Structure of PDB 8vl9 Chain A Binding Site BS01

Receptor Information

>8vl9 Chain A (length=148) Species: 9606 (Homo sapiens)

PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIH
SYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKE
RCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAH

Ligand information

• Ligand ID: A1ACI
• InChI: InChI=1S/C27H33N5O4/c1-16(33)30-24(27(2,3)4)26(36)32-15-18(34)13-23(32)25(35)28-14-17-9-10-21(22-11-12-29-31-22)20-8-6-5-7-19(17)20/h5-12,18,23-24,34H,13-15H2,1-4H3,(H,28,35)(H,29,31)(H,30,33)/t18-,23+,24-/m1/s1
• InChIKey: SURFMMPUSCEGRF-PUZWTLIVSA-N
• SMILES:
  CACTVS 3.385: CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCc2ccc(c3cc[nH]n3)c4ccccc24)C(C)(C)C
  CACTVS 3.385: CC(=O)N[CH](C(=O)N1C[CH](O)C[CH]1C(=O)NCc2ccc(c3cc[nH]n3)c4ccccc24)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(=O)NC(C(=O)N1CC(CC1C(=O)NCc2ccc(c3c2cccc3)c4cc[nH]n4)O)C(C)(C)C
  ACDLabs 12.01: CC(C)(C)C(NC(C)=O)C(=O)N1CC(O)CC1C(=O)NCc1ccc(c2cc[NH]n2)c2ccccc12
  OpenEye OEToolkits 2.0.7: CC(=O)N[C@H](C(=O)N1C[C@@H](C[C@H]1C(=O)NCc2ccc(c3c2cccc3)c4cc[nH]n4)O)C(C)(C)C
• Formula: C27 H33 N5 O4
• Name: N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide
• PDB chain: 8vl9 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8vl9 A small molecule VHL molecular glue degrader for cysteine dioxygenase 1
• Resolution: 2.5 Å
• Binding residue (original residue number in PDB): W88 Y98 P99 R107 I109 H110 S111 Y112 H115 W117
• Binding residue (residue number reindexed from 1): W28 Y38 P39 R47 I49 H50 S51 Y52 H55 W57
• Annotation score: 1

External links

• PDB: RCSB:8vl9, PDBe:8vl9, PDBj:8vl9
• PDBsum: 8vl9
• UniProt: P40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)