Structure of PDB 2hvw Chain B Binding Site BS04

Receptor Information

>2hvw Chain B (length=146) Species: 1309 (Streptococcus mutans)

RLSWQDYFMANAELISKRSTCNRAYVGAVLVKNNRIIATGYNGGVADTDN
CDDVGHEMEDGHCIRTVHAEMNALIQCAKEGISANNTEIYVTHFPCINCT
KALLQAGVKKITYNTAYRIHPFAIELMTQKEVEYVQHDVPRVKLGE

Ligand information

• Ligand ID: DDN
• InChI: InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-8,12-13H,3-4H2,(H,10,14)(H2,15,16,17)/t5-,6+,7+,8+/m0/s1
• InChIKey: ILSIYJVILUIVPM-LXGUWJNJSA-N
• SMILES:
  CACTVS 3.341: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C[CH](O)NC2=O
  CACTVS 3.341: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C[C@@H](O)NC2=O
  ACDLabs 10.04: O=C1NC(O)C=CN1C2OC(C(O)C2)COP(=O)(O)O
  OpenEye OEToolkits 1.5.0: C1C(C(OC1N2C=CC(NC2=O)O)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O)(O)O)O
• Formula: C9 H15 N2 O8 P
• Name: 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE;
  ((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE
• DrugBank: DB04280
• ZINC: ZINC000005850864
• PDB chain: 2hvw Chain B Residue 1302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2hvw Crystal structures of Streptococcus mutans 2'-deoxycytidylate deaminase and its complex with substrate analog and allosteric regulator dCTP x Mg2+.
• Resolution: 1.67 Å
• Binding residue (original residue number in PDB): C24 R26 A27 V29 N45 H65 C66 T69 H71 E73 C99 Y120 R121
• Binding residue (residue number reindexed from 1): C21 R23 A24 V26 N42 H62 C63 T66 H68 E70 C96 Y117 R118
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 3.5.4.12: dCMP deaminase.

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:2hvw, PDBe:2hvw, PDBj:2hvw
• PDBsum: 2hvw
• PubMed: 18255096
• UniProt: Q8DSE5