Structure of PDB 3da6 Chain A Binding Site BS01

Receptor Information
>3da6 Chain A (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NQFYSVEVGDSTFTVLKRYQNLKPIGSGGIVCAAYDAVLDRNVAIKKLSR
PFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVME
LMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVV
KSDCTLKILDFGLARTVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMV
RHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGL
TFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHP
YINVWYDPAREHTIEEWKELIYKEVMNS
Ligand information
Ligand IDBZ9
InChIInChI=1S/C28H23N7O/c1-17-16-24(35-28-33-22-11-5-6-12-23(22)34-28)18-8-3-4-9-19(18)25(17)36-26-20(10-7-14-30-26)21-13-15-31-27(29-2)32-21/h3-16H,1-2H3,(H,29,31,32)(H2,33,34,35)
InChIKeyJXKDTYDBDDKIPY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CNc1nccc(n1)c2cccnc2Oc3c(C)cc(Nc4[nH]c5ccccc5n4)c6ccccc36
ACDLabs 10.04n1ccc(nc1NC)c6cccnc6Oc3c2c(cccc2)c(cc3C)Nc5nc4ccccc4n5
OpenEye OEToolkits 1.5.0Cc1cc(c2ccccc2c1Oc3c(cccn3)c4ccnc(n4)NC)Nc5[nH]c6ccccc6n5
FormulaC28 H23 N7 O
NameN-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-1H-benzimidazol-2-amine
ChEMBLCHEMBL458023
DrugBank
ZINCZINC000039115026
PDB chain3da6 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3da6 Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G71 V78 A91 K93 L95 E111 L144 M146 M149 L206
Binding residue
(residue number reindexed from 1)		G26 V31 A44 K46 L48 E64 L97 M99 M102 L159
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.70,IC50=2nM
Enzymatic activity
Catalytic site (original residue number in PDB) D189 K191 N194 D207 T226
Catalytic site (residue number reindexed from 1) D142 K144 N147 D160 T169
Enzyme Commision number 2.7.11.24: mitogen-activated protein kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004707 MAP kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation

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Molecular Function
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Biological Process
External links
PDB RCSB:3da6, PDBe:3da6, PDBj:3da6
PDBsum3da6
PubMed19062275
UniProtP53779|MK10_HUMAN Mitogen-activated protein kinase 10 (Gene Name=MAPK10)

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