Structure of PDB 2gf9 Chain A Binding Site BS01

Receptor Information

>2gf9 Chain A (length=176) Species: 9606 (Homo sapiens)

LVPRGSDYMFKLLLIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKT
VYRHDKRIKLQIWDTAGQERYRTITTAYYRGAMGFLLMYDIANQESFAAV
QDWATQIKTYSWDNAQVILVGNKCDLEDERVVPAEDGRRLADDLGFEFFE
ASAKENINVKQVFERLVDVICEKMNE

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: 2gf9 Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2gf9 Crystal structure of human RAB3D in complex with GDP
• Resolution: 1.53 Å
• Binding residue (original residue number in PDB): S32 G34 K35 T36 S37 F47 N135 K136 D138 L139 S165 A166 K167
• Binding residue (residue number reindexed from 1): S19 G21 K22 T23 S24 F34 N122 K123 D125 L126 S152 A153 K154
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003924 GTPase activity
• GO:0005525 GTP binding

External links

• PDB: RCSB:2gf9, PDBe:2gf9, PDBj:2gf9
• PDBsum: 2gf9
• UniProt: O95716|RAB3D_HUMAN Ras-related protein Rab-3D (Gene Name=RAB3D)