Structure of PDB 6gfz Chain C Binding Site BS01

Receptor Information

>6gfz Chain C (length=141) Species: 9606 (Homo sapiens)

VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLT

Ligand information

• Ligand ID: EXE
• InChI: InChI=1S/C24H31FN4O4S/c1-13-20(34-12-27-13)16-8-6-15(7-9-16)10-26-22(32)19-18(25)17(31)11-29(19)23(33)21(24(3,4)5)28-14(2)30/h6-9,12,17-19,21,31H,10-11H2,1-5H3,(H,26,32)(H,28,30)/t17-,18+,19-,21+/m0/s1
• InChIKey: MNNVXLLCYGGFOQ-YOUFYPILSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[C@H](C(=O)N1C[C@H](O)[C@@H](F)[C@H]1C(=O)NCc2ccc(cc2)c3scnc3C)C(C)(C)C
  OpenEye OEToolkits 2.0.6: Cc1c(scn1)c2ccc(cc2)CNC(=O)[C@@H]3[C@@H]([C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)C)O)F
  OpenEye OEToolkits 2.0.6: Cc1c(scn1)c2ccc(cc2)CNC(=O)C3C(C(CN3C(=O)C(C(C)(C)C)NC(=O)C)O)F
  CACTVS 3.385: CC(=O)N[CH](C(=O)N1C[CH](O)[CH](F)[CH]1C(=O)NCc2ccc(cc2)c3scnc3C)C(C)(C)C
• Formula: C24 H31 F N4 O4 S
• Name: (2~{R},3~{S},4~{S})-1-[(2~{S})-2-acetamido-3,3-dimethyl-butanoyl]-3-fluoranyl-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide
• PDB chain: 6gfz Chain C Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gfz 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): P86 W88 Y98 P99 I109 H110 S111 Y112 H115 W117
• Binding residue (residue number reindexed from 1): P25 W27 Y37 P38 I48 H49 S50 Y51 H54 W56
• Annotation score: 1
• Binding affinity: MOAD: Kd=3080nM
  PDBbind-CN: -logKd/Ki=5.51,Kd=3080nM

External links

• PDB: RCSB:6gfz, PDBe:6gfz, PDBj:6gfz
• PDBsum: 6gfz
• PubMed: 29949369
• UniProt: P40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)