Structure of PDB 5xsp Chain A Binding Site BS03

Receptor Information

>5xsp Chain A (length=332) Species: 1280 (Staphylococcus aureus)

RVRARVISHALKDILAEGDKVIIMGHKRPDLDAIGAAIGVSRFAMMNNLE
AYIVLNETDIDPTLRRVMNEIDKKPELRERFITSDDAWDMMTSKTTVVIV
DTHKPELVLDENVLNKANRKVVIDHHRRGESFISNPLLIYMEPYASSTAE
LVTELLEYQPTEQRLTRLESTVMYAGIIVDTRNFTLRTGSRTFDAASYLR
AHGADTILTQHFLKDDVDTYINRSELIRTVKVEDNGIAIAHGSDDKIYHP
VTVAQAADELLSLEGIEASYVVARREDNLIGISARSLGSVNVQLTMEALG
GGGHLTNAATQLKGVTVEEAIAQLQQAITEQL

Ligand information

• Ligand ID: A
• InChI: InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: UDMBCSSLTHHNCD-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
• Formula: C10 H14 N5 O7 P
• Name: ADENOSINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL752
• DrugBank: DB00131
• ZINC: ZINC000003860156
• PDB chain: 5xsp Chain A Residue 703

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xsp Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase
• Resolution: 2.146 Å
• Binding residue (original residue number in PDB): V568 A571 Q572
• Binding residue (residue number reindexed from 1): V251 A254 Q255
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.4.-

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding

External links

• PDB: RCSB:5xsp, PDBe:5xsp, PDBj:5xsp
• PDBsum: 5xsp
• PubMed: 29203646
• UniProt: A0A0U1MUE2