Structure of PDB 1q91 Chain A Binding Site BS03

Receptor Information
>1q91 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]
RALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGR
LRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPI
KMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGA
EPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP
Ligand information
Ligand IDDPB
InChIInChI=1S/C17H19N2O8P/c1-10-8-19(16(21)18-15(10)20)14-7-12-13(26-14)9-25-17(27-12,28(22,23)24)11-5-3-2-4-6-11/h2-6,8,12-14H,7,9H2,1H3,(H,18,20,21)(H2,22,23,24)/t12-,13-,14-,17-/m0/s1
InChIKeyWTZFKHNHHRPQOU-WSMBLCCSSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1C(=CN(C(=O)N1)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4)C
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccccc4)P(=O)(O)O
CACTVS 3.341CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@@H]2C[C@@H]3O[C@@](OC[C@@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]3[C@@H](O2)CO[C@](O3)(c4ccccc4)P(=O)(O)O
FormulaC17 H19 N2 O8 P
Name(S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHONO)BENZYLIDENE-B-D-THREO-PENTOFURANOSYL]THYMINE;
DPB-T
ChEMBL
DrugBankDB02217
ZINCZINC000012501733
PDB chain1q91 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1q91 Crystal structures of the mitochondrial deoxyribonucleotidase in complex with two specific inhibitors
Resolution1.6 Å
Binding residue
(original residue number in PDB)		F49 F75 W76 V77 W96 S131 I133 K134 R163
Binding residue
(residue number reindexed from 1)		F16 F42 W43 V44 W63 S98 I100 K101 R130
Annotation score1
Binding affinityMOAD: Ki=70uM
PDBbind-CN: -logKd/Ki=4.15,Ki=70uM
Enzymatic activity
Catalytic site (original residue number in PDB) D41 D43 D176
Catalytic site (residue number reindexed from 1) D8 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:1q91, PDBe:1q91, PDBj:1q91
PDBsum1q91
PubMed15044615
UniProtQ9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

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