Structure of PDB 6di7 Chain A Binding Site BS01

Receptor Information

>6di7 Chain A (length=279) Species: 759272 (Thermochaetoides thermophila DSM 1495)

DLPQIVVVGSQSSGKSSVLENIVGRDFLPRGQGIVTRRPLVLQLINRQSD
ERLADSTDKAANLDEWGEFLHLPGQKFYDFNKIRDEINRETEAKVGRNAG
ISPAPINLRIYSPHVLNLTLVDLPGLTRVPVGDQPRDIERQIRDMILKYI
QKPNAIILAVTAANVDLANSDGLKLAREVDPEGQRTIGVLTKVDLMDEGT
DVVDILAGRIIPLRLGYVPVVNRGQRDIDNKKPITAALEAEKAFFENHKA
YRNKSAYCGTPYLARKLNLILMMHIKQTL

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: 6di7 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6di7 Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): S53 G55 K56 S57 S58 R71 K240 D242 L243 V269 N270 R271 G272 Q273
• Binding residue (residue number reindexed from 1): S12 G14 K15 S16 S17 R30 K192 D194 L195 V221 N222 R223 G224 Q225
• Annotation score: 4

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:6di7, PDBe:6di7, PDBj:6di7
• PDBsum: 6di7
• PubMed: 30087125
• UniProt: G0SFF0