Structure of PDB 5ivf Chain A Binding Site BS01

Receptor Information

>5ivf Chain A (length=308) Species: 9606 (Homo sapiens)

EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMRPREAFGFEQAVREYTLQSFGEMADNFK
SDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPV
KDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINKVPWLYVGMCFSSF
CWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQP
DLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNF
AEAVNFCT

Ligand information

• Ligand ID: 6EB
• InChI: InChI=1S/C15H14F3N5O2/c1-23-7-10(20-8-23)12-11-9(3-5-19-12)13(24)22-14(21-11)25-6-2-4-15(16,17)18/h3,5,7-8H,2,4,6H2,1H3,(H,21,22,24)
• InChIKey: GVIVKUKLHYWHES-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Cn1cnc(c1)c2nccc3c(O)nc(OCCCC(F)(F)F)nc23
  ACDLabs 12.01: c3(OCCCC(F)(F)F)nc(O)c2c(c(c1ncn(C)c1)ncc2)n3
  OpenEye OEToolkits 2.0.4: Cn1cc(nc1)c2c3c(ccn2)c(nc(n3)OCCCC(F)(F)F)O
• Formula: C15 H14 F3 N5 O2
• Name: 8-(1-methyl-1H-imidazol-4-yl)-2-(4,4,4-trifluorobutoxy)pyrido[3,4-d]pyrimidin-4-ol
• ChEMBL: CHEMBL3787534
• ZINC: ZINC000584904707
• PDB chain: 5ivf Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ivf Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds.
• Resolution: 1.683 Å
• Binding residue (original residue number in PDB): R73 Q75 Y409 A411 Y472 F480 H483 E485 K501 W503 H571
• Binding residue (residue number reindexed from 1): R62 Q64 Y135 A137 Y192 F200 H203 E205 K221 W223 H291
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.40,Kd>40uM
  BindingDB: IC50=<100nM

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:5ivf, PDBe:5ivf, PDBj:5ivf
• PDBsum: 5ivf
• PubMed: 27427228
• UniProt: P29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)