Structure of PDB 6fmk Chain C Binding Site BS01

Receptor Information

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

VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLT

Ligand information

• Ligand ID: DV8
• InChI: InChI=1S/C21H26N4O2S3/c1-12-19(30-11-23-12)16-6-4-15(5-7-16)9-22-20(28)18-8-17(27)10-25(18)21(29)13(2)24-14(3)26/h4-7,11,13,17-18,27H,8-10H2,1-3H3,(H,22,28)(H,24,26)/t13-,17+,18-/m0/s1
• InChIKey: NPFDMJWSPHYAKU-VHSSKADRSA-N
• SMILES:
  CACTVS 3.385: C[C@H](NC(C)=O)C(=S)N1C[C@H](O)C[C@H]1C(=S)NCc2ccc(cc2)c3scnc3C
  OpenEye OEToolkits 2.0.6: Cc1c(scn1)c2ccc(cc2)CNC(=S)C3CC(CN3C(=S)C(C)NC(=O)C)O
  OpenEye OEToolkits 2.0.6: Cc1c(scn1)c2ccc(cc2)CNC(=S)[C@@H]3C[C@H](CN3C(=S)[C@H](C)NC(=O)C)O
  CACTVS 3.385: C[CH](NC(C)=O)C(=S)N1C[CH](O)C[CH]1C(=S)NCc2ccc(cc2)c3scnc3C
• Formula: C21 H26 N4 O2 S3
• Name: ~{N}-[(2~{S})-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamothioyl]-4-oxidanyl-pyrrolidin-1-yl]-1-sulfanylidene-propan-2-yl]ethanamide
• ChEMBL: CHEMBL4224723
• PDB chain: 6fmk Chain C Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6fmk Thioamide substitution to probe the hydroxyproline recognition of VHL ligands.
• Resolution: 2.75 Å
• Binding residue (original residue number in PDB): W88 Y98 P99 I109 H110 S111 Y112 H115 W117
• Binding residue (residue number reindexed from 1): W27 Y37 P38 I48 H49 S50 Y51 H54 W56
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.67,Kd=21.6uM

External links

• PDB: RCSB:6fmk, PDBe:6fmk, PDBj:6fmk
• PDBsum: 6fmk
• PubMed: 29650462
• UniProt: P40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)