Structure of PDB 6bh0 Chain A Binding Site BS01

Receptor Information
>6bh0 Chain A (length=291) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTGFEQAVREYTLQSFGEMADNFKSDYF
NMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKILP
EEEEYALSGWNLNNMPVLEKVPWLYVGMCFSSFCWHIEDHWSYSINYLHW
GEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVLME
HGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDDO1
InChIInChI=1S/C22H24ClN3O3/c23-17-7-3-2-6-15(17)21(29-13-12-26-10-4-1-5-11-26)19-14-18-20(25-19)16(22(27)28)8-9-24-18/h2-3,6-9,14,21,25H,1,4-5,10-13H2,(H,27,28)/t21-/m1/s1
InChIKeyAWPYWZMMJZGPOX-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1ccnc2cc([nH]c12)[CH](OCCN3CCCCC3)c4ccccc4Cl
OpenEye OEToolkits 2.0.6c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCCCC4)Cl
CACTVS 3.385OC(=O)c1ccnc2cc([nH]c12)[C@H](OCCN3CCCCC3)c4ccccc4Cl
OpenEye OEToolkits 2.0.6c1ccc(c(c1)[C@H](c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCCCC4)Cl
ACDLabs 12.01c1cc(c(cc1)Cl)C(c3cc2c(c(C(=O)O)ccn2)n3)OCCN4CCCCC4
FormulaC22 H24 Cl N3 O3
Name2-{(R)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
ChEMBLCHEMBL4062359
DrugBank
ZINC
PDB chain6bh0 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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PDB6bh0 Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution1.985 Å
Binding residue
(original residue number in PDB)		R73 Y409 A411 W470 Y472 S479 F480 H483 K501 W503 H571
Binding residue
(residue number reindexed from 1)		R63 Y131 A133 W173 Y175 S182 F183 H186 K204 W206 H274
Annotation score1
Binding affinityMOAD: Kd=0.22uM
PDBbind-CN: -logKd/Ki=6.66,Kd=0.22uM
BindingDB: IC50=670nM,Kd=180nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y175 H186 E188 H274 A286
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6bh0, PDBe:6bh0, PDBj:6bh0
PDBsum6bh0
PubMed29537847
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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