Structure of PDB 5efb Chain D Binding Site BS02

Receptor Information

>5efb Chain D (length=355) Species: 7955 (Danio rerio)

PITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPA
RLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTC
ALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAAL
TARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGA
FFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAR
EFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIIL
EGGYNLTSISESMSMCTSMLLGDSPPSLLTPLKTSATVSINNVLRAHAPF
WSSLR

Ligand information

• Ligand ID: 5OK
• InChI: InChI=1S/C17H14N2O4S/c20-17(18-21)12-5-4-7-14-8-6-9-15(13-14)19-24(22,23)16-10-2-1-3-11-16/h1-3,5-6,8-13,19,21H,(H,18,20)/b12-5+
• InChIKey: QRPSQQUYPMFERG-LFYBBSHMSA-N
• SMILES:
  CACTVS 3.385: ONC(=O)C=CC#Cc1cccc(N[S](=O)(=O)c2ccccc2)c1
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)S(=O)(=O)Nc2cccc(c2)C#C/C=C/C(=O)NO
  CACTVS 3.385: ONC(=O)/C=C/C#Cc1cccc(N[S](=O)(=O)c2ccccc2)c1
  OpenEye OEToolkits 2.0.4: c1ccc(cc1)S(=O)(=O)Nc2cccc(c2)C#CC=CC(=O)NO
• Formula: C17 H14 N2 O4 S
• Name: Oxamflatin
• ChEMBL: CHEMBL98245
• ZINC: ZINC000003826235
• PDB chain: 5efb Chain D Residue 2004

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5efb Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
• Resolution: 2.543 Å
• Binding residue (original residue number in PDB): H463 S531 H573 H574 F583 D612 H614 F643 L712 Y745
• Binding residue (residue number reindexed from 1): H22 S90 H132 H133 F142 D171 H173 F202 L271 Y304
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=8.37,Ki=4.3nM

Enzymatic activity

• Enzyme Commision number: 3.5.1.98: histone deacetylase.

External links

• PDB: RCSB:5efb, PDBe:5efb, PDBj:5efb
• PDBsum: 5efb
• PubMed: 27454933
• UniProt: F8W4B7