Structure of PDB 5xsn Chain B Binding Site BS03

Receptor Information
>5xsn Chain B (length=333) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VRARVISHALKDILAEGDKVIIMGHKRPDLDAIGAAIGVSRFAMMNNLEA
YIVLNETDIDPTLRRVMNEIDKKPELRERFITSDDAWDMMTSKTTVVIVD
THKPELVLDENVLNKANRKVVIDHHRRGESFISNPLLIYMEPYASSTAEL
VTELLEYQPTEQRLTRLESTVMYAGIIVDTRNFTLRTGSRTFDAASYLRA
HGADTILTQHFLKDDVDTYINRSELIRTVKVEDNGIAIAHGSDDKIYHPV
TVAQAADELLSLEGIEASYVVARREDNLIGISARSLGSVNVQLTMEALGG
GGHLTNAATQLKGVTVEEAIAQLQQAITEQLSR
Ligand information
Ligand ID2BA
InChIInChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
InChIKeyPDXMFTWFFKBFIN-XPWFQUROSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=O)(OC5C(COP(=O)(O4)O)OC(C5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=O)O[CH]5[CH](O)[CH](O[CH]5CO[P](O)(=O)O[CH]4[CH]3O)n6cnc7c(N)ncnc67
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@](=O)(O[C@@H]5[C@@H](CO[P@](=O)(O4)O)O[C@H]([C@@H]5O)n6cnc7c6ncnc7N)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]5[C@@H](O)[C@@H](O[C@@H]5CO[P@](O)(=O)O[C@H]4[C@H]3O)n6cnc7c(N)ncnc67
ACDLabs 10.04O=P5(OCC7OC(n1c2ncnc(N)c2nc1)C(O)C7OP(=O)(O)OCC6OC(n3c4ncnc(N)c4nc3)C(O)C6O5)O
FormulaC20 H24 N10 O12 P2
Name(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide;
bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate
ChEMBLCHEMBL1229884
DrugBank
ZINCZINC000058661162
PDB chain5xsn Chain B Residue 703 [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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PDB5xsn Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase
Resolution2.501 Å
Binding residue
(original residue number in PDB)
V568 A571 S600 R602 G618 G619 N624 A625 A626 Q628
Binding residue
(residue number reindexed from 1)
V250 A253 S282 R284 G300 G301 N306 A307 A308 Q310
Annotation score5
Enzymatic activity
Enzyme Commision number 3.1.4.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding

View graph for
Molecular Function
External links
PDB RCSB:5xsn, PDBe:5xsn, PDBj:5xsn
PDBsum5xsn
PubMed29203646
UniProtA0A0U1MUE2

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