Structure of PDB 5ck3 Chain D Binding Site BS02

Receptor Information

>5ck3 Chain D (length=230) Species: 759272 (Thermochaetoides thermophila DSM 1495)

YTTLPSVLLIGPSGAGKTALLTLFERGPLLNPDGTSLKNPYRKPIVTSPV
AQTHTSQVPTSVELAVGANEPTSYKVDLTARKFLLIDTPGHPKLRGTTLQ
HLLNPSPPYKSKLKAVIFLLDAAALADSDGDYLSQTASYLYDVLLSLQKR
FHSSIPVLIAANKQDLFTAVPASLVKSRLEHELGRIRKTRQKFKFEEMME
FDMEVEVMGGNVIGDGPGAERWWRWIGERI

Ligand information

• Ligand ID: GTP
• InChI: InChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
• InChIKey: XKMLYUALXHKNFT-UUOKFMHZSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  CACTVS 3.370: NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  OpenEye OEToolkits 1.7.6: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
• Formula: C10 H16 N5 O14 P3
• Name: GUANOSINE-5'-TRIPHOSPHATE
• ChEMBL: CHEMBL1233147
• DrugBank: DB04137
• ZINC: ZINC000060094177
• PDB chain: 5ck3 Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ck3 Structure and Switch Cycle of SR beta as Ancestral Eukaryotic GTPase Associated with Secretory Membranes.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): S59 A61 G62 K63 T64 A65 T104 T106 S107 G149 N250 K251 D253 N328 V329 I330
• Binding residue (residue number reindexed from 1): S13 A15 G16 K17 T18 A19 T53 T55 S56 G90 N162 K163 D165 N211 V212 I213
• Annotation score: 4

External links

• PDB: RCSB:5ck3, PDBe:5ck3, PDBj:5ck3
• PDBsum: 5ck3
• PubMed: 26299945
• UniProt: G0S401