Structure of PDB 4zun Chain B Binding Site BS03

Receptor Information
>4zun 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 IDSS9
InChIInChI=1S/C8H20N2S/c9-5-4-7-10-6-2-1-3-8-11/h10-11H,1-9H2
InChIKeyUEAAWEWNMXIYCA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NCCCNCCCCCS
ACDLabs 12.01C(N)CCNCCCCCS
OpenEye OEToolkits 1.9.2C(CCNCCCN)CCS
FormulaC8 H20 N2 S
Name5-[(3-aminopropyl)amino]pentane-1-thiol
ChEMBLCHEMBL3040253
DrugBank
ZINCZINC000096282269
PDB chain4zun 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4zun Design, Synthesis, and Evaluation of Polyamine Deacetylase Inhibitors, and High-Resolution Crystal Structures of Their Complexes with Acetylpolyamine Amidohydrolase.
Resolution1.4 Å
Binding residue
(original residue number in PDB)		H159 Y168 D195 F225 Y323
Binding residue
(residue number reindexed from 1)		H159 Y168 D195 F225 Y323
Annotation score3
Binding affinityMOAD: ic50=26uM
PDBbind-CN: -logKd/Ki=4.59,IC50=26uM
BindingDB: IC50=26000nM
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:4zun, PDBe:4zun, PDBj:4zun
PDBsum4zun
PubMed26200446
UniProtQ48935|APAH_MYCRA Acetylpolyamine amidohydrolase (Gene Name=aphA)

[Back to BioLiP]