Structure of PDB 4qnq Chain B Binding Site BS01

Receptor Information
>4qnq Chain B (length=144) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQSNRELVVDFLSYKLSQKGYSWSQFSDPMAAVKQALREAGDEFELRYRR
AFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVE
SVDKEMQVLVSRIASWMATYLNDHLEPWIQENGGWDTFVDLYGN
Ligand information
Ligand ID1XJ
InChIInChI=1S/C47H55ClF3N5O6S3/c1-46(2)20-18-42(34-8-12-37(48)13-9-34)36(31-46)32-55-22-24-56(25-23-55)39-14-10-35(11-15-39)45(57)53-65(60,61)41-16-17-43(44(30-41)64(58,59)47(49,50)51)52-38(19-21-54-26-28-62-29-27-54)33-63-40-6-4-3-5-7-40/h3-17,30,38,52H,18-29,31-33H2,1-2H3,(H,53,57)/t38-/m1/s1
InChIKeyJLYAXFNOILIKPP-KXQOOQHDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC1(C)CCC(=C(CN2CCN(CC2)c3ccc(cc3)C(=O)N[S](=O)(=O)c4ccc(N[CH](CCN5CCOCC5)CSc6ccccc6)c(c4)[S](=O)(=O)C(F)(F)F)C1)c7ccc(Cl)cc7
OpenEye OEToolkits 1.7.6CC1(CCC(=C(C1)CN2CCN(CC2)c3ccc(cc3)C(=O)NS(=O)(=O)c4ccc(c(c4)S(=O)(=O)C(F)(F)F)N[C@H](CCN5CCOCC5)CSc6ccccc6)c7ccc(cc7)Cl)C
OpenEye OEToolkits 1.7.6CC1(CCC(=C(C1)CN2CCN(CC2)c3ccc(cc3)C(=O)NS(=O)(=O)c4ccc(c(c4)S(=O)(=O)C(F)(F)F)NC(CCN5CCOCC5)CSc6ccccc6)c7ccc(cc7)Cl)C
CACTVS 3.385CC1(C)CCC(=C(CN2CCN(CC2)c3ccc(cc3)C(=O)N[S](=O)(=O)c4ccc(N[C@H](CCN5CCOCC5)CSc6ccccc6)c(c4)[S](=O)(=O)C(F)(F)F)C1)c7ccc(Cl)cc7
ACDLabs 12.01Clc1ccc(cc1)C2=C(CC(C)(C)CC2)CN7CCN(c3ccc(cc3)C(=O)NS(=O)(=O)c4ccc(c(c4)S(=O)(=O)C(F)(F)F)NC(CCN5CCOCC5)CSc6ccccc6)CC7
FormulaC47 H55 Cl F3 N5 O6 S3
Name4-(4-{[2-(4-chlorophenyl)-5,5-dimethylcyclohex-1-en-1-yl]methyl}piperazin-1-yl)-N-[(4-{[(2R)-4-(morpholin-4-yl)-1-(phenylsulfanyl)butan-2-yl]amino}-3-[(trifluoromethyl)sulfonyl]phenyl)sulfonyl]benzamide
ChEMBLCHEMBL443684
DrugBankDB12340
ZINCZINC000150338726
PDB chain4qnq Chain B 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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PDB4qnq Crystal Structure Analysis of full-length Bcl-XL in complex with the inhibitor ABT-263
Resolution2.3 Å
Binding residue
(original residue number in PDB)		E96 F97 R100 Y101 F105 W137 G138 V141 S145 F146 F191 Y195
Binding residue
(residue number reindexed from 1)		E43 F44 R47 Y48 F52 W84 G85 V88 S92 F93 F138 Y142
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0019901 protein kinase binding
GO:0030276 clathrin binding
GO:0042802 identical protein binding
GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process
GO:0044877 protein-containing complex binding
GO:0051020 GTPase binding
GO:0051400 BH domain binding
GO:0051434 BH3 domain binding
GO:0097371 MDM2/MDM4 family protein binding
Biological Process
GO:0001541 ovarian follicle development
GO:0001666 response to hypoxia
GO:0001701 in utero embryonic development
GO:0001836 release of cytochrome c from mitochondria
GO:0002931 response to ischemia
GO:0006897 endocytosis
GO:0006915 apoptotic process
GO:0006979 response to oxidative stress
GO:0007005 mitochondrion organization
GO:0007281 germ cell development
GO:0007283 spermatogenesis
GO:0008406 gonad development
GO:0008584 male gonad development
GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
GO:0009314 response to radiation
GO:0009410 response to xenobiotic stimulus
GO:0009566 fertilization
GO:0009615 response to virus
GO:0010288 response to lead ion
GO:0014070 response to organic cyclic compound
GO:0021987 cerebral cortex development
GO:0032465 regulation of cytokinesis
GO:0032496 response to lipopolysaccharide
GO:0032946 positive regulation of mononuclear cell proliferation
GO:0034097 response to cytokine
GO:0034976 response to endoplasmic reticulum stress
GO:0035234 ectopic germ cell programmed cell death
GO:0036017 response to erythropoietin
GO:0036018 cellular response to erythropoietin
GO:0036466 synaptic vesicle recycling via endosome
GO:0040008 regulation of growth
GO:0042542 response to hydrogen peroxide
GO:0042981 regulation of apoptotic process
GO:0043065 positive regulation of apoptotic process
GO:0043066 negative regulation of apoptotic process
GO:0043434 response to peptide hormone
GO:0043524 negative regulation of neuron apoptotic process
GO:0044565 dendritic cell proliferation
GO:0046898 response to cycloheximide
GO:0046902 regulation of mitochondrial membrane permeability
GO:0050673 epithelial cell proliferation
GO:0051093 negative regulation of developmental process
GO:0051402 neuron apoptotic process
GO:0051602 response to electrical stimulus
GO:0051881 regulation of mitochondrial membrane potential
GO:0071230 cellular response to amino acid stimulus
GO:0071312 cellular response to alkaloid
GO:0071320 cellular response to cAMP
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor
GO:0071456 cellular response to hypoxia
GO:0071466 cellular response to xenobiotic stimulus
GO:0071480 cellular response to gamma radiation
GO:0071549 cellular response to dexamethasone stimulus
GO:0071732 cellular response to nitric oxide
GO:0071839 apoptotic process in bone marrow cell
GO:0097048 dendritic cell apoptotic process
GO:0097192 extrinsic apoptotic signaling pathway in absence of ligand
GO:0097284 hepatocyte apoptotic process
GO:1900118 negative regulation of execution phase of apoptosis
GO:1900242 regulation of synaptic vesicle endocytosis
GO:1900244 positive regulation of synaptic vesicle endocytosis
GO:1900452 regulation of long-term synaptic depression
GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
GO:1902230 negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage
GO:1902236 negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway
GO:1903077 negative regulation of protein localization to plasma membrane
GO:1905218 cellular response to astaxanthin
GO:1990646 cellular response to prolactin
GO:2000242 negative regulation of reproductive process
GO:2000302 positive regulation of synaptic vesicle exocytosis
GO:2000669 negative regulation of dendritic cell apoptotic process
GO:2000809 positive regulation of synaptic vesicle clustering
GO:2001171 positive regulation of ATP biosynthetic process
GO:2001243 negative regulation of intrinsic apoptotic signaling pathway
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005743 mitochondrial inner membrane
GO:0005759 mitochondrial matrix
GO:0005783 endoplasmic reticulum
GO:0005813 centrosome
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005905 clathrin-coated pit
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0031965 nuclear membrane
GO:0031966 mitochondrial membrane
GO:0045202 synapse
GO:0097136 Bcl-2 family protein complex
GO:0098793 presynapse

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Biological Process
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Cellular Component
External links
PDB RCSB:4qnq, PDBe:4qnq, PDBj:4qnq
PDBsum4qnq
PubMed
UniProtP53563|B2CL1_RAT Bcl-2-like protein 1 (Gene Name=Bcl2l1)

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