Structure of PDB 3dek Chain A Binding Site BS01

Receptor Information
>3dek Chain A (length=233) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DNSYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKY
EVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGP
VDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETKIPVDADFL
YAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVA
TEFESFSFDATFHAKKQIPCIVSMLTKELYFYH
Ligand information
Ligand IDRXD
InChIInChI=1S/C21H18FN3O6/c22-8-9-31-14-3-1-2-12(10-14)23-17(26)6-7-18(27)24-13-4-5-15-16(11-13)19(28)21(30)25-20(15)29/h1-5,10-11H,6-9H2,(H,23,26)(H,24,27)(H,25,29,30)
InChIKeyDQXBKUVWJSZHSI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)OCCF)NC(=O)CCC(=O)Nc2ccc3c(c2)C(=O)C(=O)NC3=O
ACDLabs 10.04FCCOc1cccc(c1)NC(=O)CCC(=O)Nc2ccc3C(=O)NC(=O)C(=O)c3c2
CACTVS 3.341FCCOc1cccc(NC(=O)CCC(=O)Nc2ccc3C(=O)NC(=O)C(=O)c3c2)c1
FormulaC21 H18 F N3 O6
NameN-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide
ChEMBL
DrugBankDB08499
ZINCZINC000039127317
PDB chain3dek Chain A Residue 300 [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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PDB3dek Isoquinoline-1,3,4-trione Derivatives Inactivate Caspase-3 by Generation of Reactive Oxygen Species
Resolution2.4 Å
Binding residue
(original residue number in PDB)		E123 C163 G165 T166 L168
Binding residue
(residue number reindexed from 1)		E90 C130 G132 T133 L135
Annotation score1
Binding affinityMOAD: ic50=27nM
PDBbind-CN: -logKd/Ki=7.57,IC50=27nM
Enzymatic activity
Catalytic site (original residue number in PDB) T62 S63 H121 G122 C163 R164
Catalytic site (residue number reindexed from 1) T29 S30 H88 G89 C130 R131
Enzyme Commision number 3.4.22.56: caspase-3.
Gene Ontology
Molecular Function
GO:0002020 protease binding
GO:0004175 endopeptidase activity
GO:0004190 aspartic-type endopeptidase activity
GO:0004197 cysteine-type endopeptidase activity
GO:0004861 cyclin-dependent protein serine/threonine kinase inhibitor activity
GO:0005123 death receptor binding
GO:0005515 protein binding
GO:0008047 enzyme activator activity
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016005 phospholipase A2 activator activity
GO:0044877 protein-containing complex binding
GO:0097153 cysteine-type endopeptidase activity involved in apoptotic process
GO:0097199 cysteine-type endopeptidase activity involved in apoptotic signaling pathway
GO:0097200 cysteine-type endopeptidase activity involved in execution phase of apoptosis
Biological Process
GO:0001554 luteolysis
GO:0001666 response to hypoxia
GO:0001782 B cell homeostasis
GO:0001818 negative regulation of cytokine production
GO:0006508 proteolysis
GO:0006915 apoptotic process
GO:0006974 DNA damage response
GO:0007413 axonal fasciculation
GO:0007507 heart development
GO:0007605 sensory perception of sound
GO:0007611 learning or memory
GO:0008627 intrinsic apoptotic signaling pathway in response to osmotic stress
GO:0009410 response to xenobiotic stimulus
GO:0009411 response to UV
GO:0009611 response to wounding
GO:0009749 response to glucose
GO:0010038 response to metal ion
GO:0010165 response to X-ray
GO:0014070 response to organic cyclic compound
GO:0016241 regulation of macroautophagy
GO:0016485 protein processing
GO:0021766 hippocampus development
GO:0030163 protein catabolic process
GO:0030182 neuron differentiation
GO:0030216 keratinocyte differentiation
GO:0030218 erythrocyte differentiation
GO:0030220 platelet formation
GO:0030889 negative regulation of B cell proliferation
GO:0031647 regulation of protein stability
GO:0032025 response to cobalt ion
GO:0032355 response to estradiol
GO:0032496 response to lipopolysaccharide
GO:0034349 glial cell apoptotic process
GO:0034612 response to tumor necrosis factor
GO:0035094 response to nicotine
GO:0035556 intracellular signal transduction
GO:0042542 response to hydrogen peroxide
GO:0043029 T cell homeostasis
GO:0043065 positive regulation of apoptotic process
GO:0043200 response to amino acid
GO:0043525 positive regulation of neuron apoptotic process
GO:0044346 fibroblast apoptotic process
GO:0045165 cell fate commitment
GO:0045786 negative regulation of cell cycle
GO:0046007 negative regulation of activated T cell proliferation
GO:0048011 neurotrophin TRK receptor signaling pathway
GO:0051146 striated muscle cell differentiation
GO:0051384 response to glucocorticoid
GO:0051402 neuron apoptotic process
GO:0051604 protein maturation
GO:0061713 anterior neural tube closure
GO:0070269 pyroptotic inflammatory response
GO:0071407 cellular response to organic cyclic compound
GO:0071887 leukocyte apoptotic process
GO:0072734 cellular response to staurosporine
GO:0097190 apoptotic signaling pathway
GO:0097193 intrinsic apoptotic signaling pathway
GO:0097194 execution phase of apoptosis
GO:0098693 regulation of synaptic vesicle cycle
GO:0140639 positive regulation of pyroptotic inflammatory response
GO:1902004 positive regulation of amyloid-beta formation
GO:1904019 epithelial cell apoptotic process
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0014069 postsynaptic density
GO:0031264 death-inducing signaling complex
GO:0043025 neuronal cell body
GO:0098978 glutamatergic synapse

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dek, PDBe:3dek, PDBj:3dek
PDBsum3dek
PubMed18768468
UniProtP42574|CASP3_HUMAN Caspase-3 (Gene Name=CASP3)

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