Structure of PDB 6dqe Chain A Binding Site BS01

Receptor Information
>6dqe Chain A (length=294) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMREYTLQSFGEMADNFKSDYFNMPVHMV
PTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEE
EEYALSGWNLNNMPVLEQSVLAKVPWLYVGMCFSSFCWHIEDHWSYSINY
LHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNV
LMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDH6A
InChIInChI=1S/C29H30N4O3/c34-29(35)24-14-15-30-26(20-24)33-27(22-10-4-1-5-11-22)25(21-31-33)28(23-12-6-2-7-13-23)36-19-18-32-16-8-3-9-17-32/h1-2,4-7,10-15,20-21,28H,3,8-9,16-19H2,(H,34,35)/t28-/m1/s1
InChIKeyHAJRSCRWEDXEKU-MUUNZHRXSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)c1ccnc(c1)n2ncc([CH](OCCN3CCCCC3)c4ccccc4)c2c5ccccc5
CACTVS 3.385OC(=O)c1ccnc(c1)n2ncc([C@H](OCCN3CCCCC3)c4ccccc4)c2c5ccccc5
ACDLabs 12.01C(=O)(O)c1ccnc(c1)n3c(c2ccccc2)c(cn3)C(c4ccccc4)OCCN5CCCCC5
OpenEye OEToolkits 2.0.6c1ccc(cc1)c2c(cnn2c3cc(ccn3)C(=O)O)C(c4ccccc4)OCCN5CCCCC5
OpenEye OEToolkits 2.0.6c1ccc(cc1)c2c(cnn2c3cc(ccn3)C(=O)O)[C@@H](c4ccccc4)OCCN5CCCCC5
FormulaC29 H30 N4 O3
Name2-(5-phenyl-4-{(R)-phenyl[2-(piperidin-1-yl)ethoxy]methyl}-1H-pyrazol-1-yl)pyridine-4-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6dqe 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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PDB6dqe Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution1.689 Å
Binding residue
(original residue number in PDB)		Y409 D412 W470 Y472 F480 H483 E485 K501 W503 L536 H571
Binding residue
(residue number reindexed from 1)		Y124 D127 W176 Y178 F186 H189 E191 K207 W209 L242 H277
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y178 H189 E191 H277 A289
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dqe, PDBe:6dqe, PDBj:6dqe
PDBsum6dqe
PubMed
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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