Structure of PDB 4zuo Chain B Binding Site BS02

Receptor Information
>4zuo 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 IDXS6
InChIInChI=1S/C9H21N3O2/c10-6-4-8-11-7-3-1-2-5-9(13)12-14/h11,14H,1-8,10H2,(H,12,13)
InChIKeyBREASWSBOVLQOH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCCNCCCCCC(=O)NO
ACDLabs 12.01C(CCNCCCCCC(NO)=O)N
OpenEye OEToolkits 1.9.2C(CCC(=O)NO)CCNCCCN
FormulaC9 H21 N3 O2
Name6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
ChEMBLCHEMBL77840
DrugBank
ZINCZINC000013725116
PDB chain4zuo Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zuo Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase.
Resolution1.33 Å
Binding residue
(original residue number in PDB)		Y19 H158 H159 Y168 D195 H197 F225 I291 Y323
Binding residue
(residue number reindexed from 1)		Y19 H158 H159 Y168 D195 H197 F225 I291 Y323
Annotation score2
Binding affinityMOAD: ic50=0.39uM
PDBbind-CN: -logKd/Ki=6.41,IC50=0.39uM
BindingDB: IC50=390nM
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:4zuo, PDBe:4zuo, PDBj:4zuo
PDBsum4zuo
PubMed26200446
UniProtQ48935|APAH_MYCRA Acetylpolyamine amidohydrolase (Gene Name=aphA)

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