Structure of PDB 1z4l Chain A Binding Site BS03

Receptor Information

>1z4l Chain A (length=194) Species: 9606 (Homo sapiens)

RALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGR
LRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPI
KMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGA
EPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP

Ligand information

• Ligand ID: TMP
• InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
• InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
• SMILES:
  CACTVS 3.341: CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
  OpenEye OEToolkits 1.5.0: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
  CACTVS 3.341: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
  ACDLabs 10.04: O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)COP(=O)(O)O
• Formula: C10 H15 N2 O8 P
• Name: THYMIDINE-5'-PHOSPHATE
• ChEMBL: CHEMBL394429
• DrugBank: DB01643
• ZINC: ZINC000001678872
• PDB chain: 1z4l Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1z4l Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): N41 D43 F49 W76 V77 W96 S131 I133 K165
• Binding residue (residue number reindexed from 1): N8 D10 F16 W43 V44 W63 S98 I100 K132
• 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:1z4l, PDBe:1z4l, PDBj:1z4l
• PDBsum: 1z4l
• PubMed: 16004879
• UniProt: Q9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)