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2QU6
Biol. Unit 2
Info
Asym.Unit (101 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (47 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE VEGFR2 KINASE DOMAIN IN COMPLEX WITH A BENZOXAZOLE INHIBITOR
Authors
:
D. A. Whittington, J. L. Kim, A. M. Long, P. Rose, Y. Gu, H. Zhao
Date
:
03 Aug 07 (Deposition) - 25 Sep 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Receptor Tyrosine Kinase, Kdr, Angiogenesis, Atp-Binding, Developmental Protein, Differentiation, Glycoprotein, Host- Virus Interaction, Immunoglobulin Domain, Membrane, Nucleotide-Binding, Phosphorylation, Polymorphism, Transferase, Transmembrane, Tyrosine-Protein Kinase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
M. H. Potashman, J. Bready, A. Coxon, T. M. Demelfi, L. Dipietro, N. Doerr, D. Elbaum, J. Estrada, P. Gallant, J. Germain, Y. Gu, J. C. Harmange, S. A. Kaufman, R. Kendall, J. L. Kim, G. N. Kumar, A. M. Long, S. Neervannan, V. F. Patel, A. Polverino, P. Rose, S. V. Plas, D. Whittington, R. Zanon, H. Zhao
Design, Synthesis, And Evaluation Of Orally Active Benzimidazoles And Benzoxazoles As Vascular Endothelial Growth Factor-2 Receptor Tyrosine Kinase Inhibitors.
J. Med. Chem. V. 50 4351 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: 4-({2-[(4-CHLORO-3-{[(2S)-1-METHYL... (857a)
1b: 4-({2-[(4-CHLORO-3-{[(2S)-1-METHYL... (857b)
2a: SULFATE ION (SO4a)
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No.
Name
Count
Type
Full Name
1
857
1
Ligand/Ion
4-({2-[(4-CHLORO-3-{[(2S)-1-METHYLPYRROLIDIN-2-YL]METHOXY}PHENYL)AMINO]-1,3-BENZOXAZOL-5-YL}OXY)-N-METHYLPYRIDINE-2-CARBOXAMIDE
2
SO4
-1
Ligand/Ion
SULFATE ION
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Sites
(0, 0)
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_046679 (V848E, chain B, )
2: VAR_036127 (G873R, chain B, )
3: VAR_VGFR2_HUMAN_CCDS3497_1_02 (G873R, chain B, )
4: VAR_063147 (P1147S, chain B, )
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_046679
V
848
E
VGFR2_HUMAN
Polymorphism
1139776
B
V
848
E
2
UniProt
VAR_036127
G
873
R
VGFR2_HUMAN
Unclassified
---
B
G
873
R
3
CancerSNP
VAR_VGFR2_HUMAN_CCDS3497_1_02
*
G
873
R
VGFR2_HUMAN
Disease (Colorectal cancer)
---
B
G
873
R
4
UniProt
VAR_063147
P
1147
S
VGFR2_HUMAN
Disease (HCI)
---
B
P
1147
S
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (B:840-868)
2: RECEPTOR_TYR_KIN_III (B:893-906)
3: PROTEIN_KINASE_TYR (B:1024-1036)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
VGFR2_HUMAN
840-868
1
-
B:840-868
2
RECEPTOR_TYR_KIN_III
PS00240
Receptor tyrosine kinase class III signature.
VGFR2_HUMAN
893-906
1
-
B:893-906
3
PROTEIN_KINASE_TYR
PS00109
Tyrosine protein kinases specific active-site signature.
VGFR2_HUMAN
1024-1036
1
-
B:1024-1036
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2qu6a_ (A:)
1b: SCOP_d2qu6b_ (B:)
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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
:
Vascular endothelial growth factor receptor 2 (kdr)
(20)
Human (Homo sapiens) [TaxId: 9606]
(20)
1a
d2qu6a_
A:
1b
d2qu6b_
B:
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2qu6B01 (B:822-918)
1b: CATH_2qu6A01 (A:817-918)
2a: CATH_2qu6A02 (A:919-1166)
2b: CATH_2qu6B02 (B:919-1165)
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(
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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
2qu6B01
B:822-918
1b
2qu6A01
A:817-918
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
2qu6A02
A:919-1166
2b
2qu6B02
B:919-1165
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Pkinase_Tyr_2qu6B01 (B:834-1160)
1b: PFAM_Pkinase_Tyr_2qu6B02 (B:834-1160)
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Clan
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PKinase
(934)
Family
:
Pkinase_Tyr
(229)
Homo sapiens (Human)
(202)
1a
Pkinase_Tyr-2qu6B01
B:834-1160
1b
Pkinase_Tyr-2qu6B02
B:834-1160
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Chain B
Asymmetric Unit 1
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Asym.Unit (101 KB)
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