Structure of PDB 4fmd Chain F Binding Site BS02

Receptor Information

>4fmd Chain F (length=149) Species: 9606 (Homo sapiens)

KLLLIGDSGVGKSCLLLRFADDTYTISTIGVDFKIRIWDTAGQERFRTIT
SSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCD
LTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRM

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: 4fmd Chain F Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4fmd Structurally Distinct Bacterial TBC-like GAPs Link Arf GTPase to Rab1 Inactivation to Counteract Host Defenses.
• Resolution: 3.05 Å
• Binding residue (original residue number in PDB): G21 G23 K24 S25 C26 Y36 K125 D127 A155 K156
• Binding residue (residue number reindexed from 1): G9 G11 K12 S13 C14 Y24 K98 D100 A128 K129
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Q70
• Catalytic site (residue number reindexed from 1): Q43
• Enzyme Commision number: 3.6.5.2: small monomeric GTPase.

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:4fmd, PDBe:4fmd, PDBj:4fmd
• PDBsum: 4fmd
• PubMed: 22939626
• UniProt: P62820|RAB1A_HUMAN Ras-related protein Rab-1A (Gene Name=RAB1A)