Structure of PDB 7d8q Chain A Binding Site BS01

Receptor Information
>7d8q Chain A (length=174) Species: 273036 (Staphylococcus aureus RF122) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIPKEGENIKIQSYKHDGKIHRVWSETTILKGTDHVVIGGNDHTLVTESD
GRTWITREPAIVYFHSEYWFNVICMFREDGIYYYCNLSSPFVCDEEALKY
IDYDLDIKVYPNGKYHLLDEDEYEQHMNQMNYPHDIDIILRRNVDILQQW
IEQKKGPFAPDFIKVWKERYKKIR
Ligand information
Ligand IDGZF
InChIInChI=1S/C10H15N5O10P2S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(24-9)1-23-26(19,20)25-27(21,22)28/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H2,21,22,28)(H3,11,13,14,18)/t3-,5+,6+,9+/m1/s1
InChIKeyQJXJXBXFIOTYHB-KHLHZJAASA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1nc(O)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O)c2n1
CACTVS 3.385Nc1nc(O)c2ncn([C@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=S)[C@H](O)[C@@H]3O)c2n1
OpenEye OEToolkits 2.0.7c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=S)(O)O)O)O)nc(nc2O)N
OpenEye OEToolkits 2.0.7c1nc2c(n1[C@@H]3[C@H]([C@H]([C@H](O3)COP(=O)(O)OP(=S)(O)O)O)O)nc(nc2O)N
FormulaC10 H15 N5 O10 P2 S
Name[(2R,3R,4S,5S)-5-(2-azanyl-6-oxidanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl bis(oxidanyl)phosphinothioyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain7d8q Chain A Residue 201 [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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PDB7d8q The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus.
Resolution1.5 Å
Binding residue
(original residue number in PDB)
H25 R26 E52 W58 Y88
Binding residue
(residue number reindexed from 1)
H21 R22 E48 W54 Y84
Annotation score3
Enzymatic activity
Enzyme Commision number 3.6.1.15: nucleoside-triphosphate phosphatase.
3.6.1.6: nucleoside diphosphate phosphatase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016787 hydrolase activity
GO:0017110 nucleoside diphosphate phosphatase activity
GO:0017111 ribonucleoside triphosphate phosphatase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7d8q, PDBe:7d8q, PDBj:7d8q
PDBsum7d8q
PubMed33955674
UniProtQ7A4T2|NTDP_STAAN Nucleoside triphosphate/diphosphate phosphatase (Gene Name=SA1684)

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