Structure of PDB 4dfn Chain A Binding Site BS01

Receptor Information
>4dfn Chain A (length=269) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKPALKDEL
LAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVK
DKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSK
ALRADENYYKAQTHGKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFS
YGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRP
GFAAVELRLRNYYYDVVNE
Ligand information
Ligand ID0K1
InChIInChI=1S/C25H28N6O2/c1-31-13-19(11-28-31)15-3-2-4-16(7-15)20-12-27-23(26)22(29-20)24(32)30-21-17-5-14-6-18(21)10-25(33,8-14)9-17/h2-4,7,11-14,17-18,21,33H,5-6,8-10H2,1H3,(H2,26,27)(H,30,32)/t14-,17-,18+,21+,25-
InChIKeyKADWYJUBGMHRCN-QWOVOEGBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cn1cc(cn1)c2cccc(c2)c3cnc(c(n3)C(=O)NC4[C@@H]5CC6C[C@H]4CC(C5)(C6)O)N
CACTVS 3.370Cn1cc(cn1)c2cccc(c2)c3cnc(N)c(n3)C(=O)NC4[C@@H]5CC6C[C@H]4CC(O)(C6)C5
CACTVS 3.370Cn1cc(cn1)c2cccc(c2)c3cnc(N)c(n3)C(=O)NC4[CH]5CC6C[CH]4CC(O)(C6)C5
ACDLabs 12.01O=C(NC3C2CC1CC3CC(O)(C1)C2)c6nc(c5cc(c4cn(nc4)C)ccc5)cnc6N
OpenEye OEToolkits 1.7.6Cn1cc(cn1)c2cccc(c2)c3cnc(c(n3)C(=O)NC4C5CC6CC4CC(C6)(C5)O)N
FormulaC25 H28 N6 O2
Name3-amino-6-[3-(1-methyl-1H-pyrazol-4-yl)phenyl]-N-[(1R,2r,3S,5s,7s)-5-hydroxyadamantan-2-yl]pyrazine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain4dfn Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dfn Pyrazine-based Syk kinase inhibitors.
Resolution2.48 Å
Binding residue
(original residue number in PDB)		L377 F382 V385 A400 M448 A451 P455 K458 L501 D512
Binding residue
(residue number reindexed from 1)		L15 F20 V23 A38 M81 A84 P88 K91 L134 D145
Annotation score1
Binding affinityMOAD: ic50=0.02uM
PDBbind-CN: -logKd/Ki=7.70,IC50=0.02uM
BindingDB: IC50=20nM
Enzymatic activity
Catalytic site (original residue number in PDB) D494 A496 R498 N499 D512 K533
Catalytic site (residue number reindexed from 1) D127 A129 R131 N132 D145 K166
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4dfn, PDBe:4dfn, PDBj:4dfn
PDBsum4dfn
PubMed22425453
UniProtP43405|KSYK_HUMAN Tyrosine-protein kinase SYK (Gene Name=SYK)

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