1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Oost, T.K.
Sun, C.
Armstrong, R.C.
Al-Assaad, A.S.
Betz, S.F.
Deckwerth, T.L.
Elmore, S.W.
Meadows, R.P.
Olejniczak, E.T.
Oleksijew, A.
Oltersdorf, T.
Rosenberg, S.H.
Shoemaker, A.R.
Zou, H.
Fesik, S.W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C25 H38 N4 O3
442.594
N-METHYLALANYL-3-METHYLVALYL-N-(1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL)PROLINAMIDE
1-[3,3-DIMETHYL-2-(2-METHYLAMINO-PROPIONYLAMINO)-BUTYRYL]-PYRROLIDINE-2-CARBOXYLIC ACID(1,2,3,4-TETRAHYDRO-NAPHTHALEN-1-YL)-AMIDE
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
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
47
4417
4426
10.1021/jm040037k
15317454
Discovery of Potent Antagonists of the Antiapoptotic Protein XIAP for the Treatment of Cancer.
2004
10.2210/pdb1tfq/pdb
pdb_00001tfq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
13424.951
Baculoviral IAP repeat-containing protein 4
BIR3 of XIAP: RESIDUES 241-356
1
man
polymer
65.409
ZINC ION
1
syn
non-polymer
442.594
N-METHYLALANYL-3-METHYLVALYL-N-(1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL)PROLINAMIDE
1
syn
non-polymer
Inhibitor of apoptosis protein 3, X-linked inhibitor of apoptosis protein, XIAP, X-linked IAP, IAP-like protein, HILP
no
no
MSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQ
HAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTT
MSDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQ
HAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTT
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
human
Homo
Escherichia
sample
BIRC4, API3, IAP3, XIAP
9606
Homo sapiens
562
Escherichia coli
plasmid
pet28b
database_2
pdbx_struct_assembly
pdbx_struct_conn_angle
pdbx_struct_oper_list
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2004-09-07
1
1
2008-04-30
1
2
2011-07-13
1
3
2022-03-02
_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_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_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.pdbx_dist_value
_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.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
NMR Structure of an Antagonists of the XIAP-Caspase-9 Interaction Complexed to the BIR3 domain of XIAP
RCSB
Y
RCSB
2004-05-27
REL
ZN
ZINC ION
998
N-METHYLALANYL-3-METHYLVALYL-N-(1,2,3,4-TETRAHYDRONAPHTHALEN-1-YL)PROLINAMIDE
1
3D_13C-separated_NOESY
3D_15N-separated_NOESY
2D_13C,15N filtered NOESY
2D_13C,15N filtered tocsy
3D_13C,15N filtered ,13C separated NOESY
20mM Tris
7.2
ambient
303
K
simulated annealing
1
minimized average structure
U-15N, 0.8mM Bir3,20mM Tris, 2mMDTT, 20mM phosphate buffer, 120mM NaCl, 90%H2O, 10%D20
90%H2O, 10%D20
U-15N,13C 0.8mM Bir3, 20mM Tris, 2mMDTT, 20mM phosphate buffer, 120mM NaCl, 100%D2O
100% D2O
Brunger
refinement
CNS
2000
600
Bruker
DRX
ZN
999
2
ZN
ZN
999
A
LIG
998
3
998
998
998
A
MET
240
n
1
MET
240
A
SER
241
n
2
SER
241
A
ASP
242
n
3
ASP
242
A
ALA
243
n
4
ALA
243
A
VAL
244
n
5
VAL
244
A
SER
245
n
6
SER
245
A
SER
246
n
7
SER
246
A
ASP
247
n
8
ASP
247
A
ARG
248
n
9
ARG
248
A
ASN
249
n
10
ASN
249
A
PHE
250
n
11
PHE
250
A
PRO
251
n
12
PRO
251
A
ASN
252
n
13
ASN
252
A
SER
253
n
14
SER
253
A
THR
254
n
15
THR
254
A
ASN
255
n
16
ASN
255
A
LEU
256
n
17
LEU
256
A
PRO
257
n
18
PRO
257
A
ARG
258
n
19
ARG
258
A
ASN
259
n
20
ASN
259
A
PRO
260
n
21
PRO
260
A
SER
261
n
22
SER
261
A
MET
262
n
23
MET
262
A
ALA
263
n
24
ALA
263
A
ASP
264
n
25
ASP
264
A
TYR
265
n
26
TYR
265
A
GLU
266
n
27
GLU
266
A
ALA
267
n
28
ALA
267
A
ARG
268
n
29
ARG
268
A
ILE
269
n
30
ILE
269
A
PHE
270
n
31
PHE
270
A
THR
271
n
32
THR
271
A
PHE
272
n
33
PHE
272
A
GLY
273
n
34
GLY
273
A
THR
274
n
35
THR
274
A
TRP
275
n
36
TRP
275
A
ILE
276
n
37
ILE
276
A
TYR
277
n
38
TYR
277
A
SER
278
n
39
SER
278
A
VAL
279
n
40
VAL
279
A
ASN
280
n
41
ASN
280
A
LYS
281
n
42
LYS
281
A
GLU
282
n
43
GLU
282
A
GLN
283
n
44
GLN
283
A
LEU
284
n
45
LEU
284
A
ALA
285
n
46
ALA
285
A
ARG
286
n
47
ARG
286
A
ALA
287
n
48
ALA
287
A
GLY
288
n
49
GLY
288
A
PHE
289
n
50
PHE
289
A
TYR
290
n
51
TYR
290
A
ALA
291
n
52
ALA
291
A
LEU
292
n
53
LEU
292
A
GLY
293
n
54
GLY
293
A
GLU
294
n
55
GLU
294
A
GLY
295
n
56
GLY
295
A
ASP
296
n
57
ASP
296
A
LYS
297
n
58
LYS
297
A
VAL
298
n
59
VAL
298
A
LYS
299
n
60
LYS
299
A
CYS
300
n
61
CYS
300
A
PHE
301
n
62
PHE
301
A
HIS
302
n
63
HIS
302
A
CYS
303
n
64
CYS
303
A
GLY
304
n
65
GLY
304
A
GLY
305
n
66
GLY
305
A
GLY
306
n
67
GLY
306
A
LEU
307
n
68
LEU
307
A
THR
308
n
69
THR
308
A
ASP
309
n
70
ASP
309
A
TRP
310
n
71
TRP
310
A
LYS
311
n
72
LYS
311
A
PRO
312
n
73
PRO
312
A
SER
313
n
74
SER
313
A
GLU
314
n
75
GLU
314
A
ASP
315
n
76
ASP
315
A
PRO
316
n
77
PRO
316
A
TRP
317
n
78
TRP
317
A
GLU
318
n
79
GLU
318
A
GLN
319
n
80
GLN
319
A
HIS
320
n
81
HIS
320
A
ALA
321
n
82
ALA
321
A
LYS
322
n
83
LYS
322
A
TRP
323
n
84
TRP
323
A
TYR
324
n
85
TYR
324
A
PRO
325
n
86
PRO
325
A
GLY
326
n
87
GLY
326
A
CYS
327
n
88
CYS
327
A
LYS
328
n
89
LYS
328
A
TYR
329
n
90
TYR
329
A
LEU
330
n
91
LEU
330
A
LEU
331
n
92
LEU
331
A
GLU
332
n
93
GLU
332
A
GLN
333
n
94
GLN
333
A
LYS
334
n
95
LYS
334
A
GLY
335
n
96
GLY
335
A
GLN
336
n
97
GLN
336
A
GLU
337
n
98
GLU
337
A
TYR
338
n
99
TYR
338
A
ILE
339
n
100
ILE
339
A
ASN
340
n
101
ASN
340
A
ASN
341
n
102
ASN
341
A
ILE
342
n
103
ILE
342
A
HIS
343
n
104
HIS
343
A
LEU
344
n
105
LEU
344
A
THR
345
n
106
THR
345
A
HIS
346
n
107
HIS
346
A
SER
347
n
108
SER
347
A
LEU
348
n
109
LEU
348
A
GLU
349
n
110
GLU
349
A
GLU
350
n
111
GLU
350
A
CYS
351
n
112
CYS
351
A
LEU
352
n
113
LEU
352
A
VAL
353
n
114
VAL
353
A
ARG
354
n
115
ARG
354
A
THR
355
n
116
THR
355
A
THR
356
n
117
THR
356
A
author_defined_assembly
1
monomeric
A
CYS
300
A
SG
CYS
61
1_555
A
ZN
999
B
ZN
ZN
1_555
A
CYS
303
A
SG
CYS
64
1_555
108.6
A
CYS
300
A
SG
CYS
61
1_555
A
ZN
999
B
ZN
ZN
1_555
A
HIS
320
A
ND1
HIS
81
1_555
110.0
A
CYS
303
A
SG
CYS
64
1_555
A
ZN
999
B
ZN
ZN
1_555
A
HIS
320
A
ND1
HIS
81
1_555
110.0
A
CYS
300
A
SG
CYS
61
1_555
A
ZN
999
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
88
1_555
109.2
A
CYS
303
A
SG
CYS
64
1_555
A
ZN
999
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
88
1_555
110.1
A
HIS
320
A
ND1
HIS
81
1_555
A
ZN
999
B
ZN
ZN
1_555
A
CYS
327
A
SG
CYS
88
1_555
109.0
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
51
A
O
LYS
299
A
O
LYS
60
A
N
VAL
298
A
N
VAL
59
A
O
LEU
307
A
O
LEU
68
1
A
ALA
243
63.16
-176.77
1
A
VAL
244
-150.92
80.29
1
A
SER
245
-159.55
-66.69
1
A
ASP
247
-147.84
-61.36
1
A
PHE
250
59.36
72.42
1
A
ASN
252
-151.81
-60.91
1
A
SER
253
-178.15
-54.37
1
A
ASN
255
-58.70
100.62
1
A
ARG
258
-170.11
-63.56
1
A
ASN
259
57.49
74.31
1
A
MET
262
-169.05
-50.38
1
A
ASP
264
-137.56
-59.76
1
A
TYR
277
-146.58
-52.06
1
A
SER
278
-129.35
-73.21
1
A
ASP
296
72.51
-56.62
1
A
LYS
297
-53.59
100.67
1
A
HIS
302
71.10
-66.69
1
A
ASP
309
60.35
65.49
1
A
SER
313
62.36
89.11
1
A
TYR
324
-161.02
87.64
1
A
LEU
344
-176.09
-49.56
1
A
LEU
348
59.63
176.69
1
A
VAL
353
71.76
-67.46
1
A
ARG
354
-166.85
51.36
minimized average
NMR Structure of an Antagonists of the XIAP-Caspase-9 Interaction Complexed to the BIR3 domain of XIAP
1
N
N
2
N
N
3
N
N
A
ASP
264
A
ASP
25
HELX_P
A
GLY
273
A
GLY
34
1
1
10
A
ASN
280
A
ASN
41
HELX_P
A
GLY
288
A
GLY
49
1
2
9
A
ASP
315
A
ASP
76
HELX_P
A
TYR
324
A
TYR
85
1
3
10
A
CYS
327
A
CYS
88
HELX_P
A
HIS
343
A
HIS
104
1
4
17
metalc
2.102
A
CYS
300
A
SG
CYS
61
1_555
A
ZN
999
B
ZN
ZN
1_555
metalc
2.104
A
CYS
303
A
SG
CYS
64
1_555
A
ZN
999
B
ZN
ZN
1_555
metalc
2.205
A
HIS
320
A
ND1
HIS
81
1_555
A
ZN
999
B
ZN
ZN
1_555
metalc
2.104
A
CYS
327
A
SG
CYS
88
1_555
A
ZN
999
B
ZN
ZN
1_555
APOPTOSIS
COMPLEX, ligand-PROTEIN, APOPTOSIS, BIR, XIAP
BIRC4_HUMAN
UNP
1
241
P98170
SDAVSSDRNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQH
AKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVRTT
241
356
1TFQ
241
356
P98170
A
1
2
117
1
initiating methionine
MET
240
1TFQ
A
P98170
UNP
1
3
anti-parallel
anti-parallel
A
PHE
289
A
PHE
50
A
ALA
291
A
ALA
52
A
VAL
298
A
VAL
59
A
CYS
300
A
CYS
61
A
GLY
306
A
GLY
67
A
LEU
307
A
LEU
68
BINDING SITE FOR RESIDUE ZN A 999
A
ZN
999
Software
4
BINDING SITE FOR RESIDUE 998 A 998
A
998
998
Software
8
A
CYS
300
A
CYS
61
4
1_555
A
CYS
303
A
CYS
64
4
1_555
A
HIS
320
A
HIS
81
4
1_555
A
CYS
327
A
CYS
88
4
1_555
A
LYS
297
A
LYS
58
8
1_555
A
LYS
299
A
LYS
60
8
1_555
A
GLY
306
A
GLY
67
8
1_555
A
LEU
307
A
LEU
68
8
1_555
A
THR
308
A
THR
69
8
1_555
A
ASP
309
A
ASP
70
8
1_555
A
GLN
319
A
GLN
80
8
1_555
A
TRP
323
A
TRP
84
8
1_555