Structure of PDB 8pfh Chain B Binding Site BS01

Receptor Information

>8pfh Chain B (length=287) Species: 4932 (Saccharomyces cerevisiae)

GYVGFANLPKQWHRRSIKNGFSFNLLCVGPDGIGKTTLMKTLFNNDDIEA
NLVKEQRHKVKIKSYESVIEENGVKLNLNVIDTEGFGDFLNNDQKSWDPI
IKEIDSRFDQYLDAENKINRHSINDKRIHACLYFIEPTGHYLKPLDLKFM
QSVYEKCNLIPVIAKSDILTDEEILSFKKTIMNQLIQSNIELFKPPIYSN
DDAENSHLSERLFSSLPYAVIGSNDIVENYSGNQVRGRSYPWGVIEVDND
NHSDFNLLKNLLIKQFMEELKERTSKILYENYRSSKL

Ligand information

• Ligand ID: GDP
• InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: QGWNDRXFNXRZMB-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.385: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
• Formula: C10 H15 N5 O11 P2
• Name: GUANOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL384759
• DrugBank: DB04315
• ZINC: ZINC000008215481
• PDB chain: 8pfh Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8pfh Crystal structure of the yeast septin complex Shs1-Cdc12-Cdc3-Cdc10
• Resolution: 3.24 Å
• Binding residue (original residue number in PDB): H262 I290 E295
• Binding residue (residue number reindexed from 1): H140 I168 E173
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0005525 GTP binding

External links

• PDB: RCSB:8pfh, PDBe:8pfh, PDBj:8pfh
• PDBsum: 8pfh
• PubMed: 38184752
• UniProt: P32457|CDC3_YEAST Cell division control protein 3 (Gene Name=CDC3)