Structure of PDB 5myd Chain C Binding Site BS01

Receptor Information

>5myd Chain C (length=164) Species: 1739434 (Staphylococcus sp. HMSC068C09)

MTNTLTTDQLQELLQIQKEFDDRIPTLNLGDSKIAYVVEFFEWFNTLETF
KNWKKKPGKPLDVQLDELADILAFGLSIANQQGFEEYDRDLFFESFDEEY
FLDFPYLRNQDMIYDMMSEFYDDDLTSIRRLVIVFKIAEQLYTIDQLIDA
YKKKMKRNHERQDG

Ligand information

• Ligand ID: DUP
• InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
• InChIKey: XZLLMTSKYYYJLH-SHYZEUOFSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O)(N[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
• Formula: C9 H16 N3 O13 P3
• Name: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
• ChEMBL: CHEMBL1232397
• DrugBank: DB01965
• PDB chain: 5myd Chain C Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5myd Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Q17 F20 D21 D70 F74 K154 N158
• Binding residue (residue number reindexed from 1): Q17 F20 D21 D70 F74 K154 N158
• Annotation score: 3
• Binding affinity: MOAD: ic50=13.9uM

Enzymatic activity

• Enzyme Commision number: 3.6.1.23: dUTP diphosphatase.

Gene Ontology

Molecular Function

• GO:0004170 dUTP diphosphatase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:5myd, PDBe:5myd, PDBj:5myd
• PDBsum: 5myd
• PubMed: 28892519
• UniProt: A0A2D0TC86