Structure of PDB 1yvd Chain A Binding Site BS02

Receptor Information

>1yvd Chain A (length=166) Species: 10090 (Mus musculus)

SLRELKVCLLGDTGVGKSSIVWRFVEDSFDPNINPTIGASFMTKTVQYQN
ELHKFLIWDTAGQERFRALAPMYYRGSAAAIIVYDITKEETFSTLKNWVR
ELRQHGPPSIVVAIAGNKCDLTDVREVMERDAKDYADSIHAIFVETSAKN
AININELFIEISRRIP

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: 1yvd Chain A Residue 900

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yvd Structural basis of family-wide Rab GTPase recognition by rabenosyn-5.
• Resolution: 1.93 Å
• Binding residue (original residue number in PDB): T14 G15 G17 K18 S19 S20 F30 P32 I34 P36 T37 G63 N118 K119 D121 L122 S148 K150
• Binding residue (residue number reindexed from 1): T13 G14 G16 K17 S18 S19 F29 P31 I33 P35 T36 G62 N117 K118 D120 L121 S147 K149
• Annotation score: 3

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:1yvd, PDBe:1yvd, PDBj:1yvd
• PDBsum: 1yvd
• PubMed: 16034420
• UniProt: P35285|RB22A_MOUSE Ras-related protein Rab-22A (Gene Name=Rab22a)