Structure of PDB 6bgw Chain A Binding Site BS01

Receptor Information
>6bgw 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 IDDKS
InChIInChI=1S/C22H22ClF2N3O3/c23-16-4-2-1-3-14(16)20(31-12-11-28-9-6-22(24,25)7-10-28)18-13-17-19(27-18)15(21(29)30)5-8-26-17/h1-5,8,13,20,27H,6-7,9-12H2,(H,29,30)/t20-/m0/s1
InChIKeyQCUMGQXPGZQHID-FQEVSTJZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1ccnc2cc([nH]c12)[C@@H](OCCN3CCC(F)(F)CC3)c4ccccc4Cl
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCC(CC4)(F)F)Cl
OpenEye OEToolkits 2.0.6c1ccc(c(c1)[C@@H](c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCC(CC4)(F)F)Cl
ACDLabs 12.01c4ccc(Cl)c(C(c2cc1c(c(C(=O)O)ccn1)n2)OCCN3CCC(F)(CC3)F)c4
CACTVS 3.385OC(=O)c1ccnc2cc([nH]c12)[CH](OCCN3CCC(F)(F)CC3)c4ccccc4Cl
FormulaC22 H22 Cl F2 N3 O3
Name2-{(S)-(2-chlorophenyl)[2-(4,4-difluoropiperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6bgw 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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PDB6bgw Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution1.644 Å
Binding residue
(original residue number in PDB)		Y409 D412 W470 Y472 F480 C481 H483 N493 K501 W503 H571
Binding residue
(residue number reindexed from 1)		Y136 D139 W191 Y193 F201 C202 H204 N214 K222 W224 H292
Annotation score1
Binding affinityMOAD: Kd=0.21uM
PDBbind-CN: -logKd/Ki=6.68,Kd=0.21uM
BindingDB: IC50=4500nM,Kd=210nM
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:6bgw, PDBe:6bgw, PDBj:6bgw
PDBsum6bgw
PubMed29537847
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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