Structure of PDB 8fy1 Chain A Binding Site BS01

Receptor Information
>8fy1 Chain A (length=144) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIH
SYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKE
RCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQE
Ligand information
Ligand IDYF8
InChIInChI=1S/C82H105ClF3N11O11S4/c1-56(58-18-20-60(21-19-58)75-57(2)87-55-110-75)88-78(102)71-48-66(98)52-97(71)79(103)76(80(3,4)5)90-73(99)16-12-7-8-13-17-74(100)96-42-38-94(39-43-96)54-81(6)34-32-69(59-22-26-63(83)27-23-59)62(50-81)51-93-36-40-95(41-37-93)65-28-24-61(25-29-65)77(101)91-112(106,107)68-30-31-70(72(49-68)111(104,105)82(84,85)86)89-64(33-35-92-44-46-108-47-45-92)53-109-67-14-10-9-11-15-67/h9-11,14-15,18-31,49,55-56,64,66,71,76,89,98H,7-8,12-13,16-17,32-48,50-54H2,1-6H3,(H,88,102)(H,90,99)(H,91,101)/t56-,64+,66+,71-,76+,81+/m0/s1
InChIKeyKQEMZZJSHJCPSI-RYFXIQSLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1c(scn1)c2ccc(cc2)C(C)NC(=O)C3CC(CN3C(=O)C(C(C)(C)C)NC(=O)CCCCCCC(=O)N4CCN(CC4)CC5(CCC(=C(C5)CN6CCN(CC6)c7ccc(cc7)C(=O)NS(=O)(=O)c8ccc(c(c8)S(=O)(=O)C(F)(F)F)NC(CCN9CCOCC9)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)CCCCCCC(=O)N2CCN(CC2)C[C@]3(C)CCC(=C(CN4CCN(CC4)c5ccc(cc5)C(=O)N[S](=O)(=O)c6ccc(N[C@H](CCN7CCOCC7)CSc8ccccc8)c(c6)[S](=O)(=O)C(F)(F)F)C3)c9ccc(Cl)cc9)C(C)(C)C)c%10ccc(cc%10)c%11scnc%11C
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)CCCCCCC(=O)N4CCN(CC4)C[C@@]5(CCC(=C(C5)CN6CCN(CC6)c7ccc(cc7)C(=O)NS(=O)(=O)c8ccc(c(c8)S(=O)(=O)C(F)(F)F)N[C@H](CCN9CCOCC9)CSc1ccccc1)c1ccc(cc1)Cl)C)[O]
CACTVS 3.385C[CH](NC(=O)[CH]1C[CH]([O])CN1C(=O)[CH](NC(=O)CCCCCCC(=O)N2CCN(CC2)C[C]3(C)CCC(=C(CN4CCN(CC4)c5ccc(cc5)C(=O)N[S](=O)(=O)c6ccc(N[CH](CCN7CCOCC7)CSc8ccccc8)c(c6)[S](=O)(=O)C(F)(F)F)C3)c9ccc(Cl)cc9)C(C)(C)C)c%10ccc(cc%10)c%11scnc%11C
ACDLabs 12.01O=S(=O)(c1cc(ccc1NC(CSc1ccccc1)CCN1CCOCC1)S(=O)(=O)NC(=O)c1ccc(cc1)N1CCN(CC1)CC=1CC(C)(CCC=1c1ccc(Cl)cc1)CN1CCN(CC1)C(=O)CCCCCCC(=O)NC(C(=O)N1CC(O)CC1C(=O)NC(C)c1ccc(cc1)c1scnc1C)C(C)(C)C)C(F)(F)F
FormulaC82 H104 Cl F3 N11 O11 S4
NameN-[8-(4-{[(1R,3R,4S)-4-(4-chlorophenyl)-1-methyl-3-{[4-(4-{[4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-(trifluoromethanesulfonyl)benzene-1-sulfonyl]carbamoyl}phenyl)piperazin-1-yl]methyl}cyclohexyl]methyl}piperazin-1-yl)-8-oxooctanoyl]-3-methyl-L-valyl-(4R)-4-hydroxy-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide
ChEMBL
DrugBank
ZINC
PDB chain8fy1 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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PDB8fy1 Development and crystal structures of a potent second-generation dual degrader of BCL-2 and BCL-xL.
Resolution2.56 Å
Binding residue
(original residue number in PDB)
R69 W88 Y98 P99 L101 I109 H110 S111 Y112 H115 W117
Binding residue
(residue number reindexed from 1)
R9 W28 Y38 P39 L41 I49 H50 S51 Y52 H55 W57
Annotation score1
Enzymatic activity
Enzyme Commision number ?
External links
PDB RCSB:8fy1, PDBe:8fy1, PDBj:8fy1
PDBsum8fy1
PubMed38548768
UniProtP40337|VHL_HUMAN von Hippel-Lindau disease tumor suppressor (Gene Name=VHL)

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