Structure of PDB 4zup Chain B Binding Site BS02

Receptor Information
>4zup Chain B (length=341) Species: 40837 (Mycoplana ramosa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVIFSEDHKLRNAKTELYGGELVPPFEAPFRAEWILAAVKEAGFDDVVA
PARHGLETVLKVHDAGYLNFLETAWDRWKAAGYKGEAIATSFPVRRTSPR
IPTDIEGQIGYYCNAAETAISPGTWEAALSSMASAIDGADLIAAGHKAAF
SLCRPPGHHAGIDMFGGYCFINNAAVAAQRLLDKGAKKIAILDVDFHHGN
GTQDIFYERGDVFFASLHGDPAEAFPHFLGYAEETGKGAGAGTTANYPMG
RGTPYSVWGEALTDSLKRIAAFGAEAIVVSLGVDTFEQDPISFFKLTSPD
YITMGRTIAASGVPLLVVMEGGYGVPEIGLNVANVLKGVAG
Ligand information
Ligand ID5XA
InChIInChI=1S/C5H12N2O2/c6-4-2-1-3-5(8)7-9/h9H,1-4,6H2,(H,7,8)
InChIKeyYEOWNCJWBHIJNK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C(CCN)CC(=O)NO
CACTVS 3.385NCCCCC(=O)NO
ACDLabs 12.01ONC(=O)CCCCN
FormulaC5 H12 N2 O2
Name5-amino-N-hydroxypentanamide
ChEMBL
DrugBank
ZINC
PDB chain4zup Chain B Residue 405 [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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PDB4zup Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase.
Resolution1.421 Å
Binding residue
(original residue number in PDB)		E117 H158 H159 Y168 D195 H197 F225 Y323
Binding residue
(residue number reindexed from 1)		E117 H158 H159 Y168 D195 H197 F225 Y323
Annotation score1
Binding affinityMOAD: ic50=0.17uM
PDBbind-CN: -logKd/Ki=6.77,IC50=0.17uM
Enzymatic activity
Enzyme Commision number 3.5.1.-
3.5.1.48: acetylspermidine deacetylase.
3.5.1.62: acetylputrescine deacetylase.
Gene Ontology
Molecular Function
GO:0004407 histone deacetylase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047609 acetylputrescine deacetylase activity
GO:0047611 acetylspermidine deacetylase activity
Biological Process
GO:0006338 chromatin remodeling

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4zup, PDBe:4zup, PDBj:4zup
PDBsum4zup
PubMed26200446
UniProtQ48935|APAH_MYCRA Acetylpolyamine amidohydrolase (Gene Name=aphA)

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