Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T57943 | Target Info | |||
| Target Name | Caspase-3 (CASP3) | ||||
| Synonyms | Yama protein; SREBP cleavage activity 1; SCA-1; Protein Yama; Cysteine protease CPP32; Caspase 3; CPP32; CPP-32; CASP-3; Apopain | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | CASP3 | ||||
| Biochemical Class | Peptidase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Cysteinesulfonic Acid | Ligand Info | |||||
| Structure Description | Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors | PDB:3DEK | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
DNSYKMDYPE
43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAR164 GTELDCGIET174 KIPVDADFLY195 AYSTAPGYYS 205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI235 LTRVNRKVAT245 EFESFSFDAT 255 FHAKKQIPCI265 VSMLTKELYF275 YH
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: (10S)-3,3-dimethyl-8-{[(2S)-2-(phenoxymethyl)pyrrolidin-1-yl]sulfonyl}-2,3,4,10-tetrahydropyrimido[1,2-a]indol-10-ol | Ligand Info | |||||
| Structure Description | 3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as Potent Non-Peptidic Inhibitors of Caspase-3 | PDB:3H0E | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [2] |
| PDB Sequence |
DNSYKMDYPE
43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAC163 RGTELDCGIE173 DDMACHKIPV189 EADFLYAYST 199 APGYYSWRNS209 KDGSWFIQSL219 CAMLKQYADK229 LEFMHILTRV239 NRKVATEFES 249 FSFDATFHAK259 KQIPCIVSML269 TKELYFY
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MET61
4.228
THR62
4.652
SER120
3.743
HIS121
3.153
GLY122
2.891
GLU123
3.488
PHE128
4.531
ALA162
3.963
CYS163
1.941
GLY165
4.720
THR166
3.537
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| Ligand Name: 5-[4-(1-Carboxymethyl-2-oxo-propylcarbamoyl)-benzylsulfamoyl]-2-hydroxy-benzoic acid | Ligand Info | |||||
| Structure Description | Caspase-3 tethered to irreversible inhibitor | PDB:1NMS | ||||
| Method | X-ray diffraction | Resolution | 1.70 Å | Mutation | No | [3] |
| PDB Sequence |
DNSYKMDYPE
43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAC163 RGTELDCGIE173 TDDDMACHKI187 PVDADFLYAY 197 STAPGYYSWR207 NSKDGSWFIQ217 SLCAMLKQYA227 DKLEFMHILT237 RVNRKVATEF 247 ESFSFDATFH257 AKKQIPCIVS267 MLTKELYFYH277
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .161 or .1612 or .1613 or :3161;style chemicals stick;color identity;select .A:62 or .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:209 or .A:214 or .A:248 or .A:249 or .A:250 or .A:256; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(3-{2-[(5-Methanesulfonyl-thiophene-2-carbonyl)-amino]-ethyldisulfanylmethyl}-benzenesulfonylamino)-4-oxo-pentanoic acid | Ligand Info | |||||
| Structure Description | Extendend Tethering: In Situ Assembly of Inhibitors | PDB:1NMQ | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [3] |
| PDB Sequence |
DNSYKMDYPE
43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAC163 RGTELDCGIE173 TDDDCHKIPV189 DADFLYAYST 199 APGYYSWRNS209 KDGSWFIQSL219 CAMLKQYADK229 LEFMHILTRV239 NRKVATEFES 249 FSFDATFHAK259 KQIPCIVSML269 TKELYFYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .160 or .1602 or .1603 or :3160;style chemicals stick;color identity;select .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .A:204 or .A:205 or .A:206 or .A:207 or .A:208 or .A:209 or .A:214 or .A:248 or .A:249 or .A:250 or .A:251 or .A:256; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: N-[3-(2-fluoroethoxy)phenyl]-N'-(1,3,4-trioxo-1,2,3,4-tetrahydroisoquinolin-6-yl)butanediamide | Ligand Info | |||||
| Structure Description | Crystal Structures of Caspase-3 with Bound Isoquinoline-1,3,4-trione Derivative Inhibitors | PDB:3DEK | ||||
| Method | X-ray diffraction | Resolution | 2.40 Å | Mutation | No | [1] |
| PDB Sequence |
DNSYKMDYPE
43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAR164 GTELDCGIET174 KIPVDADFLY195 AYSTAPGYYS 205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI235 LTRVNRKVAT245 EFESFSFDAT 255 FHAKKQIPCI265 VSMLTKELYF275 YH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .RXD or .RXD2 or .RXD3 or :3RXD;style chemicals stick;color identity;select .A:121 or .A:122 or .A:123 or .A:124 or .A:165 or .A:166 or .A:168 or .A:204 or .A:256; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (4S)-5-[[(2S)-1-[2-(carboxymethyl)-2-[(3S)-3-hydroxy-4-oxo-4-(2-phenylethylamino)butanoyl]hydrazinyl]-3-methyl-1-oxobutan-2-yl]amino]-5-oxo-4-(phenylmethoxycarbonylamino)pentanoic acid | Ligand Info | |||||
| Structure Description | Crystal structures of caspase-3 in complex with aza-peptide epoxide inhibitors. | PDB:2CNO | ||||
| Method | X-ray diffraction | Resolution | 1.95 Å | Mutation | No | [4] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIETD> Chain B HKIPVEADFL 194 YAYSTAPGYY204 SWRNSKDGSW214 FIQSLCAMLK224 QYADKLEFMH234 ILTRVNRKVA 244 TEFESFSFDA254 TFHAKKQIPC264 IVSMLTKELY274 FYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .M60 or .M602 or .M603 or :3M60;style chemicals stick;color identity;select .A:63 or .A:64 or .A:65 or .A:120 or .A:121 or .A:122 or .A:123 or .A:161 or .A:162 or .A:163 or .A:165 or .A:166 or .B:204 or .B:205 or .B:206 or .B:207 or .B:208 or .B:209 or .B:214 or .B:248 or .B:249 or .B:250 or .B:256; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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SER63[A]
4.047
ARG64[A]
2.752
SER65[A]
2.685
SER120[A]
3.552
HIS121[A]
3.098
GLY122[A]
2.939
GLU123[A]
3.181
GLN161[A]
3.156
ALA162[A]
3.608
CYS163[A]
1.877
GLY165[A]
3.237
THR166[A]
3.401
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| Ligand Name: (3S)-3-({[(5S,10aS)-2-{(2S)-4-carboxy-2-[(phenylacetyl)amino]butyl}-1,3-dioxo-2,3,5,7,8,9,10,10a-octahydro-1H-[1,2,4]triazolo[1,2-a]cinnolin-5-yl]carbonyl}amino)-4-oxopentanoic acid | Ligand Info | |||||
| Structure Description | Caspase 3 Bound to a covalent inhibitor | PDB:3KJF | ||||
| Method | X-ray diffraction | Resolution | 2.00 Å | Mutation | No | [5] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAC163 RGTELDCGIE173 > Chain B SGVDDDMACH 185 KIPVDADFLY195 AYSTAPGYYS205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI 235 LTRVNRKVAT245 EFESFSFDAT255 FHAKKQIPCI265 VSMLTKELYF275 YH |
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B92 or .B922 or .B923 or :3B92;style chemicals stick;color identity;select .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .B:204 or .B:205 or .B:206 or .B:207 or .B:208 or .B:209 or .B:210 or .B:214 or .B:248 or .B:249 or .B:250 or .B:256; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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ARG64[A]
2.830
SER120[A]
3.805
HIS121[A]
3.154
GLY122[A]
2.962
GLN161[A]
3.015
ALA162[A]
4.014
CYS163[A]
1.804
TYR204[B]
3.605
SER205[B]
2.880
TRP206[B]
3.336
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| Ligand Name: 3-(2-{5-Tert-butyl-3-[(4-methyl-furazan-3-ylmethyl)-amino]-2-oxo-2H-pyrazin-1-YL}-butyrylamino)-5-(hexyl-methyl-amino)-4-oxo-pentanoic acid anion | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A PRYAZINONE INHIBITOR | PDB:1RHJ | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .PZN or .PZN2 or .PZN3 or :3PZN;style chemicals stick;color identity;select .A:176 or .A:179 or .A:236 or .A:237 or .A:238 or .A:239 or .A:283 or .A:284 or .A:285 or .A:287 or .A:288 or .A:290 or .B:338 or .B:339 or .B:340 or .B:341 or .B:342 or .B:343 or .B:348 or .B:381H or .B:381C or .B:381B or .B:381A; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET176[A]
4.553
ARG179[A]
2.719
SER236[A]
3.877
HIS237[A]
3.371
GLY238[A]
3.085
GLU239[A]
4.149
GLN283[A]
3.115
ALA284[A]
3.449
CYS285[A]
1.853
GLY287[A]
4.621
THR288[A]
4.045
LEU290[A]
4.988
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| Ligand Name: Methyl (3s)-3-[(Tert-Butoxycarbonyl)amino]-4-Oxopentanoate | Ligand Info | |||||
| Structure Description | Caspase-3 Binds Diverse P4 Residues in Peptides | PDB:3GJR | ||||
| Method | X-ray diffraction | Resolution | 2.20 Å | Mutation | No | [7] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 43 MGLCIIINNK53 NFHKSTGMTS63 RSGTDVDAAN73 LRETFRNLKY83 EVRNKNDLTR 93 EEIVELMRDV103 SKEDHSKRSS113 FVCVLLSHGE123 EGIIFGTNGP133 VDLKKITNFF 143 RGDRCRSLTG153 KPKLFIIQAC163 RGTELDCGIE173 T> Chain B KIPVEADFLY 195 AYSTAPGYYS205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI235 LTRVNRKVAT 245 EFESFSFDAT255 FHAKKQIPCI265 VSMLTKELYF275 YH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .DZE or .DZE2 or .DZE3 or :3DZE;style chemicals stick;color identity;select .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .B:204 or .B:205 or .B:206 or .B:207; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3S)-3-{[(5-Bromopyridin-3-YL)carbonyl]amino}-4-oxobutanoic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR | PDB:1RE1 | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NA3 or .NA32 or .NA33 or :3NA3;style chemicals stick;color identity;select .A:179 or .A:236 or .A:237 or .A:238 or .A:283 or .A:284 or .A:285 or .B:338 or .B:339 or .B:340 or .B:341; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 4-[5-(2-Carboxy-1-formyl-ethylcarbamoyl)-pyridin-3-YL]-benzoic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A NICOTINIC ACID ALDEHYDE INHIBITOR | PDB:1RHM | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .NA4 or .NA42 or .NA43 or :3NA4;style chemicals stick;color identity;select .A:179 or .A:236 or .A:237 or .A:238 or .A:283 or .A:284 or .A:285 or .B:338 or .B:339 or .B:340 or .B:341 or .B:381H or .B:381C; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3S)-3-[({(2S)-5-[(N-Acetyl-L-alpha-aspartyl)amino]-4-oxo-1,2,4,5,6,7-hexahydroazepino[3,2,1-HI]indol-2-YL}carbonyl)amino]-5-(benzylsulfanyl)-4-oxopentanoic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A 5,6,7 TRICYCLIC PEPTIDOMIMETIC INHIBITOR | PDB:1RHU | ||||
| Method | X-ray diffraction | Resolution | 2.51 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .3CY or .3CY2 or .3CY3 or :33CY;style chemicals stick;color identity;select .A:176 or .A:179 or .A:236 or .A:237 or .A:238 or .A:239 or .A:244 or .A:283 or .A:284 or .A:285 or .A:287 or .A:288 or .B:338 or .B:339 or .B:340 or .B:341 or .B:342 or .B:343 or .B:348 or .B:381H or .B:381B or .B:381C or .B:381A or .B:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET176[A]
3.885
ARG179[A]
2.752
SER236[A]
4.055
HIS237[A]
2.501
GLY238[A]
3.805
GLU239[A]
3.440
PHE244[A]
4.619
GLN283[A]
3.069
ALA284[A]
4.686
CYS285[A]
1.795
GLY287[A]
4.918
THR288[A]
3.353
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| Ligand Name: 1-Methyl-5-(2-phenoxymethyl-pyrrolidine-1-sulfonyl)-1h-indole-2,3-dione | Ligand Info | |||||
| Structure Description | THE 2.8 ANGSTROM CRYSTAL STRUCTURE OF CASPASE-3 (APOPAIN OR CPP32)IN COMPLEX WITH AN ISATIN SULFONAMIDE INHIBITOR. | PDB:1GFW | ||||
| Method | X-ray diffraction | Resolution | 2.80 Å | Mutation | No | [8] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIE> Chain B HKIPVDADFL 194 YAYSTAPGYY204 SWRNSKDGSW214 FIQSLCAMLK224 QYADKLEFMH234 ILTRVNRKVA 244 TEFESFSFDA254 TFHAKKQIPC264 IVSMLTKELY274 FYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .MSI or .MSI2 or .MSI3 or :3MSI;style chemicals stick;color identity;select .A:61 or .A:65 or .A:120 or .A:121 or .A:122 or .A:123 or .A:162 or .A:163 or .B:204 or .B:205 or .B:206 or .B:207 or .B:209 or .B:256; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: (3S)-5-[(2-Chloro-6-fluorobenzyl)sulfanyl]-3-{[N-({2-ethoxy-5-[(1E)-3-methoxy-3-oxoprop-1-enyl]phenyl}acetyl)-D-valyl]amino}-4-oxopentanoic acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A CINNAMIC ACID METHYL ESTER INHIBITOR | PDB:1RHR | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .CNE or .CNE2 or .CNE3 or :3CNE;style chemicals stick;color identity;select .A:176 or .A:179 or .A:236 or .A:237 or .A:238 or .A:239 or .A:283 or .A:284 or .A:285 or .A:287 or .A:288 or .B:338 or .B:339 or .B:340 or .B:341 or .B:342 or .B:348 or .B:381A or .B:381B or .B:381C or .B:381H or .B:381; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET176[A]
3.234
ARG179[A]
2.455
SER236[A]
3.867
HIS237[A]
2.541
GLY238[A]
2.799
GLU239[A]
3.325
GLN283[A]
4.047
ALA284[A]
4.963
CYS285[A]
1.831
GLY287[A]
3.112
THR288[A]
4.077
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| Ligand Name: 5-S-Benzyl-3-({n-[(5-Bromo-2-Methoxyphenyl)acetyl]-L-Valyl}amino)-2,3-Dideoxy-5-Thio-D-Erythro-Pentonic Acid | Ligand Info | |||||
| Structure Description | CRYSTAL STRUCTURE OF THE COMPLEX OF CASPASE-3 WITH A BROMOMETHOXYPHENYL INHIBITOR | PDB:1RHQ | ||||
| Method | X-ray diffraction | Resolution | 3.00 Å | Mutation | Yes | [6] |
| PDB Sequence |
> Chain A
DNSYKMDYPE 162 MGLCIIINNK171 NFHKSTGMTS178 RSGTDVDAAN188 LRETFRNLKY198 EVRNKNDLTR 208 EEIVELMRDV218 SKEDHSKRSS229 FVCVLLSHGE239 EGIIFGTNGP255 VDLKKITNFF 265 RGDRCRSLTG275 KPKLFIIQAC285 RGTELDCGIE295 > Chain B KIPVEADFLY 329 AYSTAPGYYS339 WRNSKDGSWF349 IQSLCAMLKQ359 YADKLEFMHI369 LTRVNRKVAT 379 EFESFSFDAT381G FHAKKQIPCI389 VSMLTKELYF400 Y
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .0ZZ or .0ZZ2 or .0ZZ3 or :30ZZ;style chemicals stick;color identity;select .A:176 or .A:177 or .A:179 or .A:236 or .A:237 or .A:238 or .A:239 or .A:244 or .A:283 or .A:284 or .A:285 or .A:287 or .A:288 or .B:338 or .B:339 or .B:340 or .B:341 or .B:381A or .B:381B or .B:381C or .B:381H or .B:381; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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MET176[A]
4.436
THR177[A]
4.804
ARG179[A]
2.635
SER236[A]
2.495
HIS237[A]
3.170
GLY238[A]
3.126
GLU239[A]
3.345
PHE244[A]
3.566
GLN283[A]
3.931
ALA284[A]
3.891
CYS285[A]
1.809
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| Ligand Name: Tosylphenylalanyl chloromethyl ketone | Ligand Info | |||||
| Structure Description | Caspase-3:CAS329306 | PDB:2XYG | ||||
| Method | X-ray diffraction | Resolution | 1.54 Å | Mutation | No | [9] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIET> Chain B HKIPVEADFL 194 YAYSTAPGYY204 SWRNSKDGSW214 FIQSLCAMLK224 QYADKLEFMH234 ILTRVNRKVA 244 TEFESFSFDA254 TFHAKKQIPC264 IVSMLTKELY274 FYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TQ8 or .TQ82 or .TQ83 or :3TQ8;style chemicals stick;color identity;select .A:59 or .A:60 or .A:61 or .A:62 or .A:121 or .A:122 or .A:123 or .A:128 or .A:163 or .A:165 or .A:166 or .B:204 or .B:205; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 2-Hydroxy-5-(2-mercapto-ethylsulfamoyl)-benzoic acid | Ligand Info | |||||
| Structure Description | Structure of Casp-3 with tethered salicylate | PDB:1NME | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [3] |
| PDB Sequence |
KIPVDADFLY
195 AYSTAPGYYS205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI235 LTRVNRKVAT 245 EFESFSFDAT255 FHAKKQIPCI265 VSMLTKELYF275 YH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .159 or .1592 or .1593 or :3159;style chemicals stick;color identity;select .B:204 or .B:206 or .B:207 or .B:208 or .B:209 or .B:214 or .B:248 or .B:249 or .B:250; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 3-(2-Mercapto-acetylamino)-4-oxo-pentanoic acid | Ligand Info | |||||
| Structure Description | Structure of Casp-3 with tethered salicylate | PDB:1NME | ||||
| Method | X-ray diffraction | Resolution | 1.60 Å | Mutation | No | [3] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIET> Chain B KIPVDADFLY 195 AYSTAPGYYS205 WRNSKDGSWF215 IQSLCAMLKQ225 YADKLEFMHI235 LTRVNRKVAT 245 EFESFSFDAT255 FHAKKQIPCI265 VSMLTKELYF275 YH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .158 or .1582 or .1583 or :3158;style chemicals stick;color identity;select .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .B:204 or .B:205 or .B:206 or .B:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: Z-L-Phe chloromethyl ketone | Ligand Info | |||||
| Structure Description | Caspase-3:CAS26049945 | PDB:2XYP | ||||
| Method | X-ray diffraction | Resolution | 1.86 Å | Mutation | No | [9] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIET> Chain B HKIPVEADFL 194 YAYSTAPGYY204 SWRNSKDGSW214 FIQSLCAMLK224 QYADKLEFMH234 ILTRVNRKVA 244 TEFESFSFDA254 TFHAKKQIPC264 IVSMLTKELY274 FYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .XVE or .XVE2 or .XVE3 or :3XVE;style chemicals stick;color identity;select .A:59 or .A:60 or .A:61 or .A:62 or .A:120 or .A:121 or .A:122 or .A:123 or .A:128 or .A:163 or .A:165 or .A:166 or .B:204 or .B:256; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Ligand Name: 5-Chloro-4-oxopentanoic acid | Ligand Info | |||||
| Structure Description | Caspase-3:CAS60254719 | PDB:2XYH | ||||
| Method | X-ray diffraction | Resolution | 1.89 Å | Mutation | No | [9] |
| PDB Sequence |
> Chain A
SGISLDNSYK 38 MDYPEMGLCI48 IINNKNFHKS58 TGMTSRSGTD68 VDAANLRETF78 RNLKYEVRNK 88 NDLTREEIVE98 LMRDVSKEDH108 SKRSSFVCVL118 LSHGEEGIIF128 GTNGPVDLKK 138 ITNFFRGDRC148 RSLTGKPKLF158 IIQACRGTEL168 DCGIET> Chain B HKIPVEADFL 194 YAYSTAPGYY204 SWRNSKDGSW214 FIQSLCAMLK224 QYADKLEFMH234 ILTRVNRKVA 244 TEFESFSFDA254 TFHAKKQIPC264 IVSMLTKELY274 FYH
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Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .TQ9 or .TQ92 or .TQ93 or :3TQ9;style chemicals stick;color identity;select .A:64 or .A:120 or .A:121 or .A:122 or .A:161 or .A:162 or .A:163 or .B:204 or .B:205 or .B:207; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Isoquinoline-1,3,4-trione derivatives inactivate caspase-3 by generation of reactive oxygen species. J Biol Chem. 2008 Oct 31;283(44):30205-15. | ||||
| REF 2 | 3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as potent non-peptidic inhibitors of caspase-3. Bioorg Med Chem. 2009 Nov 15;17(22):7755-68. | ||||
| REF 3 | In situ assembly of enzyme inhibitors using extended tethering. Nat Biotechnol. 2003 Mar;21(3):308-14. | ||||
| REF 4 | Exploring the S4 and S1 prime subsite specificities in caspase-3 with aza-peptide epoxide inhibitors. Biochemistry. 2006 Aug 1;45(30):9059-67. | ||||
| REF 5 | Kinetic and structural characterization of caspase-3 and caspase-8 inhibition by a novel class of irreversible inhibitors. Biochim Biophys Acta. 2010 Sep;1804(9):1817-31. | ||||
| REF 6 | Reducing the peptidyl features of caspase-3 inhibitors: a structural analysis. J Med Chem. 2004 May 6;47(10):2466-74. | ||||
| REF 7 | Caspase-3 binds diverse P4 residues in peptides as revealed by crystallography and structural modeling. Apoptosis. 2009 May;14(5):741-52. | ||||
| REF 8 | Potent and selective nonpeptide inhibitors of caspases 3 and 7 inhibit apoptosis and maintain cell functionality. J Biol Chem. 2000 May 26;275(21):16007-14. | ||||
| REF 9 | In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Aug 1;67(Pt 8):842-50. | ||||
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