Structure of PDB 6g22 Chain A Binding Site BS02

Receptor Information
>6g22 Chain A (length=193) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRL
RPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIK
MFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAE
PTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP
Ligand information
Ligand ID2O2
InChIInChI=1S/C18H20N2O11P2/c21-16-11(6-7-32(23,24)25)9-20(17(22)19-16)15-8-13-14(30-15)10-29-18(31-13,33(26,27)28)12-4-2-1-3-5-12/h1-7,9,13-15H,8,10H2,(H,19,21,22)(H2,23,24,25)(H2,26,27,28)/b7-6+/t13-,14-,15-,18-/m1/s1
InChIKeyAYSYVLQGVXZPIY-OAIWFRFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)[C@]2(OC[C@@H]3[C@H](O2)C[C@@H](O3)N4C=C(C(=O)NC4=O)/C=C/P(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)/C=C/C1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
ACDLabs 12.01O=P(O)(O)/C=C/C1=CN(C(=O)NC1=O)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4
OpenEye OEToolkits 1.7.6c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)C=CP(=O)(O)O)P(=O)(O)O
CACTVS 3.385O[P](O)(=O)C=CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O
FormulaC18 H20 N2 O11 P2
Name1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000263620255
PDB chain6g22 Chain A Residue 305 [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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PDB6g22 Structure-based optimization of bisphosphonate nucleoside inhibitors of human 5'(3')-deoxyribonucleotidases
Resolution1.85 Å
Binding residue
(original residue number in PDB)		D43 F49 F75 W76 V77 W96 S131 I133 K134 R163
Binding residue
(residue number reindexed from 1)		D9 F15 F41 W42 V43 W62 S97 I99 K100 R129
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.56,Ki=27.7nM
Enzymatic activity
Catalytic site (original residue number in PDB) D41 D43 D176
Catalytic site (residue number reindexed from 1) D7 D9 D142
Enzyme Commision number 3.1.3.-
Gene Ontology
Molecular Function
GO:0008253 5'-nucleotidase activity
Biological Process
GO:0009264 deoxyribonucleotide catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:6g22, PDBe:6g22, PDBj:6g22
PDBsum6g22
PubMed
UniProtQ9NPB1|NT5M_HUMAN 5'(3')-deoxyribonucleotidase, mitochondrial (Gene Name=NT5M)

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