Structure of PDB 7d8l Chain A Binding Site BS01

Receptor Information
>7d8l Chain A (length=174) Species: 158879 (Staphylococcus aureus subsp. aureus N315) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIPKEGENIKIQSYKHDGKIHRVWSETTILKGTDHVVIGGNDHTLVTESD
GRTWITREPAIVYFHSEYWFNVICMFREDGIYYYCNLSSPFVCDEEALKY
IDYDLDIKVYPNGKYHLLDEDEYEQHMNQMNYPHDIDIILRRNVDILQQW
IEQKKGPFAPDFIKVWKERYKKIR
Ligand information
Ligand IDGSP
InChIInChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXOFLBQFBSOEHOG-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
ACDLabs 10.04S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O13 P3 S
Name5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
ChEMBLCHEMBL1204628
DrugBankDB01864
ZINCZINC000008217391
PDB chain7d8l 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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PDB7d8l The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		H25 R26 N45 W58 T60 M79 Y88
Binding residue
(residue number reindexed from 1)		H21 R22 N41 W54 T56 M75 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:7d8l, PDBe:7d8l, PDBj:7d8l
PDBsum7d8l
PubMed33955674
UniProtQ7A4T2|NTDP_STAAN Nucleoside triphosphate/diphosphate phosphatase (Gene Name=SA1684)

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