Structure of PDB 2yfd Chain A Binding Site BS02

Receptor Information

>2yfd Chain A (length=138) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

PPTNAERLHEFHRAIGATPERPTPPPPELLRLRQTLLDEESAEVRAEIDH
LLARQAAGEALSAGDLAPLAHELADLLYVTYGALDQLGIDADAVFAEVHR
ANLSKASGPRRADGKQLKPEGWRPADVRGVIERLQHAP

Ligand information

• Ligand ID: UMP
• 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:
  ACDLabs 12.01: O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
  CACTVS 3.370: O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
  CACTVS 3.370: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.7.6: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
• Formula: C9 H13 N2 O8 P
• Name: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
  DUMP
• ChEMBL: CHEMBL211312
• DrugBank: DB03800
• ZINC: ZINC000004228260
• PDB chain: 2yfd Chain A Residue 1147

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2yfd Structural and Functional Insights Into Dr2231 Protein, the Mazg-Like Nucleoside Triphosphate Pyrophosphohydrolase from Deinococcus Radiodurans.
• Resolution: 1.767 Å
• Binding residue (original residue number in PDB): N109 K112 K122 Q123 K125
• Binding residue (residue number reindexed from 1): N102 K105 K115 Q116 K118
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.6.1.19: Transferred entry: 3.6.1.9.

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding
• GO:0047429 nucleoside triphosphate diphosphatase activity

External links

• PDB: RCSB:2yfd, PDBe:2yfd, PDBj:2yfd
• PDBsum: 2yfd
• PubMed: 21733847
• UniProt: Q9RS96