Structure of PDB 8fy2 Chain A Binding Site BS01

Receptor Information
>8fy2 Chain A (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRI
HSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLK
ERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAH
Ligand information
Ligand IDYFH
InChIInChI=1S/C83H105ClF3N13O11S4/c1-55(57-12-14-59(15-13-57)76-56(2)88-54-113-76)89-79(105)72-43-66(101)47-100(72)80(106)77(81(3,4)5)91-74(102)49-94-30-32-95(33-31-94)50-75(103)98-40-36-96(37-41-98)53-82(6)28-26-70(58-16-20-62(84)21-17-58)61(45-82)46-93-34-38-97(39-35-93)64-22-18-60(19-23-64)78(104)92-115(109,110)69-24-25-71(73(44-69)114(107,108)83(85,86)87)90-63(52-112-68-10-8-7-9-11-68)27-29-99-48-67-42-65(99)51-111-67/h7-25,44,54-55,63,65-67,72,77,90,101H,26-43,45-53H2,1-6H3,(H,89,105)(H,91,102)(H,92,104)/t55-,63+,65+,66-,67+,72-,77+,82+/m0/s1
InChIKeyBSXCOLDAQWGIQN-DTQJYWAGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](NC(=O)[CH]1C[CH](O)CN1C(=O)[CH](NC(=O)CN2CCN(CC2)CC(=O)N3CCN(CC3)C[C]4(C)CCC(=C(CN5CCN(CC5)c6ccc(cc6)C(=O)N[S](=O)(=O)c7ccc(N[CH](CCN8C[CH]9C[CH]8CO9)CSc%10ccccc%10)c(c7)[S](=O)(=O)C(F)(F)F)C4)c%11ccc(Cl)cc%11)C(C)(C)C)c%12ccc(cc%12)c%13scnc%13C
OpenEye OEToolkits 2.0.7Cc1c(scn1)c2ccc(cc2)C(C)NC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)CN4CCN(CC4)CC(=O)N5CCN(CC5)CC6(CCC(=C(C6)CN7CCN(CC7)c8ccc(cc8)C(=O)NS(=O)(=O)c9ccc(c(c9)S(=O)(=O)C(F)(F)F)NC(CCN1CC2CC1CO2)CSc1ccccc1)c1ccc(cc1)Cl)C)O
CACTVS 3.385C[C@H](NC(=O)[C@@H]1C[C@H](O)CN1C(=O)[C@@H](NC(=O)CN2CCN(CC2)CC(=O)N3CCN(CC3)C[C@]4(C)CCC(=C(CN5CCN(CC5)c6ccc(cc6)C(=O)N[S](=O)(=O)c7ccc(N[C@H](CCN8C[C@H]9C[C@@H]8CO9)CSc%10ccccc%10)c(c7)[S](=O)(=O)C(F)(F)F)C4)c%11ccc(Cl)cc%11)C(C)(C)C)c%12ccc(cc%12)c%13scnc%13C
OpenEye OEToolkits 2.0.7Cc1c(scn1)c2ccc(cc2)[C@H](C)NC(=O)[C@@H]3C[C@@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)CN4CCN(CC4)CC(=O)N5CCN(CC5)C[C@@]6(CCC(=C(C6)CN7CCN(CC7)c8ccc(cc8)C(=O)NS(=O)(=O)c9ccc(c(c9)S(=O)(=O)C(F)(F)F)N[C@H](CCN1C[C@H]2C[C@@H]1CO2)CSc1ccccc1)c1ccc(cc1)Cl)C)O
ACDLabs 12.01O=S(=O)(c1cc(ccc1NC(CSc1ccccc1)CCN1CC2CC1CO2)S(=O)(=O)NC(=O)c1ccc(cc1)N1CCN(CC1)CC=1CC(C)(CCC=1c1ccc(Cl)cc1)CN1CCN(CC1)C(=O)CN1CCN(CC1)CC(=O)NC(C(=O)N1CC(O)CC1C(=O)NC(C)c1ccc(cc1)c1scnc1C)C(C)(C)C)C(F)(F)F
FormulaC83 H105 Cl F3 N13 O11 S4
NameN-({4-[2-(4-{[(4R)-4'-chloro-4-methyl-6-{[4-(4-{[4-{[(2R)-4-[(1R,4R)-2-oxa-5-azabicyclo[2.2.1]heptan-5-yl]-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}-2,3,4,5-tetrahydro[1,1'-biphenyl]-4-yl]methyl}piperazin-1-yl)-2-oxoethyl]piperazin-1-yl}acetyl)-3-methyl-L-valyl-(4S)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide
ChEMBL
DrugBank
ZINC
PDB chain8fy2 Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8fy2 Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.
Resolution2.98 Å
Binding residue
(original residue number in PDB)
F76 P86 W88 Y98 P99 L101 R107 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)
F17 P27 W29 Y39 P40 L42 R48 I50 H51 S52 Y53 H56 W58
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:8fy2, PDBe:8fy2, PDBj:8fy2
PDBsum8fy2
PubMed38548768
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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