Structure of PDB 2efe Chain C Binding Site BS01

Receptor Information

>2efe Chain C (length=246) Species: 3702 (Arabidopsis thaliana)

MRKPSAGDFVKSIKSFIVSFSNNAPDPEKDCAMVQEFFSKMEAAFRAHPL
WSGCSEEELDSAGDGLEKYVMTKLFTRVFASNTEEVIADEKLFQKMSLVQ
QFISPENLDIQPTFQNESSWLLAQKELQKINMYKAPRDKLVCILNCCKVI
NNLLLNASIASNENAPGADEFLPVLIYVTIKANPPQLHSNLLYIQRYRRE
SKLVGEAAYFFTNILSAESFISNIDAKSISLDEAEFEKNMESARAR

Ligand information

• Ligand ID: GNH
• InChI: InChI=1S/C10H16N6O10P2/c11-10-14-7-4(8(19)15-10)13-2-16(7)9-6(18)5(17)3(25-9)1-24-28(22,23)26-27(12,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H3,12,20,21)(H3,11,14,15,19)/t3-,5-,6-,9-/m1/s1
• InChIKey: ZGPDMUBRWRJAQQ-UUOKFMHZSA-N
• SMILES:
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](N)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](N)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(N)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(N)O)O)O)N=C(NC2=O)N
• Formula: C10 H16 N6 O10 P2
• Name: AMINOPHOSPHONIC ACID-GUANYLATE ESTER
• DrugBank: DB02623
• PDB chain: 2efe Chain D Residue 2200

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2efe GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5/Vps9 system
• Resolution: 2.08 Å
• Binding residue (original residue number in PDB): N180 D185
• Binding residue (residue number reindexed from 1): N164 D169
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005085 guanyl-nucleotide exchange factor activity

Biological Process

• GO:0016192 vesicle-mediated transport

External links

• PDB: RCSB:2efe, PDBe:2efe, PDBj:2efe
• PDBsum: 2efe
• PubMed: 20833725
• UniProt: Q9LT31|VPS9A_ARATH Vacuolar protein sorting-associated protein 9A (Gene Name=VPS9A)