Structure of PDB 4p9c Chain I Binding Site BS03

Receptor Information

>4p9c Chain I (length=135) Species: 1137745 (Cyanophage S-TIM5)

MKPEIKEAYMKTAELFSQVSNCKRMKVGAIVVKNGSILAHGWNGTPSGFH
TNCCELEDGSTNPFVLHAEQNALVKMAKSSESIDGSELFCTHSPCPDCSK
MIAQAGVKKVYYRNEYRITDGIDVLQQLGVEVEKM

Ligand information

• Ligand ID: DU
• InChI: InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
• InChIKey: JSRLJPSBLDHEIO-SHYZEUOFSA-N
• SMILES:
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
• Formula: C9 H13 N2 O8 P
• Name: 2'-DEOXYURIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL211312
• DrugBank: DB03800
• ZINC: ZINC000004228260
• PDB chain: 4p9c Chain I Residue 203

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4p9c The First Crystal Structure of a dTTP-bound Deoxycytidylate Deaminase Validates and Details the Allosteric-Inhibitor Binding Site.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): R24 V27 N43 T61 H67 E69 Y116 R117
• Binding residue (residue number reindexed from 1): R24 V27 N43 T61 H67 E69 Y116 R117
• Annotation score: 3

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003824 catalytic activity
• GO:0004132 dCMP deaminase activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006220 pyrimidine nucleotide metabolic process

External links

• PDB: RCSB:4p9c, PDBe:4p9c, PDBj:4p9c
• PDBsum: 4p9c
• PubMed: 25404739
• UniProt: H6WFU3