Structure of PDB 6pia Chain A Binding Site BS03

Receptor Information

>6pia Chain A (length=345) Species: 1658765 (Marinobacter subterrani)

GSMKTVFSPLHSRRHVKTELDGGLLIEPHEKPSRAETILARVKDQALGEI
LEPEEFGLGPVKRVHTADYVSFLETCWDEWVAAGKRGEAIPTFWVGRGMR
ARLPKDIDGRLGYYSLGADTSISDGTWEAARASANVALTAQKLVAEGERA
AFALCRPPGHHAHADVFGGYCFFNNAAIAAQAFRDQGYGKVAVLDVDFHH
GNGTQAIFYDRSDVLTISLHGDPDLVFPHFLGFEDETGEGDGEAYNLNIV
FPPDTPFSIWSQGLEKACERIRTFAPDALVVALGVDTFEEDPISFFKLTS
GDYLKLGKRLEQLGLPTVFTMEGGYDVDAIGVNAVNVMQGFEGKS

Ligand information

• Ligand ID: XS6
• InChI: InChI=1S/C9H21N3O2/c10-6-4-8-11-7-3-1-2-5-9(13)12-14/h11,14H,1-8,10H2,(H,12,13)
• InChIKey: BREASWSBOVLQOH-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: NCCCNCCCCCC(=O)NO
  ACDLabs 12.01: C(CCNCCCCCC(NO)=O)N
  OpenEye OEToolkits 1.9.2: C(CCC(=O)NO)CCNCCCN
• Formula: C9 H21 N3 O2
• Name: 6-[(3-aminopropyl)amino]-N-hydroxyhexanamide
• ChEMBL: CHEMBL77840
• ZINC: ZINC000013725116
• PDB chain: 6pia Chain A Residue 407

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6pia Structure and Function of the Acetylpolyamine Amidohydrolase from the Deep Earth HalophileMarinobacter subterrani.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): E17 L18 D19 D117 H158 H159 G167 Y168 D195 H197 F225 Y323
• Binding residue (residue number reindexed from 1): E19 L20 D21 D119 H160 H161 G169 Y170 D197 H199 F227 Y325
• Annotation score: 1
• Binding affinity: MOAD: ic50=550uM
  PDBbind-CN: -logKd/Ki=4.96,Kd=11.0uM

Gene Ontology

Molecular Function

• GO:0004407 histone deacetylase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006338 chromatin remodeling

External links

• PDB: RCSB:6pia, PDBe:6pia, PDBj:6pia
• PDBsum: 6pia
• PubMed: 31436969
• UniProt: A0A0J7JFD7