Structure of PDB 6dq5 Chain A Binding Site BS01

Receptor Information
>6dq5 Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTVREYTLQSFGEMADNFKSDYFNMPVHM
VPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPE
EEEYALSGWNLNNMPVLEQSVLAHINVKVPWLYVGMCFSSFCWHIEDHWS
YSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTI
MNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFC
Ligand information
Ligand IDH6G
InChIInChI=1S/C20H24N6O3/c1-2-18(27)26-11-5-10-25(12-13-26)17-14-16(22-9-7-19(28)29)23-20(24-17)15-6-3-4-8-21-15/h2-4,6,8,14H,1,5,7,9-13H2,(H,28,29)(H,22,23,24)
InChIKeyGQZPLTPYSQYTFB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C=CC(=O)N1CCCN(CC1)c2cc(nc(n2)c3ccccn3)NCCC(=O)O
ACDLabs 12.01C1CCN(CCN1C(=O)/C=C)c2cc(NCCC(=O)O)nc(n2)c3ccccn3
CACTVS 3.385OC(=O)CCNc1cc(nc(n1)c2ccccn2)N3CCCN(CC3)C(=O)C=C
FormulaC20 H24 N6 O3
NameN-[6-(4-acryloyl-1,4-diazepan-1-yl)-2-(pyridin-2-yl)pyrimidin-4-yl]-beta-alanine
ChEMBLCHEMBL4283844
DrugBank
ZINC
PDB chain6dq5 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6dq5 Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		R73 Y409 Y472 F480 C481 H483 E485 K501
Binding residue
(residue number reindexed from 1)		R62 Y125 Y183 F191 C192 H194 E196 K212
Annotation score1
Binding affinityMOAD: Kd=6.4uM
PDBbind-CN: -logKd/Ki=5.19,Kd=6.4uM
BindingDB: Kd=6000nM,IC50=71000nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y183 H194 E196 H282 A294
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dq5, PDBe:6dq5, PDBj:6dq5
PDBsum6dq5
PubMed30392349
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

[Back to BioLiP]