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3DKC
Asym. Unit
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Asym.Unit (62 KB)
Biol.Unit 1 (59 KB)
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(1)
Title
:
STRUCTURE OF MET RECEPTOR TYROSINE KINASE IN COMPLEX WITH ATP
Authors
:
J. Hendle
Date
:
24 Jun 08 (Deposition) - 07 Jul 09 (Release) - 22 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.52
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Drug Discovery, C-Met Kinase, Fragment Based, Membrane, Receptor, Transmembrane, Oncoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. G. Buchanan, J. Hendle, P. S. Lee, C. R. Smith, P. Y. Bounaud, K. A. Jessen, C. M. Tang, N. H. Huser, J. D. Felce, K. J. Froning, M. C. Peterman, B. E. Aubol, S. F. Gessert, J. M. Sauder, K. D. Schwinn, M. Russell, I. A. Rooney, J. Adams, B. C. Leon, T. H. Do, J. M. Blaney, P. A. Sprengeler, D. A. Thompson, L. Smyth, L. A. Pelletier, S. Atwell, K. Holme, S. R. Wasserman, S. Emtage, S. K. Burley, S. H. Reich
Sgx523 Is An Exquisitely Selective, Atp-Competitive Inhibitor Of The Met Receptor Tyrosine Kinase With Antitumo Activity In Vivo.
Mol. Cancer Ther. V. 8 3181 2009
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
2a: CHLORIDE ION (CLa)
3a: MAGNESIUM ION (MGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
CL
1
Ligand/Ion
CHLORIDE ION
3
MG
1
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:104 , ASN A:1209 , ASP A:1222
BINDING SITE FOR RESIDUE MG A 2
2
AC2
SOFTWARE
HOH A:42 , LYS A:1179 , GLY A:1346 , GLU A:1347 , HIS A:1348
BINDING SITE FOR RESIDUE CL A 3
3
AC3
SOFTWARE
HOH A:15 , HOH A:26 , HOH A:41 , HOH A:70 , HOH A:76 , HOH A:78 , HOH A:81 , HOH A:96 , HOH A:104 , HOH A:118 , HOH A:163 , ILE A:1084 , GLY A:1085 , GLY A:1087 , HIS A:1088 , GLY A:1090 , ALA A:1108 , LYS A:1110 , PRO A:1158 , MET A:1160 , ASP A:1204 , ARG A:1208 , ASN A:1209 , MET A:1211 , ASP A:1222
BINDING SITE FOR RESIDUE ATP A 1
[
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]
SAPs(SNPs)/Variants
(19, 19)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_032485 (V1092I, chain A, )
02: VAR_032486 (H1094L, chain A, )
03: VAR_032487 (H1094R, chain A, )
04: VAR_032488 (H1094Y, chain A, )
05: VAR_032489 (H1106D, chain A, )
06: VAR_006286 (M1131T, chain A, )
07: VAR_032490 (T1173I, chain A, )
08: VAR_006287 (V1188L, chain A, )
09: VAR_006288 (L1195V, chain A, )
10: VAR_006289 (V1220I, chain A, )
11: VAR_006291 (D1228H, chain A, )
12: VAR_006290 (D1228N, chain A, )
13: VAR_006292 (Y1230C, chain A, )
14: VAR_032491 (Y1230D, chain A, )
15: VAR_006293 (Y1230H, chain A, )
16: VAR_032492 (K1244R, chain A, )
17: VAR_032493 (M1250I, chain A, )
18: VAR_006294 (M1250T, chain A, )
19: VAR_064857 (V1294I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_032485
V
1092
I
MET_HUMAN
Disease (RCCP)
---
A
V
1092
I
02
UniProt
VAR_032486
H
1094
L
MET_HUMAN
Disease (RCCP)
---
A
H
1094
L
03
UniProt
VAR_032487
H
1094
R
MET_HUMAN
Disease (RCCP)
---
A
H
1094
R
04
UniProt
VAR_032488
H
1094
Y
MET_HUMAN
Disease (RCCP)
---
A
H
1094
Y
05
UniProt
VAR_032489
H
1106
D
MET_HUMAN
Disease (RCCP)
---
A
H
1106
D
06
UniProt
VAR_006286
M
1131
T
MET_HUMAN
Disease (RCCP)
---
A
M
1131
T
07
UniProt
VAR_032490
T
1173
I
MET_HUMAN
Disease (HCC)
---
A
T
1173
I
08
UniProt
VAR_006287
V
1188
L
MET_HUMAN
Disease (RCCP)
---
A
V
1188
L
09
UniProt
VAR_006288
L
1195
V
MET_HUMAN
Disease (RCCP)
---
A
L
1195
V
10
UniProt
VAR_006289
V
1220
I
MET_HUMAN
Disease (RCCP)
---
A
V
1220
I
11
UniProt
VAR_006291
D
1228
H
MET_HUMAN
Disease (RCCP)
---
A
D
1228
H
12
UniProt
VAR_006290
D
1228
N
MET_HUMAN
Disease (RCCP)
---
A
D
1228
N
13
UniProt
VAR_006292
Y
1230
C
MET_HUMAN
Disease (RCCP)
---
A
Y
1230
C
14
UniProt
VAR_032491
Y
1230
D
MET_HUMAN
Disease (RCCP)
---
A
Y
1230
D
15
UniProt
VAR_006293
Y
1230
H
MET_HUMAN
Disease (RCCP)
---
A
Y
1230
H
16
UniProt
VAR_032492
K
1244
R
MET_HUMAN
Disease (HCC)
---
A
K
1244
R
17
UniProt
VAR_032493
M
1250
I
MET_HUMAN
Disease (HCC)
---
A
M
1250
I
18
UniProt
VAR_006294
M
1250
T
MET_HUMAN
Disease (RCCP)
---
A
M
1250
T
19
UniProt
VAR_064857
V
1294
I
MET_HUMAN
Unclassified
---
A
V
1294
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:1084-1110)
2: PROTEIN_KINASE_TYR (A:1200-1212)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
MET_HUMAN
1084-1110
1
A:1084-1110
2
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
MET_HUMAN
1200-1212
1
A:1200-1212
[
close PROSITE info
]
Exons
(7, 7)
Info
All Exons
Exon 1.18b (A:1051-1087)
Exon 1.19 (A:1087-1114)
Exon 1.20 (A:1114-1174)
Exon 1.21 (A:1175-1211)
Exon 1.22 (A:1211-1266)
Exon 1.23 (A:1267-1312)
Exon 1.24b (A:1312-1362)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.17/1.18b
2: Boundary 1.18b/1.19
3: Boundary 1.19/1.20
4: Boundary 1.20/1.21
5: Boundary 1.21/1.22
6: Boundary 1.22/1.23
7: Boundary 1.23/1.24b
8: Boundary 1.24b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1c
ENST00000397752
1c
ENSE00001865305
chr7:
116312446-116312631
186
MET_HUMAN
-
0
0
-
-
1.3c
ENST00000397752
3c
ENSE00001238915
chr7:
116339125-116340338
1214
MET_HUMAN
1-400
400
0
-
-
1.6
ENST00000397752
6
ENSE00000717722
chr7:
116371722-116371913
192
MET_HUMAN
401-464
64
0
-
-
1.7
ENST00000397752
7
ENSE00000717724
chr7:
116380004-116380138
135
MET_HUMAN
465-509
45
0
-
-
1.8
ENST00000397752
8
ENSE00000717726
chr7:
116380906-116381079
174
MET_HUMAN
510-567
58
0
-
-
1.9b
ENST00000397752
9b
ENSE00000717728
chr7:
116395409-116395569
161
MET_HUMAN
568-621
54
0
-
-
1.10
ENST00000397752
10
ENSE00000717730
chr7:
116397491-116397593
103
MET_HUMAN
621-655
35
0
-
-
1.11b
ENST00000397752
11b
ENSE00000717732
chr7:
116397692-116397828
137
MET_HUMAN
656-701
46
0
-
-
1.12a
ENST00000397752
12a
ENSE00000717735
chr7:
116398513-116398674
162
MET_HUMAN
701-755
55
0
-
-
1.13b
ENST00000397752
13b
ENSE00001530016
chr7:
116399445-116399544
100
MET_HUMAN
755-788
34
0
-
-
1.14
ENST00000397752
14
ENSE00000717791
chr7:
116403104-116403322
219
MET_HUMAN
789-861
73
0
-
-
1.15a
ENST00000397752
15a
ENSE00000717803
chr7:
116409699-116409845
147
MET_HUMAN
862-910
49
0
-
-
1.16
ENST00000397752
16
ENSE00000717811
chr7:
116411552-116411708
157
MET_HUMAN
911-963
53
0
-
-
1.17
ENST00000397752
17
ENSE00000717833
chr7:
116411903-116412043
141
MET_HUMAN
963-1010
48
0
-
-
1.18b
ENST00000397752
18b
ENSE00000717861
chr7:
116414935-116415165
231
MET_HUMAN
1010-1087
78
1
A:1051-1087
37
1.19
ENST00000397752
19
ENSE00000717879
chr7:
116417443-116417523
81
MET_HUMAN
1087-1114
28
1
A:1087-1114
28
1.20
ENST00000397752
20
ENSE00000717895
chr7:
116418830-116419011
182
MET_HUMAN
1114-1174
61
1
A:1114-1174
61
1.21
ENST00000397752
21
ENSE00000717902
chr7:
116422042-116422151
110
MET_HUMAN
1175-1211
37
1
A:1175-1211
37
1.22
ENST00000397752
22
ENSE00000717928
chr7:
116423358-116423523
166
MET_HUMAN
1211-1266
56
1
A:1211-1266
56
1.23
ENST00000397752
23
ENSE00000717937
chr7:
116435709-116435845
137
MET_HUMAN
1267-1312
46
1
A:1267-1312
46
1.24b
ENST00000397752
24b
ENSE00000881894
chr7:
116435941-116438440
2500
MET_HUMAN
1312-1390
79
1
A:1312-1362
51
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3dkca_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Hepatocyte growth factor receptor, c-MET
(34)
Human (Homo sapiens) [TaxId: 9606]
(34)
1a
d3dkca_
A:
[
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]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3dkcA01 (A:1061-1159)
2a: CATH_3dkcA02 (A:1160-1362)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Human (Homo sapiens)
(1036)
1a
3dkcA01
A:1061-1159
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Human (Homo sapiens)
(1049)
2a
3dkcA02
A:1160-1362
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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]
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(currently selected atoms:
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)
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Chain A
Asymmetric Unit 1
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