Structure of PDB 6bgv Chain A Binding Site BS01

Receptor Information

>6bgv 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 ID

DQG

InChI

InChI=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-/m0/s1

InChIKey

AWPYWZMMJZGPOX-NRFANRHFSA-N

SMILES

Software	SMILES
CACTVS 3.385	OC(=O)c1ccnc2cc([nH]c12)[CH](OCCN3CCCCC3)c4ccccc4Cl
ACDLabs 12.01	c4ccc(Cl)c(C(c2cc1c(c(C(=O)O)ccn1)n2)OCCN3CCCCC3)c4
OpenEye OEToolkits 2.0.6	c1ccc(c(c1)[C@@H](c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCCCC4)Cl
OpenEye OEToolkits 2.0.6	c1ccc(c(c1)C(c2cc3c([nH]2)c(ccn3)C(=O)O)OCCN4CCCCC4)Cl
CACTVS 3.385	OC(=O)c1ccnc2cc([nH]c12)[C@@H](OCCN3CCCCC3)c4ccccc4Cl

Formula

C22 H24 Cl N3 O3

Name

2-{(S)-(2-chlorophenyl)[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid

PDB chain

6bgv 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	6bgv Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution	1.592 Å
Binding residue (original residue number in PDB)	Y409 D412 W470 Y472 F480 C481 H483 K501 W503 H571
Binding residue (residue number reindexed from 1)	Y136 D139 W191 Y193 F201 C202 H204 K222 W224 H292
Annotation score	1
Binding affinity	MOAD: Kd=0.18uM PDBbind-CN: -logKd/Ki=6.74,Kd=0.18uM BindingDB: Kd=60nM,IC50=590nM

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

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