Structure of PDB 4rkf Chain B Binding Site BS01

Receptor Information

>4rkf Chain B (length=172) Species: 7227 (Drosophila melanogaster)

QNFDYMFKLLIIGNSSVGKTSFLFRYADDSFTSAFVSTVGIDFKVKTVFR
HDKRVKLQIWDTAGLERYRTITTAYYRGAMGFILMYDVTNEDSFNSVQDW
VTQIKTYSWDNAQVILVGNKCDMEDQRVISFERGRQLADQLGVEFFETSA
KENVNVKAVFERLVDIICDKMS

Ligand information

• Ligand ID: GNP
• InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
• InChIKey: UQABYHGXWYXDTK-UUOKFMHZSA-N
• SMILES:
  ACDLabs 10.04: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
• Formula: C10 H17 N6 O13 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
• ChEMBL: CHEMBL1233085
• DrugBank: DB02082
• ZINC: ZINC000037868676
• PDB chain: 4rkf Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4rkf Structures of Drosophila melanogaster Rab2 and Rab3 bound to GMPPNP.
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): S30 S31 G33 K34 T35 S36 F46 S48 F50 S52 T53 G79 N134 K135 D137 M138 S164 A165 K166
• Binding residue (residue number reindexed from 1): S15 S16 G18 K19 T20 S21 F31 S33 F35 S37 T38 G64 N119 K120 D122 M123 S149 A150 K151
• Annotation score: 3

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:4rkf, PDBe:4rkf, PDBj:4rkf
• PDBsum: 4rkf
• PubMed: 25615965
• UniProt: P25228|RAB3_DROME Ras-related protein Rab-3 (Gene Name=Rab3)