Structure of PDB 3lco Chain A Binding Site BS01

Receptor Information
>3lco Chain A (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KIIEFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKED
AVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGGP
VLVITEYCCYGDLLNFLRRKAEAMLGPSGRPLELRDLLHFSSQVAQGMAF
LASKNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMNDSNYIVRLPVKWM
APESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDG
YQMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQAQ
Ligand information
Ligand IDLC0
InChIInChI=1S/C23H24N6O4/c1-29-12-16(9-27-29)19-10-26-22(24)23(28-19)33-14-17-8-20(31-3)21(11-25-17)32-13-15-4-6-18(30-2)7-5-15/h4-12H,13-14H2,1-3H3,(H2,24,26)
InChIKeyFYNJLBSSIPLISK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COc1ccc(COc2cnc(COc3nc(cnc3N)c4cnn(C)c4)cc2OC)cc1
OpenEye OEToolkits 1.7.0Cn1cc(cn1)c2cnc(c(n2)OCc3cc(c(cn3)OCc4ccc(cc4)OC)OC)N
FormulaC23 H24 N6 O4
Name3-({4-methoxy-5-[(4-methoxybenzyl)oxy]pyridin-2-yl}methoxy)-5-(1-methyl-1H-pyrazol-4-yl)pyrazin-2-amine
ChEMBLCHEMBL1087662
DrugBank
ZINCZINC000049112169
PDB chain3lco Chain A Residue 999 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3lco Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		L588 A614 K616 V647 E664 C666 L785 G795 D796 F797
Binding residue
(residue number reindexed from 1)		L30 A56 K58 V89 E106 C108 L167 G177 D178 F179
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.84,IC50=143nM
BindingDB: IC50=143nM
Enzymatic activity
Catalytic site (original residue number in PDB) D778 R782 N783 D796
Catalytic site (residue number reindexed from 1) D160 R164 N165 D178
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:3lco, PDBe:3lco, PDBj:3lco
PDBsum3lco
PubMed20137931
UniProtP07333|CSF1R_HUMAN Macrophage colony-stimulating factor 1 receptor (Gene Name=CSF1R)

[Back to BioLiP]