Structure of PDB 1q92 Chain A Binding Site BS02

Receptor Information

>1q92 Chain A (length=195) Species: 9606 (Homo sapiens)

GRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYG
RLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSP
IKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITG
AEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP

Ligand information

• Ligand ID: DRM
• InChI: InChI=1S/C10H15N2O6P/c13-9-4-5-12(10(14)11-9)7-2-1-3-8(7)18-6-19(15,16)17/h4-5,7-8H,1-3,6H2,(H,11,13,14)(H2,15,16,17)/t7-,8-/m1/s1
• InChIKey: KKXMDNJBVSYDQL-HTQZYQBOSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C[C@H]([C@@H](C1)OCP(=O)(O)O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=P(O)(O)COC2CCCC2N1C=CC(=O)NC1=O
  CACTVS 3.341: O[P](O)(=O)CO[C@@H]1CCC[C@H]1N2C=CC(=O)NC2=O
  OpenEye OEToolkits 1.5.0: C1CC(C(C1)OCP(=O)(O)O)N2C=CC(=O)NC2=O
  CACTVS 3.341: O[P](O)(=O)CO[CH]1CCC[CH]1N2C=CC(=O)NC2=O
• Formula: C10 H15 N2 O6 P
• Name: {[(1R,2S)-2-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)CYCLOPENTYL]OXY}METHYLPHOSPHONIC ACID;
  1-TRANS-(2-PHOSPHONOMETHOXYCYCLOPENTYL)URACIL;
  PMCP-U
• ZINC: ZINC000024790285
• PDB chain: 1q92 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1q92 Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): D43 F49 F75 W76 V77 F102 S131 I133 K165 R177
• Binding residue (residue number reindexed from 1): D11 F17 F43 W44 V45 F70 S99 I101 K133 R145
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D41 D43 D176
• Catalytic site (residue number reindexed from 1): D9 D11 D144
• 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:1q92, PDBe:1q92, PDBj:1q92
• PDBsum: 1q92
• PubMed: 15044615
• UniProt: Q9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)