Structure of PDB 1z4m Chain A Binding Site BS02

Receptor Information

>1z4m Chain A (length=194) Species: 9606 (Homo sapiens)

RALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGR
LRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPI
KMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGA
EPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP

Ligand information

• Ligand ID: U5P
• InChI: InChI=1S/C9H13N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: DJJCXFVJDGTHFX-XVFCMESISA-N
• SMILES:
  ACDLabs 10.04: O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=O)(O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H13 N2 O9 P
• Name: URIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL214393
• DrugBank: DB03685
• ZINC: ZINC000002123545
• PDB chain: 1z4m Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1z4m Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): N41 D43 F49 W76 S78 W96 T130 S131 I133
• Binding residue (residue number reindexed from 1): N8 D10 F16 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:1z4m, PDBe:1z4m, PDBj:1z4m
• PDBsum: 1z4m
• PubMed: 16004879
• UniProt: Q9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)