Structure of PDB 8fy2 Chain D Binding Site BS01

Receptor Information
>8fy2 Chain D (length=141) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYDNREIVMKYIHYKLSQRGYEWDGPVPPVVHLTLRQAGDDFSRRYRRDF
AEMSSQLHLTPFTARGRFATVVEELFRDGVNWGRIVAFFEFGGVMCVESV
NREMSPLVDNIALWMTEYLNRHLHTWIQDNGGWDAFVELYG
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)
D103 F104 R107 Y108 E114 N143 W144 G145 A149 L201 Y202
Binding residue
(residue number reindexed from 1)
D41 F42 R45 Y46 E52 N81 W82 G83 A87 L139 Y140
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

View graph for
Biological Process

View graph for
Cellular Component
External links
PDB RCSB:8fy2, PDBe:8fy2, PDBj:8fy2
PDBsum8fy2
PubMed38548768
UniProtP10415|BCL2_HUMAN Apoptosis regulator Bcl-2 (Gene Name=BCL2)

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