Structure of PDB 6bh1 Chain A Binding Site BS01

Receptor Information

>6bh1 Chain A (length=297) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTQAVREYTLQSFGEMADNFKSDYFNMP
VHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKI
LPEEEEYALSGWNLNNMPVLEQSVLKVPWLYVGMCFSSFCWHIEDHWSYS
INYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMN
PNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT

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

6bh1 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	6bh1 Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution	1.932 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)	Y128 D131 W179 Y181 F189 C190 H192 N202 K210 W212 H280
Annotation score	1
Binding affinity	MOAD: Kd=0.06uM PDBbind-CN: -logKd/Ki=7.22,Kd=0.06uM 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)	Y181 H192 E194 H280 A292
Enzyme Commision number	1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

PDB	RCSB:6bh1, PDBe:6bh1, PDBj:6bh1
PDBsum	6bh1
PubMed	29537847
UniProt	P29375\|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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