Structure of PDB 5ivc Chain A Binding Site BS01

Receptor Information
>5ivc 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 ID6E7
InChIInChI=1S/C20H17N3O3/c24-19(23-9-6-14-4-2-1-3-5-14)15-7-10-21-17(12-15)18-13-16(20(25)26)8-11-22-18/h1-5,7-8,10-13H,6,9H2,(H,23,24)(H,25,26)
InChIKeyDSGOLESVOJUGOK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1ccc(cc1)CCNC(=O)c2ccnc(c2)c3cc(ccn3)C(=O)O
CACTVS 3.385OC(=O)c1ccnc(c1)c2cc(ccn2)C(=O)NCCc3ccccc3
ACDLabs 12.01c1(cc(ccn1)C(NCCc2ccccc2)=O)c3nccc(C(=O)O)c3
FormulaC20 H17 N3 O3
Name4'-[(2-phenylethyl)carbamoyl][2,2'-bipyridine]-4-carboxylic acid
ChEMBLCHEMBL2169917
DrugBank
ZINCZINC000095556198
PDB chain5ivc 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]
PDB5ivc Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
Resolution1.573 Å
Binding residue
(original residue number in PDB)		R73 Y409 A411 F480 H483 E485 K501 W503 H571
Binding residue
(residue number reindexed from 1)		R62 Y135 A137 F200 H203 E205 K221 W223 H291
Annotation score1
Binding affinityMOAD: Kd=1.2uM
PDBbind-CN: -logKd/Ki=5.92,Kd=1.2uM
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:5ivc, PDBe:5ivc, PDBj:5ivc
PDBsum5ivc
PubMed27427228
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

[Back to BioLiP]