Structure of PDB 7vek Chain A Binding Site BS02

Receptor Information

>7vek Chain A (length=452) Species: 3527 (Phytolacca americana)

QLHVVFFPIMAHGHMIPTLDIARLFAARNVRATIITTPLNAHTFTKAIEM
NGSPTIHLELFKFPAQDVGLPEGCENLEQALGSSLIEKFFKGVGLLREQL
EAYLEKTRPNCLVADMFFPWATDSAAKFNIPRLVFHGTSFFSLCALEVVR
LYEPHKNVSSDEELFSLPLFPHDIKMMRLQLPEDVWKHEKAEGKTRLKLI
KESELKSYGVIVNSFYELEPNYAEFFRKELGRRAWNIGPVSLCNRHECLK
WLNSKKKNSVIYICFGSTAHQIAPQLYEIAMALEASGQEFIWVVRNNDDS
WLPRGFEQRVEGKGLIIRGWAPQVLILEHEAIGAFVTHCGWNSTLEGITA
GVPMVTWPIFAEQFYNEKLVNQILKIGVPVGANKWSRETSIEDVIKKDAI
EKALREIMVGDEAEERRSRAKKLKEMAWKAVEEGGSSYSDLSALIEELRG
YH

Ligand information

• Ligand ID: U2F
• InChI: InChI=1S/C15H23FN2O16P2/c16-8-11(23)9(21)5(3-19)32-14(8)33-36(28,29)34-35(26,27)30-4-6-10(22)12(24)13(31-6)18-2-1-7(20)17-15(18)25/h1-2,5-6,8-14,19,21-24H,3-4H2,(H,26,27)(H,28,29)(H,17,20,25)/t5-,6-,8-,9-,10-,11-,12-,13-,14-/m1/s1
• InChIKey: NGTCPFGWXMBZEP-NQQHDEILSA-N
• SMILES:
  ACDLabs 10.04: O=P(OC1OC(C(O)C(O)C1F)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)F)O)O
  CACTVS 3.341: OC[C@H]1O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](F)[C@@H](O)[C@@H]1O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)F)O)O
  CACTVS 3.341: OC[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](F)[CH](O)[CH]1O
• Formula: C15 H23 F N2 O16 P2
• Name: URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE
• ChEMBL: CHEMBL593830
• DrugBank: DB03488
• ZINC: ZINC000016051573
• PDB chain: 7vek Chain A Residue 503

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7vek Structural basis for substrate recognition in the Phytolacca americana glycosyltransferase PaGT3.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G19 G146 C289 S292 T293 W352 A353 Q355 H370 G372 W373 N374 S375 E378 F392 E394 Q395
• Binding residue (residue number reindexed from 1): G13 G137 C264 S267 T268 W320 A321 Q323 H338 G340 W341 N342 S343 E346 F360 E362 Q363
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.4.1.-

Gene Ontology

Molecular Function

• GO:0008194 UDP-glycosyltransferase activity
• GO:0016757 glycosyltransferase activity
• GO:0035251 UDP-glucosyltransferase activity
• GO:0046527 glucosyltransferase activity

External links

• PDB: RCSB:7vek, PDBe:7vek, PDBj:7vek
• PDBsum: 7vek
• PubMed: 35234151
• UniProt: B5MGN9