Structure of PDB 5ef8 Chain A Binding Site BS02

Receptor Information
>5ef8 Chain A (length=357) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPA
RLATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTC
ALLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAAL
TARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGA
FFPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIAR
EFAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIIL
EGGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHA
PFWSSLR
Ligand information
Ligand IDLBH
InChIInChI=1S/C21H23N3O2/c1-15-18(19-4-2-3-5-20(19)23-15)12-13-22-14-17-8-6-16(7-9-17)10-11-21(25)24-26/h2-11,22-23,26H,12-14H2,1H3,(H,24,25)/b11-10+
InChIKeyFPOHNWQLNRZRFC-ZHACJKMWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1[nH]c2ccccc2c1CCNCc3ccc(/C=C/C(=O)NO)cc3
OpenEye OEToolkits 2.0.4Cc1c(c2ccccc2[nH]1)CCNCc3ccc(cc3)/C=C/C(=O)NO
CACTVS 3.385Cc1[nH]c2ccccc2c1CCNCc3ccc(C=CC(=O)NO)cc3
OpenEye OEToolkits 2.0.4Cc1c(c2ccccc2[nH]1)CCNCc3ccc(cc3)C=CC(=O)NO
FormulaC21 H23 N3 O2
NamePanobinostat
ChEMBLCHEMBL483254
DrugBankDB06603
ZINCZINC000022010649
PDB chain5ef8 Chain A Residue 2004 [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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PDB5ef8 Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		D460 H463 P464 S531 H573 H574 F583 D612 H614 F643 Y745
Binding residue
(residue number reindexed from 1)		D19 H22 P23 S90 H132 H133 F142 D171 H173 F202 Y304
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.85,Ki=1.4nM
Enzymatic activity
Enzyme Commision number 3.5.1.98: histone deacetylase.
External links