HOH
363
B
HOH
223
3
HOH
HOH
364
B
HOH
156
3
HOH
HOH
365
B
HOH
241
3
HOH
HOH
366
B
HOH
39
3
HOH
HOH
367
B
3.880
3.880
29.310
29.310
Phaser MODE: MR_AUTO
MET
17
n
1
MET
17
A
GLN
18
n
2
GLN
18
A
ILE
19
n
3
ILE
19
A
PRO
20
n
4
PRO
20
A
ALA
21
n
5
ALA
21
A
SER
22
n
6
SER
22
A
GLU
23
n
7
GLU
23
A
GLN
24
n
8
GLN
24
A
GLU
25
n
9
GLU
25
A
THR
26
n
10
THR
26
A
LEU
27
n
11
LEU
27
A
VAL
28
n
12
VAL
28
A
ARG
29
n
13
ARG
29
A
PRO
30
n
14
PRO
30
A
LYS
31
n
15
LYS
31
A
PRO
32
n
16
PRO
32
A
LEU
33
n
17
LEU
33
A
LEU
34
n
18
LEU
34
A
LEU
35
n
19
LEU
35
A
LYS
36
n
20
LYS
36
A
LEU
37
n
21
LEU
37
A
LEU
38
n
22
LEU
38
A
LYS
39
n
23
LYS
39
A
SER
40
n
24
SER
40
A
VAL
41
n
25
VAL
41
A
GLY
42
n
26
GLY
42
A
ALA
43
n
27
ALA
43
A
GLN
44
n
28
GLN
44
A
LYS
45
n
29
LYS
45
A
ASP
46
n
30
ASP
46
A
THR
47
n
31
THR
47
A
TYR
48
n
32
TYR
48
A
THR
49
n
33
THR
49
A
MET
50
n
34
MET
50
A
LYS
51
n
35
LYS
51
A
GLU
52
n
36
GLU
52
A
VAL
53
n
37
VAL
53
A
LEU
54
n
38
LEU
54
A
PHE
55
n
39
PHE
55
A
TYR
56
n
40
TYR
56
A
LEU
57
n
41
LEU
57
A
GLY
58
n
42
GLY
58
A
GLN
59
n
43
GLN
59
A
TYR
60
n
44
TYR
60
A
ILE
61
n
45
ILE
61
A
MET
62
n
46
MET
62
A
THR
63
n
47
THR
63
A
LYS
64
n
48
LYS
64
A
ARG
65
n
49
ARG
65
A
LEU
66
n
50
LEU
66
A
TYR
67
n
51
TYR
67
A
ASP
68
n
52
ASP
68
A
GLU
69
n
53
GLU
69
A
LYS
70
n
54
LYS
70
A
GLN
71
n
55
GLN
71
A
GLN
72
n
56
GLN
72
A
HIS
73
n
57
HIS
73
A
ILE
74
n
58
ILE
74
A
VAL
75
n
59
VAL
75
A
TYR
76
n
60
TYR
76
A
CYS
77
n
61
CYS
77
A
SER
78
n
62
SER
78
A
ASN
79
n
63
ASN
79
A
ASP
80
n
64
ASP
80
A
LEU
81
n
65
LEU
81
A
LEU
82
n
66
LEU
82
A
GLY
83
n
67
GLY
83
A
ASP
84
n
68
ASP
84
A
LEU
85
n
69
LEU
85
A
PHE
86
n
70
PHE
86
A
GLY
87
n
71
GLY
87
A
VAL
88
n
72
VAL
88
A
PRO
89
n
73
PRO
89
A
SER
90
n
74
SER
90
A
PHE
91
n
75
PHE
91
A
SER
92
n
76
SER
92
A
VAL
93
n
77
VAL
93
A
LYS
94
n
78
LYS
94
A
GLU
95
n
79
GLU
95
A
HIS
96
n
80
HIS
96
A
ARG
97
n
81
ARG
97
A
LYS
98
n
82
LYS
98
A
ILE
99
n
83
ILE
99
A
TYR
100
n
84
TYR
100
A
THR
101
n
85
THR
101
A
MET
102
n
86
MET
102
A
ILE
103
n
87
ILE
103
A
TYR
104
n
88
TYR
104
A
ARG
105
n
89
ARG
105
A
ASN
106
n
90
ASN
106
A
LEU
107
n
91
LEU
107
A
VAL
108
n
92
VAL
108
A
VAL
109
n
93
VAL
109
A
VAL
110
n
94
VAL
110
A
n
95
111
A
n
96
112
A
n
97
113
A
n
98
114
A
n
1
17
B
GLN
18
n
2
GLN
18
B
ILE
19
n
3
ILE
19
B
PRO
20
n
4
PRO
20
B
ALA
21
n
5
ALA
21
B
SER
22
n
6
SER
22
B
GLU
23
n
7
GLU
23
B
GLN
24
n
8
GLN
24
B
GLU
25
n
9
GLU
25
B
THR
26
n
10
THR
26
B
LEU
27
n
11
LEU
27
B
VAL
28
n
12
VAL
28
B
ARG
29
n
13
ARG
29
B
PRO
30
n
14
PRO
30
B
LYS
31
n
15
LYS
31
B
PRO
32
n
16
PRO
32
B
LEU
33
n
17
LEU
33
B
LEU
34
n
18
LEU
34
B
LEU
35
n
19
LEU
35
B
LYS
36
n
20
LYS
36
B
LEU
37
n
21
LEU
37
B
LEU
38
n
22
LEU
38
B
LYS
39
n
23
LYS
39
B
SER
40
n
24
SER
40
B
VAL
41
n
25
VAL
41
B
GLY
42
n
26
GLY
42
B
ALA
43
n
27
ALA
43
B
GLN
44
n
28
GLN
44
B
LYS
45
n
29
LYS
45
B
ASP
46
n
30
ASP
46
B
THR
47
n
31
THR
47
B
TYR
48
n
32
TYR
48
B
THR
49
n
33
THR
49
B
MET
50
n
34
MET
50
B
LYS
51
n
35
LYS
51
B
GLU
52
n
36
GLU
52
B
VAL
53
n
37
VAL
53
B
LEU
54
n
38
LEU
54
B
PHE
55
n
39
PHE
55
B
TYR
56
n
40
TYR
56
B
LEU
57
n
41
LEU
57
B
GLY
58
n
42
GLY
58
B
GLN
59
n
43
GLN
59
B
TYR
60
n
44
TYR
60
B
ILE
61
n
45
ILE
61
B
MET
62
n
46
MET
62
B
THR
63
n
47
THR
63
B
LYS
64
n
48
LYS
64
B
ARG
65
n
49
ARG
65
B
LEU
66
n
50
LEU
66
B
TYR
67
n
51
TYR
67
B
ASP
68
n
52
ASP
68
B
GLU
69
n
53
GLU
69
B
LYS
70
n
54
LYS
70
B
GLN
71
n
55
GLN
71
B
GLN
72
n
56
GLN
72
B
HIS
73
n
57
HIS
73
B
ILE
74
n
58
ILE
74
B
VAL
75
n
59
VAL
75
B
TYR
76
n
60
TYR
76
B
CYS
77
n
61
CYS
77
B
SER
78
n
62
SER
78
B
ASN
79
n
63
ASN
79
B
ASP
80
n
64
ASP
80
B
LEU
81
n
65
LEU
81
B
LEU
82
n
66
LEU
82
B
GLY
83
n
67
GLY
83
B
ASP
84
n
68
ASP
84
B
LEU
85
n
69
LEU
85
B
PHE
86
n
70
PHE
86
B
GLY
87
n
71
GLY
87
B
VAL
88
n
72
VAL
88
B
PRO
89
n
73
PRO
89
B
SER
90
n
74
SER
90
B
PHE
91
n
75
PHE
91
B
SER
92
n
76
SER
92
B
VAL
93
n
77
VAL
93
B
LYS
94
n
78
LYS
94
B
GLU
95
n
79
GLU
95
B
HIS
96
n
80
HIS
96
B
ARG
97
n
81
ARG
97
B
LYS
98
n
82
LYS
98
B
ILE
99
n
83
ILE
99
B
TYR
100
n
84
TYR
100
B
THR
101
n
85
THR
101
B
MET
102
n
86
MET
102
B
ILE
103
n
87
ILE
103
B
TYR
104
n
88
TYR
104
B
ARG
105
n
89
ARG
105
B
ASN
106
n
90
ASN
106
B
LEU
107
n
91
LEU
107
B
VAL
108
n
92
VAL
108
B
VAL
109
n
93
VAL
109
B
VAL
110
n
94
VAL
110
B
ASN
111
n
95
ASN
111
B
GLN
112
n
96
GLN
112
B
GLN
113
n
97
GLN
113
B
GLU
114
n
98
GLU
114
B
0.3069
0.3950
0.1780
0.5952
0.3736
4.2051
-0.0300
0.0028
0.0036
-0.0222
0.0170
-0.0340
0.1976
0.1766
0.0130
0.0277
0.0035
-0.0071
0.0134
0.0035
0.0303
refined
9.5938
-3.9201
-22.0759
X-RAY DIFFRACTION
1.2204
-0.0615
-0.7898
0.8863
0.0731
3.1978
0.0130
0.0469
-0.0409
-0.0359
-0.0272
-0.0294
0.0644
-0.2253
0.0143
0.0071
-0.0114
0.0015
0.0336
-0.0108
0.0824
refined
2.0244
-1.2072
-44.7590
X-RAY DIFFRACTION
A
17
A
110
X-RAY DIFFRACTION
1
B
18
B
114
X-RAY DIFFRACTION
2
author_defined_assembly
1
monomeric
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
TYR
48
A
O
TYR
32
A
N
VAL
28
A
N
VAL
12
A
N
ARG
29
A
N
ARG
13
A
O
VAL
108
A
O
VAL
92
A
N
VAL
75
A
N
VAL
59
A
O
PHE
91
A
O
PHE
75
B
O
TYR
48
B
O
TYR
32
B
N
VAL
28
B
N
VAL
12
B
N
ARG
29
B
N
ARG
13
B
O
VAL
108
B
O
VAL
92
B
N
VAL
75
B
N
VAL
59
B
O
PHE
91
B
O
PHE
75
1
B
CE
LYS
94
B
CE
LYS
78
1
Y
1
B
NZ
LYS
94
B
NZ
LYS
78
1
Y
1
B
CG
GLN
113
B
CG
GLN
97
1
Y
1
B
CD
GLN
113
B
CD
GLN
97
1
Y
1
B
OE1
GLN
113
B
OE1
GLN
97
1
Y
1
B
NE2
GLN
113
B
NE2
GLN
97
1
Y
1
B
CB
GLU
114
B
CB
GLU
98
1
Y
1
B
CG
GLU
114
B
CG
GLU
98
1
Y
1
B
CD
GLU
114
B
CD
GLU
98
1
Y
1
B
OE1
GLU
114
B
OE1
GLU
98
1
Y
1
B
OE2
GLU
114
B
OE2
GLU
98
1
Y
1
A
ASN
111
A
ASN
95
1
Y
1
A
GLN
112
A
GLN
96
1
Y
1
A
GLN
113
A
GLN
97
1
Y
1
A
GLU
114
A
GLU
98
1
Y
1
B
MET
17
B
MET
1
1
Y
1
16.48
2.30
115.30
131.78
B
B
B
CA
CB
CG
LEU
LEU
LEU
37
37
37
N
65.130
26.6860
9.710
2.2700
0.0000
-0.0000
0.6300
-0.0000
-2.8900
0.9490
0.9080
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.2470
0.1881
0.1910
2.0000
30.0000
600
11285
5.0000
83.2900
0.2466
0.1874
0.8231
9.9200
0.1510
0.2619
0.2110
RANDOM
1
THROUGHOUT
0.000
MOLECULAR REPLACEMENT
0.2620
0.2110
0.8000
0.8000
1.2000
3TJ2
MAXIMUM LIKELIHOOD
MASK
2.0000
30.0000
114
1742
20.51
27.99
66
0
1562
191
0.013
0.019
1687
0.005
0.020
1651
1.874
2.042
2288
1.247
3.000
3799
5.956
5.000
195
45.265
24.118
68
19.811
15.000
319
11.821
15.000
8
0.103
0.200
251
0.008
0.021
1835
0.004
0.020
379
1.241
1.853
771
1.222
1.850
770
1.892
2.760
963
1
A
1
5464
X-RAY DIFFRACTION
interatomic distance
0.150
0.050
2
B
1
5464
X-RAY DIFFRACTION
interatomic distance
0.150
0.050
0.2920
0.2770
2.0520
48
840
888
20
85.3800
1.739
48.893
4ZGK
11908
11908
0.071
0.151
0.132
1
3.500
6.300
46290
3.900
84.800
0.322
2.000
2.110
2.300
6232
1756
0.186
0.322
1
3.400
3.500
0
86.800
0.290
2.110
2.240
2.500
6077
1639
0.161
0.290
1
3.900
3.700
0
86.500
0.294
2.240
2.390
1.900
6322
1553
0.159
0.294
1
4.400
4.100
0
86.200
0.221
2.390
2.580
3.200
6051
1461
0.116
0.221
1
5.200
4.100
0
86.300
0.183
2.580
2.830
3.700
5223
1326
0.098
0.183
1
5.900
3.900
0
85.200
0.128
2.830
3.160
5.000
4293
1169
0.073
0.128
1
7.400
3.700
0
83.700
0.103
3.160
3.650
5.900
4245
1049
0.054
0.103
1
9.600
4.000
0
83.300
0.089
3.650
4.470
6.300
3688
880
0.046
0.089
1
11.500
4.200
0
81.800
0.091
4.470
6.320
6.500
2563
682
0.051
0.091
1
11.000
3.800
0
79.900
0.096
6.320
29.305
4.300
1596
393
0.047
0.096
1
11.400
4.100
0
78.900
data reduction
MOSFLM
7.0.9
data scaling
SCALA
3.3.21
phasing
PHASER
2.5.5
refinement
REFMAC
5.8.0049
data extraction
PDB_EXTRACT
3.15
Structure of Mdm2 with low molecular weight inhibitor.
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
A
PRO
20
A
PRO
4
HELX_P
A
GLU
25
A
GLU
9
1
AA1
6
A
LYS
31
A
LYS
15
HELX_P
A
VAL
41
A
VAL
25
1
AA2
11
A
MET
50
A
MET
34
HELX_P
A
LYS
64
A
LYS
48
1
AA3
15
A
ASP
80
A
ASP
64
HELX_P
A
GLY
87
A
GLY
71
1
AA4
8
A
GLU
95
A
GLU
79
HELX_P
A
ARG
105
A
ARG
89
1
AA5
11
B
PRO
20
B
PRO
4
HELX_P
B
GLU
25
B
GLU
9
1
AA6
6
B
LYS
31
B
LYS
15
HELX_P
B
VAL
41
B
VAL
25
1
AA7
11
B
MET
50
B
MET
34
HELX_P
B
LYS
64
B
LYS
48
1
AA8
15
B
ASP
80
B
ASP
64
HELX_P
B
GLY
87
B
GLY
71
1
AA9
8
B
GLU
95
B
GLU
79
HELX_P
B
ARG
105
B
ARG
89
1
AB1
11
LIGASE
p53-Mdm2/MdmX interaction, inhibitor, ligase
A
B
A
GLN
18
A
GLN
2
A
VAL
109
A
VAL
93
0
B
GLN
18
B
GLN
2
B
VAL
109
B
VAL
93
0
MDM2_HUMAN
UNP
1
18
Q00987
QIPASEQETLVRPKPLLLKLLKSVGAQKDTYTMKEVLFYLGQYIMTKRLYDEKQQHIVYCSNDLLGDLFGVPSFSVKEHR
KIYTMIYRNLVVVNQQE
18
114
4ZGK
18
114
Q00987
A
1
2
98
18
114
4ZGK
18
114
Q00987
B
1
2
98
1
initiating methionine
MET
17
4ZGK
A
Q00987
UNP
1
2
initiating methionine
MET
17
4ZGK
B
Q00987
UNP
1
3
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
TYR
48
A
TYR
32
A
THR
49
A
THR
33
A
LEU
27
A
LEU
11
A
PRO
30
A
PRO
14
A
LEU
107
A
LEU
91
A
VAL
109
A
VAL
93
A
ILE
74
A
ILE
58
A
TYR
76
A
TYR
60
A
SER
90
A
SER
74
A
SER
92
A
SER
76
B
TYR
48
B
TYR
32
B
THR
49
B
THR
33
B
LEU
27
B
LEU
11
B
PRO
30
B
PRO
14
B
LEU
107
B
LEU
91
B
VAL
109
B
VAL
93
B
ILE
74
B
ILE
58
B
TYR
76
B
TYR
60
B
SER
90
B
SER
74
B
SER
92
B
SER
76
binding site for residue 4NX A 201
A
4NX
201
Software
12
binding site for residue 4NX B 201
B
4NX
201
Software
12
A
LEU
54
A
LEU
38
12
1_555
A
PHE
55
A
PHE
39
12
1_555
A
GLY
58
A
GLY
42
12
1_555
A
TYR
67
A
TYR
51
12
1_555
A
VAL
93
A
VAL
77
12
1_555
A
HIS
96
A
HIS
80
12
1_555
A
ILE
99
A
ILE
83
12
1_555
A
TYR
100
A
TYR
84
12
1_555
A
HOH
304
E
HOH
12
1_555
A
HOH
309
E
HOH
12
1_555
A
HOH
327
E
HOH
12
1_555
B
LYS
51
B
LYS
35
12
1_555
A
LYS
51
A
LYS
35
12
1_555
B
LEU
54
B
LEU
38
12
1_555
B
PHE
55
B
PHE
39
12
1_555
B
GLY
58
B
GLY
42
12
1_555
B
ILE
61
B
ILE
45
12
1_555
B
TYR
67
B
TYR
51
12
1_555
B
VAL
93
B
VAL
77
12
1_555
B
HIS
96
B
HIS
80
12
1_555
B
ILE
99
B
ILE
83
12
1_555
B
TYR
100
B
TYR
84
12
1_555
B
HOH
318
F
HOH
12
1_555
B
HOH
323
F
HOH
12
1_555
19
P 21 21 21