Structure of PDB 1z4q Chain A Binding Site BS03

Receptor Information
>1z4q Chain A (length=194) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RALRVLVNMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGR
LRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPI
KMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGA
EPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP
Ligand information
Ligand IDD4M
InChIInChI=1S/C10H13N2O7P/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(19-8)5-18-20(15,16)17/h2-4,7-8H,5H2,1H3,(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1
InChIKeyXLPGURCDSRIXFL-JGVFFNPUSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1NC(=O)N(C=C1C)C2OC(C=C2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2C=CC(O2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C=C[C@H](O2)COP(=O)(O)O
CACTVS 3.341CC1=CN([CH]2O[CH](CO[P](O)(O)=O)C=C2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)C=C2)C(=O)NC1=O
FormulaC10 H13 N2 O7 P
Name[(5R)-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-2,5-DIHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE;
2',3'-DIDEOXY-2',3-DIDEHYDROTHYMIDINE 5'-MONOPHOSPHATE;
2',3'-DEHYDRO-2',3'-DEOXY-THYMIDINE 5'-MONOPHOSPHATE
ChEMBLCHEMBL403328
DrugBankDB04672
ZINCZINC000006521243
PDB chain1z4q Chain A Residue 1489 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1z4q Structural basis for substrate specificity of the human mitochondrial deoxyribonucleotidase
Resolution2.05 Å
Binding residue
(original residue number in PDB)		N41 D43 F49 F75 W76 V77 W96 F102 S131 I133 K165
Binding residue
(residue number reindexed from 1)		N8 D10 F16 F42 W43 V44 W63 F69 S98 I100 K132
Annotation score1
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1z4q, PDBe:1z4q, PDBj:1z4q
PDBsum1z4q
PubMed16004879
UniProtQ9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

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