Structure of PDB 3vf8 Chain A Binding Site BS01

Receptor Information
>3vf8 Chain A (length=265) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYLDRKLLTLEDKELGSGNFGTVKKGYYQMVVKTVAVKILPALKDELLAE
ANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKN
IIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALR
ADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQ
KPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFA
AVELRLRNYYYDVVN
Ligand information
Ligand ID0JE
InChIInChI=1S/C17H21FN6O2/c1-4-24(5-2)17(25)22-13-9-19-23-15(13)16-20-11-7-10(18)14(26-6-3)8-12(11)21-16/h7-9H,4-6H2,1-3H3,(H,19,23)(H,20,21)(H,22,25)
InChIKeyUJXIKUVGGQECLJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCN(CC)C(=O)Nc1cn[nH]c1c2[nH]c3cc(c(cc3n2)OCC)F
ACDLabs 12.01O=C(Nc3c(c2nc1cc(OCC)c(F)cc1n2)nnc3)N(CC)CC
CACTVS 3.370CCOc1cc2nc([nH]c2cc1F)c3[nH]ncc3NC(=O)N(CC)CC
FormulaC17 H21 F N6 O2
Name3-[5-(5-ethoxy-6-fluoro-1H-benzimidazol-2-yl)-1H-pyrazol-4-yl]-1,1-diethylurea
ChEMBLCHEMBL2017551
DrugBank
ZINCZINC000084587050
PDB chain3vf8 Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vf8 X-ray crystallographic structure-based design of selective thienopyrazole inhibitors for interleukin-2-inducible tyrosine kinase.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		L377 A400 M450 A451 E452 G454 P455 L501 S511
Binding residue
(residue number reindexed from 1)		L15 A36 M80 A81 E82 G84 P85 L131 S141
Annotation score1
Binding affinityMOAD: ic50=150nM
PDBbind-CN: -logKd/Ki=6.82,IC50=150nM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512 K533
Catalytic site (residue number reindexed from 1) D124 A126 R128 N129 D142 K163
Enzyme Commision number 2.7.10.2: non-specific protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3vf8, PDBe:3vf8, PDBj:3vf8
PDBsum3vf8
PubMed22464456
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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