Structure of PDB 3lcd Chain A Binding Site BS01

Receptor Information
>3lcd Chain A (length=290) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GNSYTFIDPTQLPYNEKWEFPRNNLQFGKTLGAGAFGKVVEATAFGLGKE
DAVLKVAVKMLKSTAHADEKEALMSELKIMSHLGQHENIVNLLGACTHGG
PVLVITEYCCYGDLLNFLRRKAEADLDPLELRDLLHFSSQVAQGMAFLAS
KNCIHRDVAARNVLLTNGHVAKIGDFGLARDIMSNYIVKGNARLPVKWMA
PESIFDCVYTVQSDVWSYGILLWEIFSLGLNPYPGILVNSKFYKLVKDGY
QMAQPAFAPKNIYSIMQACWALEPTHRPTFQQICSFLQEQ
Ligand information
Ligand IDBDY
InChIInChI=1S/C27H30Cl2N6O/c28-22-6-3-7-23(29)21(22)15-32-26-25(30)31-16-24(33-26)18-8-10-19(11-9-18)27(36)35-14-4-5-20(35)17-34-12-1-2-13-34/h3,6-11,16,20H,1-2,4-5,12-15,17H2,(H2,30,31)(H,32,33)/t20-/m1/s1
InChIKeyPVBCEWZVPUKFNT-HXUWFJFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Nc1ncc(nc1NCc2c(Cl)cccc2Cl)c3ccc(cc3)C(=O)N4CCC[C@@H]4CN5CCCC5
OpenEye OEToolkits 1.7.0c1cc(c(c(c1)Cl)CNc2c(ncc(n2)c3ccc(cc3)C(=O)N4CCC[C@@H]4CN5CCCC5)N)Cl
OpenEye OEToolkits 1.7.0c1cc(c(c(c1)Cl)CNc2c(ncc(n2)c3ccc(cc3)C(=O)N4CCCC4CN5CCCC5)N)Cl
CACTVS 3.352Nc1ncc(nc1NCc2c(Cl)cccc2Cl)c3ccc(cc3)C(=O)N4CCC[CH]4CN5CCCC5
FormulaC27 H30 Cl2 N6 O
NameN~3~-(2,6-dichlorobenzyl)-5-(4-{[(2R)-2-(pyrrolidin-1-ylmethyl)pyrrolidin-1-yl]carbonyl}phenyl)pyrazine-2,3-diamine
ChEMBL
DrugBank
ZINCZINC000044460263
PDB chain3lcd 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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PDB3lcd Structure-based drug design enables conversion of a DFG-in binding CSF-1R kinase inhibitor to a DFG-out binding mode
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L588 G589 A614 Y665 C666 G669 L785
Binding residue
(residue number reindexed from 1)		L31 G32 A57 Y108 C109 G112 L164
Annotation score1
Binding affinityMOAD: ic50=40nM
PDBbind-CN: -logKd/Ki=7.40,IC50=40nM
Enzymatic activity
Catalytic site (original residue number in PDB) D778 A780 R782 N783 D796 N814
Catalytic site (residue number reindexed from 1) D157 A159 R161 N162 D175 N191
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3lcd, PDBe:3lcd, PDBj:3lcd
PDBsum3lcd
PubMed20137931
UniProtP07333|CSF1R_HUMAN Macrophage colony-stimulating factor 1 receptor (Gene Name=CSF1R)

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