Structure of PDB 1z4i Chain A Binding Site BS02

Receptor Information

>1z4i Chain A (length=194) Species: 9606 (Homo sapiens)

RALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGR
LRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPI
KMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGA
EPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP

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: 1z4i Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1z4i Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase
• Resolution: 1.98 Å
• Binding residue (original residue number in PDB): N41 M42 D43 W76 S78 W96 T130 S131 I133
• Binding residue (residue number reindexed from 1): N8 M9 D10 W43 S45 W63 T97 S98 I100
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): N41 D43 D176
• Catalytic site (residue number reindexed from 1): N8 D10 D143
• Enzyme Commision number: 3.1.3.-

Gene Ontology

Molecular Function

• GO:0008253 5'-nucleotidase activity

Biological Process

• GO:0009264 deoxyribonucleotide catabolic process

External links

• PDB: RCSB:1z4i, PDBe:1z4i, PDBj:1z4i
• PDBsum: 1z4i
• PubMed: 16004879
• UniProt: Q9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)