Structure of PDB 8fy1 Chain D Binding Site BS01

Receptor Information
>8fy1 Chain D (length=147) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGYDNREIVMKYIHYKLSQRGYEWDAGSPVPPVVHLTLRQAGDDFSRRYR
RDFAEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCV
ESVNREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYGPSM
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
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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)
F104 R107 Y108 D111 F124 R129 T132 V133 E136 N143 W144 G145 R146 V148 E152 F198 L201 Y202 P204 S205
Binding residue
(residue number reindexed from 1)
F45 R48 Y49 D52 F65 R70 T73 V74 E77 N84 W85 G86 R87 V89 E93 F139 L142 Y143 P145 S146
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Biological Process
GO:0042981 regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
Cellular Component
GO:0016020 membrane

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Biological Process

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Cellular Component
External links
PDB RCSB:8fy1, PDBe:8fy1, PDBj:8fy1
PDBsum8fy1
PubMed38548768
UniProtP10415|BCL2_HUMAN Apoptosis regulator Bcl-2 (Gene Name=BCL2)

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