Structure of PDB 3dpk Chain A Binding Site BS01

Receptor Information
>3dpk Chain A (length=279) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRWKIIESSYTFIDPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLG
AVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGP
VLVITEYCCYGDLLNFLRRQLSSRDLLHFSSQVAQGMAFLASKNCIHRDV
AARNVLLTNGHVAKIGDFGLARDIMNDSNYIVRLPVKWMAPESIFDCVYT
VQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGYQMAQPAFAPK
NIYSIMQACWALEPTHRPTFQQICSFLQE
Ligand information
Ligand ID8C5
InChIInChI=1S/C27H34N6O3/c1-36-31-26(35)23-18-33(21-7-3-2-4-8-21)25-22(24(23)34)17-28-27(30-25)29-20-11-9-19(10-12-20)13-16-32-14-5-6-15-32/h9-12,17-18,21H,2-8,13-16H2,1H3,(H,31,35)(H,28,29,30)
InChIKeyLYINTIKJROJCGF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(NOC)C2=CN(c1nc(ncc1C2=O)Nc3ccc(cc3)CCN4CCCC4)C5CCCCC5
CACTVS 3.341CONC(=O)C1=CN(C2CCCCC2)c3nc(Nc4ccc(CCN5CCCC5)cc4)ncc3C1=O
OpenEye OEToolkits 1.5.0CONC(=O)C1=CN(c2c(cnc(n2)Nc3ccc(cc3)CCN4CCCC4)C1=O)C5CCCCC5
FormulaC27 H34 N6 O3
Name8-cyclohexyl-N-methoxy-5-oxo-2-{[4-(2-pyrrolidin-1-ylethyl)phenyl]amino}-5,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide
ChEMBLCHEMBL490080
DrugBank
ZINCZINC000039136227
PDB chain3dpk Chain A Residue 923 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dpk Pyrido[2,3-d]pyrimidin-5-ones: a novel class of antiinflammatory macrophage colony-stimulating factor-1 receptor inhibitors
Resolution1.95 Å
Binding residue
(original residue number in PDB)		A614 K616 E633 M637 T663 Y665 C666 G669 L785 F797
Binding residue
(residue number reindexed from 1)		A56 K58 E75 M79 T105 Y107 C108 G111 L156 F168
Annotation score1
Binding affinityMOAD: ic50=4.1nM
PDBbind-CN: -logKd/Ki=8.39,IC50=4.1nM
Enzymatic activity
Catalytic site (original residue number in PDB) D778 A780 R782 N783 D796 N805
Catalytic site (residue number reindexed from 1) D149 A151 R153 N154 D167 N176
Enzyme Commision number 2.7.10.1: receptor protein-tyrosine kinase.
Gene Ontology
Molecular Function
GO:0004672 protein kinase activity
GO:0004713 protein tyrosine kinase activity
GO:0004714 transmembrane receptor protein tyrosine kinase activity
GO:0005524 ATP binding
Biological Process
GO:0006468 protein phosphorylation
GO:0007169 cell surface receptor protein tyrosine kinase signaling pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dpk, PDBe:3dpk, PDBj:3dpk
PDBsum3dpk
PubMed19193011
UniProtP07333|CSF1R_HUMAN Macrophage colony-stimulating factor 1 receptor (Gene Name=CSF1R);
P11362|FGFR1_HUMAN Fibroblast growth factor receptor 1 (Gene Name=FGFR1)

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