0.013972
0.000000
0.000000
-0.000000
0.013972
0.000000
0.000000
-0.000000
0.009464
0.00000
0.00000
0.00000
Chessari, G.
Buck, I.M.
Day, J.E.H.
Day, P.J.
Iqbal, A.
Johnson, C.N.
Lewis, E.J.
Martins, V.
Miller, D.
Reader, M.
Rees, D.C.
Rich, S.J.
Tamanini, E.
Vitorino, M.
Ward, G.A.
Williams, P.A.
Williams, G.
Wilsher, N.E.
Woolford, A.J.-A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
71.571
71.571
105.666
C8 H13 Br N3 1
231.113
4-(4-bromo-1H-pyrazol-1-yl)piperidinium
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
Zn 2
65.409
ZINC ION
non-polymer
US
J.Med.Chem.
JMCMAR
0151
0022-2623
58
6574
6588
10.1021/acs.jmedchem.5b00706
26218264
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Discovery of a Non-Alanine Lead Series with Dual Activity Against cIAP1 and XIAP.
2015
100
1
CCD
2008-10-08
ADSC QUANTUM 4
SINGLE WAVELENGTH
M
x-ray
1
.9834
1.0
ID23-1
ESRF
.9834
SYNCHROTRON
ESRF BEAMLINE ID23-1
12686.206
E3 ubiquitin-protein ligase XIAP
6.3.2.-
residues 245-354
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
231.113
4-(4-bromo-1H-pyrazol-1-yl)piperidinium
1
syn
non-polymer
18.015
water
56
nat
water
Baculoviral IAP repeat-containing protein 4,IAP-like protein,hILP,Inhibitor of apoptosis protein 3,hIAP3,X-linked inhibitor of apoptosis protein,X-linked IAP
no
no
GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY
PGCKYLLEQKGQEYINNIHLTHSLEECLVR
GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY
PGCKYLLEQKGQEYINNIHLTHSLEECLVR
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
Human
Image clone
sample
1
110
XIAP, API3, BIRC4, IAP3
9606
Homo sapiens
469008
Escherichia coli BL21(DE3)
Biological sequence
pET 28b
2.32
1.35
47
Blocks
VAPOR DIFFUSION, HANGING DROP
7.5
3.9M NaCl, 0.1M HEPES/NaOHpH=7.5
277
repository
Initial release
Database references
1
0
2015-08-12
1
1
2015-09-09
5C0K contains the same protein but with a different ligand
N
RCSB
Y
PDBE
2015-06-12
REL
REL
1
A
O
HOH
556
6.00
ZN
ZINC ION
4WJ
4-(4-bromo-1H-pyrazol-1-yl)piperidinium
HOH
water
ZN
1
2
ZN
ZN
401
A
L01
1
3
4WJ
4WJ
402
A
HOH
8
4
HOH
HOH
501
A
HOH
3
4
HOH
HOH
502
A
HOH
54
4
HOH
HOH
503
A
HOH
1
4
HOH
HOH
504
A
HOH
18
4
HOH
HOH
505
A
HOH
53
4
HOH
HOH
506
A
HOH
13
4
HOH
HOH
507
A
HOH
42
4
HOH
HOH
508
A
HOH
44
4
HOH
HOH
509
A
HOH
36
4
HOH
HOH
510
A
HOH
38
4
HOH
HOH
511
A
HOH
40
4
HOH
HOH
512
A
HOH
43
4
HOH
HOH
513
A
HOH
55
4
HOH
HOH
514
A
HOH
33
4
HOH
HOH
515
A
HOH
5
4
HOH
HOH
516
A
HOH
39
4
HOH
HOH
517
A
HOH
34
4
HOH
HOH
518
A
HOH
26
4
HOH
HOH
519
A
HOH
56
4
HOH
HOH
520
A
HOH
2
4
HOH
HOH
521
A
HOH
27
4
HOH
HOH
522
A
HOH
32
4
HOH
HOH
523
A
HOH
59
4
HOH
HOH
524
A
HOH
6
4
HOH
HOH
525
A
HOH
20
4
HOH
HOH
526
A
HOH
31
4
HOH
HOH
527
A
HOH
16
4
HOH
HOH
528
A
HOH
63
4
HOH
HOH
529
A
HOH
30
4
HOH
HOH
530
A
HOH
52
4
HOH
HOH
531
A
HOH
25
4
HOH
HOH
532
A
HOH
7
4
HOH
HOH
533
A
HOH
51
4
HOH
HOH
534
A
HOH
65
4
HOH
HOH
535
A
HOH
14
4
HOH
HOH
536
A
HOH
21
4
HOH
HOH
537
A
HOH
66
4
HOH
HOH
538
A
HOH
12
4
HOH
HOH
539
A
HOH
15
4
HOH
HOH
540
A
HOH
47
4
HOH
HOH
541
A
HOH
17
4
HOH
HOH
542
A
HOH
11
4
HOH
HOH
543
A
HOH
35
4
HOH
HOH
544
A
HOH
4
4
HOH
HOH
545
A
HOH
19
4
HOH
HOH
546
A
HOH
23
4
HOH
HOH
547
A
HOH
24
4
HOH
HOH
548
A
HOH
9
4
HOH
HOH
549
A
HOH
67
4
HOH
HOH
550
A
HOH
50
4
HOH
HOH
551
A
HOH
62
4
HOH
HOH
552
A
HOH
61
4
HOH
HOH
553
A
HOH
22
4
HOH
HOH
554
A
HOH
64
4
HOH
HOH
555
A
HOH
29
4
HOH
HOH
556
A
n
1
245
A
n
2
246
A
n
3
247
A
n
4
248
A
ASN
249
n
5
ASN
249
A
PHE
250
n
6
PHE
250
A
PRO
251
n
7
PRO
251
A
ASN
252
n
8
ASN
252
A
SER
253
n
9
SER
253
A
THR
254
n
10
THR
254
A
ASN
255
n
11
ASN
255
A
LEU
256
n
12
LEU
256
A
PRO
257
n
13
PRO
257
A
ARG
258
n
14
ARG
258
A
ASN
259
n
15
ASN
259
A
PRO
260
n
16
PRO
260
A
SER
261
n
17
SER
261
A
MET
262
n
18
MET
262
A
ALA
263
n
19
ALA
263
A
ASP
264
n
20
ASP
264
A
TYR
265
n
21
TYR
265
A
GLU
266
n
22
GLU
266
A
ALA
267
n
23
ALA
267
A
ARG
268
n
24
ARG
268
A
ILE
269
n
25
ILE
269
A
PHE
270
n
26
PHE
270
A
THR
271
n
27
THR
271
A
PHE
272
n
28
PHE
272
A
GLY
273
n
29
GLY
273
A
THR
274
n
30
THR
274
A
TRP
275
n
31
TRP
275
A
ILE
276
n
32
ILE
276
A
TYR
277
n
33
TYR
277
A
SER
278
n
34
SER
278
A
VAL
279
n
35
VAL
279
A
ASN
280
n
36
ASN
280
A
LYS
281
n
37
LYS
281
A
GLU
282
n
38
GLU
282
A
GLN
283
n
39
GLN
283
A
LEU
284
n
40
LEU
284
A
ALA
285
n
41
ALA
285
A
ARG
286
n
42
ARG
286
A
ALA
287
n
43
ALA
287
A
GLY
288
n
44
GLY
288
A
PHE
289
n
45
PHE
289
A
TYR
290
n
46
TYR
290
A
ALA
291
n
47
ALA
291
A
LEU
292
n
48
LEU
292
A
GLY
293
n
49
GLY
293
A
GLU
294
n
50
GLU
294
A
GLY
295
n
51
GLY
295
A
ASP
296
n
52
ASP
296
A
LYS
297
n
53
LYS
297
A
VAL
298
n
54
VAL
298
A
LYS
299
n
55
LYS
299
A
CYS
300
n
56
CYS
300
A
PHE
301
n
57
PHE
301
A
HIS
302
n
58
HIS
302
A
CYS
303
n
59
CYS
303
A
GLY
304
n
60
GLY
304
A
GLY
305
n
61
GLY
305
A
GLY
306
n
62
GLY
306
A
LEU
307
n
63
LEU
307
A
THR
308
n
64
THR
308
A
ASP
309
n
65
ASP
309
A
TRP
310
n
66
TRP
310
A
LYS
311
n
67
LYS
311
A
PRO
312
n
68
PRO
312
A
SER
313
n
69
SER
313
A
GLU
314
n
70
GLU
314
A
ASP
315
n
71
ASP
315
A
PRO
316
n
72
PRO
316
A
TRP
317
n
73
TRP
317
A
GLU
318
n
74
GLU
318
A
GLN
319
n
75
GLN
319
A
HIS
320
n
76
HIS
320
A
ALA
321
n
77
ALA
321
A
LYS
322
n
78
LYS
322
A
TRP
323
n
79
TRP
323
A
TYR
324
n
80
TYR
324
A
PRO
325
n
81
PRO
325
A
GLY
326
n
82
GLY
326
A
CYS
327
n
83
CYS
327
A
LYS
328
n
84
LYS
328
A
TYR
329
n
85
TYR
329
A
LEU
330
n
86
LEU
330
A
LEU
331
n
87
LEU
331
A
GLU
332
n
88
GLU
332
A
GLN
333
n
89
GLN
333
A
LYS
334
n
90
LYS
334
A
GLY
335
n
91
GLY
335
A
GLN
336
n
92
GLN
336
A
GLU
337
n
93
GLU
337
A
TYR
338
n
94
TYR
338
A
ILE
339
n
95
ILE
339
A
ASN
340
n
96
ASN
340
A
ASN
341
n
97
ASN
341
A
ILE
342
n
98
ILE
342
A
HIS
343
n
99
HIS
343
A
LEU
344
n
100
LEU
344
A
THR
345
n
101
THR
345
A
HIS
346
n
102
HIS
346
A
SER
347
n
103
SER
347
A
LEU
348
n
104
LEU
348
A
GLU
349
n
105
GLU
349
A
GLU
350
n
106
GLU
350
A
CYS
351
n
107
CYS
351
A
LEU
352
n
108
LEU
352
A
VAL
353
n
109
VAL
353
A
ARG
354
n
110
ARG
354
A
6.7377
-0.8019
1.0612
2.7624
-0.6141
3.5585
0.1032
-0.3739
0.0479
0.3117
-0.0476
0.0561
-0.0985
-0.0020
-0.0556
0.0419
-0.0181
0.0093
0.0809
-0.0296
0.0129
refined
-17.3482
-28.7670
-4.0275
X-RAY DIFFRACTION
A
249
A
354
X-RAY DIFFRACTION
1
software_defined_assembly
PISA
1
monomeric
0
0
6670
A
CYS
300
A
SG
CYS
56
1_555
A
ZN
401
B
ZN
ZN
1_555
A
CYS
303
A
SG
CYS
59
1_555
106.5
A
CYS
300
A
SG
CYS
56
1_555
A
ZN
401
B
ZN
ZN
1_555
A
HIS
320
A
NE2
HIS
76
1_555
99.8
A
CYS
303
A
SG
CYS
59
1_555
A
ZN
401
B
ZN
ZN
1_555
A
HIS
320
A
NE2
HIS
76
1_555
112.4
A
CYS
300
A
SG
CYS
56
1_555
A
ZN
401
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
83
1_555
118.9
A
CYS
303
A
SG
CYS
59
1_555
A
ZN
401
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
83
1_555
113.4
A
HIS
320
A
NE2
HIS
76
1_555
A
ZN
401
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
83
1_555
105.1
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
290
A
N
TYR
46
A
O
LYS
299
A
O
LYS
55
A
N
VAL
298
A
N
VAL
54
A
O
LEU
307
A
O
LEU
63
1
A
HOH
541
D
HOH
1
A
GLY
245
A
GLY
1
1
Y
1
A
SER
246
A
SER
2
1
Y
1
A
HIS
247
A
HIS
3
1
Y
1
A
MET
248
A
MET
4
1
Y
1
A
CYS
351
-73.65
44.49
45.118
0.66
-0.00
-0.00
0.66
-0.00
-1.32
0.934
0.904
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
0.23234
0.19979
0.20144
2.60
71.57
473
8443
5.3
99.38
11.222
0.136
RANDOM
1
THROUGHOUT
0.236
0.205
0.80
0.80
1.20
MAXIMUM LIKELIHOOD
MASK
2.60
71.57
56
935
13
0
866
0.011
0.019
907
0.009
0.027
13
1.419
1.924
1230
0.188
1.072
32
5.319
5.000
105
36.855
24.255
47
18.622
15.000
148
12.281
15.000
4
0.118
0.200
118
0.000
0.021
718
0.000
0.013
2
2.528
6.381
423
4.393
7.120
481
4.388
7.121
482
11.434
14.956
304
0.252
0.291
2.666
35
612
20
99.39
2.59
71.57
5C0L
8972
8972
2.0
0.071
1
7.8
3.6
99.5
0.335
2.59
2.63
2.2
1
99.5
refinement
REFMAC
5.8.0107
E3 ubiquitin-protein ligase XIAP (E.C.6.3.2.-)
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 2
1
N
N
2
N
N
3
N
N
4
N
N
A
ASN
259
A
ASN
15
HELX_P
A
ALA
263
A
ALA
19
5
AA1
5
A
ASP
264
A
ASP
20
HELX_P
A
THR
271
A
THR
27
1
AA2
8
A
ASN
280
A
ASN
36
HELX_P
A
ALA
287
A
ALA
43
1
AA3
8
A
ASP
315
A
ASP
71
HELX_P
A
TYR
324
A
TYR
80
1
AA4
10
A
CYS
327
A
CYS
83
HELX_P
A
CYS
351
A
CYS
107
1
AA5
25
metalc
2.247
A
CYS
300
A
SG
CYS
56
1_555
A
ZN
401
B
ZN
ZN
1_555
metalc
2.307
A
CYS
303
A
SG
CYS
59
1_555
A
ZN
401
B
ZN
ZN
1_555
metalc
2.148
A
HIS
320
A
NE2
HIS
76
1_555
A
ZN
401
B
ZN
ZN
1_555
metalc
2.343
A
CYS
327
A
SG
CYS
83
1_555
A
ZN
401
B
ZN
ZN
1_555
LIGASE
ligase
XIAP_HUMAN
UNP
1
245
P98170
SSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWY
PGCKYLLEQKGQEYINNIHLTHSLEECLVR
245
354
5C0L
245
354
P98170
A
1
1
110
1
SER
conflict
GLY
245
5C0L
A
P98170
UNP
245
1
1
ASP
conflict
HIS
247
5C0L
A
P98170
UNP
247
3
1
ARG
conflict
MET
248
5C0L
A
P98170
UNP
248
4
3
anti-parallel
anti-parallel
A
PHE
289
A
PHE
45
A
ALA
291
A
ALA
47
A
VAL
298
A
VAL
54
A
CYS
300
A
CYS
56
A
GLY
306
A
GLY
62
A
LEU
307
A
LEU
63
binding site for residue ZN A 401
A
ZN
401
Software
4
binding site for residue 4WJ A 402
A
4WJ
402
Software
6
A
CYS
300
A
CYS
56
4
1_555
A
CYS
303
A
CYS
59
4
1_555
A
HIS
320
A
HIS
76
4
1_555
A
CYS
327
A
CYS
83
4
1_555
A
LEU
307
A
LEU
63
6
1_555
A
THR
308
A
THR
64
6
1_555
A
ASP
309
A
ASP
65
6
1_555
A
GLU
314
A
GLU
70
6
1_555
A
GLN
319
A
GLN
75
6
1_555
A
TRP
323
A
TRP
79
6
1_555
91
P 41 2 2