Structure of PDB 6vik Chain B Binding Site BS01

Receptor Information

>6vik Chain B (length=173) Species: 10090 (Mus musculus)

FASLDRVKVLVLGDSGVGKSSLVHLLCHNQVLGNPSWTVGCSVHDYKEGT
PEEKTYYIELWDVGGSVKSTRAVFYNSVNGIILVHDLTNKKSSQNLYRWS
LEVNQIPLLVIGTKLDQIHETKRHEVLIRTAFLAEDFNAEEINLDCTNPR
SSAAGSSNAVKLSRFFDKVIEKR

Ligand information

• Ligand ID: GSP
• InChI: InChI=1S/C10H16N5O13P3S/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(26-9)1-25-29(19,20)27-30(21,22)28-31(23,24)32/h2-3,5-6,9,16-17H,1H2,(H,19,20)(H,21,22)(H2,23,24,32)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: XOFLBQFBSOEHOG-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(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)O[P](O)(O)=S)[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)(O)OP(=S)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.341: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
  ACDLabs 10.04: S=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
• Formula: C10 H16 N5 O13 P3 S
• Name: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
• ChEMBL: CHEMBL1204628
• DrugBank: DB01864
• ZINC: ZINC000008217391
• PDB chain: 6vik Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6vik Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): S15 G16 G18 K19 S20 S21 K148 D150 D179 C180
• Binding residue (residue number reindexed from 1): S15 G16 G18 K19 S20 S21 K114 D116 D145 C146
• Annotation score: 1

External links

• PDB: RCSB:6vik, PDBe:6vik, PDBj:6vik
• PDBsum: 6vik
• PubMed: 32220963
• UniProt: Q9D4V7|RABL3_MOUSE Rab-like protein 3 (Gene Name=Rabl3)