Structure of PDB 4w9g Chain F Binding Site BS01

Receptor Information

>4w9g Chain F (length=144) Species: 9606 (Homo sapiens)

VLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKER
CLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQER

Ligand information

• Ligand ID: 3JV
• InChI: InChI=1S/C22H29N3O3S/c1-14-7-15(5-6-17(14)19-11-23-13-29-19)10-24-21(28)18-8-16(26)12-25(18)20(27)9-22(2,3)4/h5-7,11,13,16,18,26H,8-10,12H2,1-4H3,(H,24,28)/t16-,18+/m1/s1
• InChIKey: QBAUKFDDQIMOAJ-AEFFLSMTSA-N
• SMILES:
  CACTVS 3.385: Cc1cc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)CC(C)(C)C)ccc1c3scnc3
  OpenEye OEToolkits 1.9.2: Cc1cc(ccc1c2cncs2)CNC(=O)C3CC(CN3C(=O)CC(C)(C)C)O
  OpenEye OEToolkits 1.9.2: Cc1cc(ccc1c2cncs2)CNC(=O)[C@@H]3C[C@H](CN3C(=O)CC(C)(C)C)O
  CACTVS 3.385: Cc1cc(CNC(=O)[CH]2C[CH](O)CN2C(=O)CC(C)(C)C)ccc1c3scnc3
  ACDLabs 12.01: O=C(N1CC(O)CC1C(=O)NCc3cc(c(c2scnc2)cc3)C)CC(C)(C)C
• Formula: C22 H29 N3 O3 S
• Name: (4R)-1-(3,3-dimethylbutanoyl)-4-hydroxy-N-[3-methyl-4-(1,3-thiazol-5-yl)benzyl]-L-prolinamide
• ChEMBL: CHEMBL3344080
• ZINC: ZINC000098208456
• PDB chain: 4w9g Chain F Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4w9g Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.
• Resolution: 2.7 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: BindingDB: Kd=6530nM

External links

• PDB: RCSB:4w9g, PDBe:4w9g, PDBj:4w9g
• PDBsum: 4w9g
• PubMed: 25166285
• UniProt: P40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)