Structure of PDB 1wog Chain C Binding Site BS03

Receptor Information

>1wog Chain C (length=303) Species: 1299 (Deinococcus radiodurans)

GPAHLPYGGIPTFARAPLVQPDGDWQADVAALGVPFDIALGFRPGARFAP
RALREASLRSVPPFTGLDGKTRLQGVTFADAGDVILPSLEPQLAHDRITE
AARQVRGRCRVPVFLGGDHSVSYPLLRAFADVPDLHVVQLDAHLDFTDTR
NDTKWSNSSPFRRACEALPNLVHITTVGLRGLRFDPEAVAAARARGHTII
PMDDVTADLAGVLAQLPRGQNVYFSVDVDGFDPAVIPGTSSPEPDGLTYA
QGMKILAAAAANNTVVGLDLVELAPNLDPTGRSELLMARLVMETLCEVFD
HVL

Ligand information

• Ligand ID: 16D
• InChI: InChI=1S/C6H16N2/c7-5-3-1-2-4-6-8/h1-8H2
• InChIKey: NAQMVNRVTILPCV-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C(CCCN)CCN
  ACDLabs 10.04
  CACTVS 3.341: NCCCCCCN
• Formula: C6 H16 N2
• Name: HEXANE-1,6-DIAMINE;
  1,6-DIAMINOHEXANE
• ChEMBL: CHEMBL303004
• DrugBank: DB03260
• ZINC: ZINC000001543408
• PDB chain: 1wog Chain C Residue 1403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1wog Crystal structure of agmatinase reveals structural conservation and inhibition mechanism of the ureohydrolase superfamily
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H145 D147 N159 S160
• Binding residue (residue number reindexed from 1): H143 D145 N157 S158
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): H121 D143 H145 D147 N159 D229 D231 E274
• Catalytic site (residue number reindexed from 1): H119 D141 H143 D145 N157 D227 D229 E272
• Enzyme Commision number: 3.5.3.11: agmatinase.

Gene Ontology

Molecular Function

• GO:0008783 agmatinase activity
• GO:0016787 hydrolase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0046872 metal ion binding

Biological Process

• GO:0033389 putrescine biosynthetic process from arginine, using agmatinase

External links

• PDB: RCSB:1wog, PDBe:1wog, PDBj:1wog
• PDBsum: 1wog
• PubMed: 15355972
• UniProt: Q9RZ04