Structure of PDB 6bgu Chain A Binding Site BS01

Receptor Information
>6bgu Chain A (length=309) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTPREAFGFEQAVREYTLQSFGEMADNF
KSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFP
VKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSS
FCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQ
PDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYN
FAEAVNFCT
Ligand information
Ligand IDDKP
InChIInChI=1S/C18H17ClN2O3/c1-2-9-24-17(11-5-3-4-6-13(11)19)15-10-14-16(21-15)12(18(22)23)7-8-20-14/h3-8,10,17,21H,2,9H2,1H3,(H,22,23)/t17-/m1/s1
InChIKeyNXCXDWJNFKFGCO-QGZVFWFLSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c3cccc(C(c1nc2c(c1)nccc2C(=O)O)OCCC)c3Cl
OpenEye OEToolkits 2.0.6CCCOC(c1ccccc1Cl)c2cc3c([nH]2)c(ccn3)C(=O)O
OpenEye OEToolkits 2.0.6CCCO[C@H](c1ccccc1Cl)c2cc3c([nH]2)c(ccn3)C(=O)O
CACTVS 3.385CCCO[CH](c1[nH]c2c(c1)nccc2C(O)=O)c3ccccc3Cl
CACTVS 3.385CCCO[C@@H](c1[nH]c2c(c1)nccc2C(O)=O)c3ccccc3Cl
FormulaC18 H17 Cl N2 O3
Name2-[(R)-(2-chlorophenyl)(propoxy)methyl]-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6bgu Chain A Residue 601 [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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PDB6bgu Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution1.684 Å
Binding residue
(original residue number in PDB)		R73 Y409 A411 Y472 F480 H483 N493 K501 W503 Q535 H571
Binding residue
(residue number reindexed from 1)		R63 Y136 A138 Y193 F201 H204 N214 K222 W224 Q256 H292
Annotation score1
Binding affinityMOAD: Kd=0.53uM
PDBbind-CN: -logKd/Ki=6.28,Kd=0.53uM
BindingDB: IC50=<100nM,Kd=530nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y193 H204 E206 H292 A304
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6bgu, PDBe:6bgu, PDBj:6bgu
PDBsum6bgu
PubMed29537847
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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