Structure of PDB 6bgx Chain A Binding Site BS01

Receptor Information

>6bgx Chain A (length=308) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMRPREAFGFEQAVREYTLQSFGEMADNFK
SDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPV
KDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSSF
CWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQP
DLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNF
AEAVNFCT

Ligand information

Ligand ID

DKV

InChI

InChI=1S/C22H21ClF2N2O3/c23-16-4-2-1-3-14(16)20(30-12-13-5-8-22(24,25)9-6-13)18-11-17-19(27-18)15(21(28)29)7-10-26-17/h1-4,7,10-11,13,20,27H,5-6,8-9,12H2,(H,28,29)/t20-/m0/s1

InChIKey

OZTBUBVWGCXOMR-FQEVSTJZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.6	c1ccc(c(c1)[C@@H](c2cc3c([nH]2)c(ccn3)C(=O)O)OCC4CCC(CC4)(F)F)Cl
OpenEye OEToolkits 2.0.6	c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCC4CCC(CC4)(F)F)Cl
CACTVS 3.385	OC(=O)c1ccnc2cc([nH]c12)[CH](OCC3CCC(F)(F)CC3)c4ccccc4Cl
CACTVS 3.385	OC(=O)c1ccnc2cc([nH]c12)[C@@H](OCC3CCC(F)(F)CC3)c4ccccc4Cl
ACDLabs 12.01	c2(nc1c(C(=O)O)ccnc1c2)C(c3ccccc3Cl)OCC4CCC(F)(CC4)F

Formula

C22 H21 Cl F2 N2 O3

Name

2-{(S)-(2-chlorophenyl)[(4,4-difluorocyclohexyl)methoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid

ChEMBL

DrugBank

ZINC

PDB chain

6bgx Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6bgx Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution	1.882 Å
Binding residue (original residue number in PDB)	Y409 Y472 F480 C481 H483 D486 K501 W503 H571
Binding residue (residue number reindexed from 1)	Y135 Y192 F200 C201 H203 D206 K221 W223 H291
Annotation score	1
Binding affinity	MOAD: Kd=0.47uM PDBbind-CN: -logKd/Ki=6.33,Kd=0.47uM BindingDB: Kd=470nM,IC50=22000nM

Enzymatic activity

Catalytic site (original residue number in PDB)	Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1)	Y192 H203 E205 H291 A303
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

PDB	RCSB:6bgx, PDBe:6bgx, PDBj:6bgx
PDBsum	6bgx
PubMed	29537847
UniProt	P29375\|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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