Binding Site Information of Target
| Target General Information | Top | ||||
|---|---|---|---|---|---|
| Target ID | T14731 | Target Info | |||
| Target Name | NAD-dependent deacetylase sirtuin-1 (SIRT1) | ||||
| Synonyms | hSIRT1; hSIR2; SIR2L1; SIR2-like protein 1; Regulatory protein SIR2 homolog 1; NAD-dependent protein deacetylase sirtuin-1 | ||||
| Target Type | Clinical trial Target | ||||
| Gene Name | SIRT1 | ||||
| Biochemical Class | Carbon-nitrogen hydrolase | ||||
| UniProt ID | |||||
| Drug Binding Sites of Target | Top | |||||
|---|---|---|---|---|---|---|
| Ligand Name: Resveratrol | Ligand Info | |||||
| Structure Description | Crystal structure of SIRT1 in complex with resveratrol and an AMC-containing peptide | PDB:5BTR | ||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
DNLLFGDEII
153 TNGSDWTPRP180 RIGPYTFVQQ190 HLMIGTDPRT200 ILKDLLPETI210 PPPELDDMTL 220 WQIVINILSE230 PPKRKKRKDI240 NTIEDAVKLL250 QESKKIIVLT260 GAGVSVSSGI 270 PDFRSRDGIY280 ARLAVDFPDL290 PDPQAMFDIE300 YFRKDPRPFF310 KFAKEIYPGQ 320 FQPSLCHKFI330 ALSDKEGKLL340 RNYTQNIDTL350 EQVAGIQRII360 QCHGSFATAS 370 CLICKYKVDC380 EAVRGDIFNQ390 VVPRCPRCPA400 DEPLAIMKPE410 IVFFGENLPE 420 QFHRAMKYDK430 DEVDLLIVIG440 SSLKVRPVAL450 IPSSIPHEVP460 QILINREPLP 470 HLHFDVELLG480 DCDVIINELC490 HRLGGEYAKL500 SSNPVKLSEI510 TEQYLFLPPN 648 RYIFHGAEVY658
|
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|
|
THR209
3.360
PRO212
3.605
GLU214
4.582
PRO291
4.328
ASP292
2.270
GLN294
3.329
ALA295
3.460
ASP298
2.260
PHE414
3.593
LYS444
3.303
VAL445
3.906
LEU202
3.712
LEU206
3.637
THR209
4.689
ILE210
3.940
PRO211
3.149
PRO212
3.973
|
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| Ligand Name: Norleucine | Ligand Info | |||||
| Structure Description | SIRT1/Activator/Substrate Complex | PDB:4ZZJ | ||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 NGGSQYLFLP646 PNRYIFHGAE656 VYSD
|
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| Ligand Name: Carba-Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||||
| Structure Description | SIRT1/Activator/Substrate Complex | PDB:4ZZJ | ||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 NGGSQYLFLP646 PNRYIFHGAE656 VYSD
|
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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 .CNA or .CNA2 or .CNA3 or :3CNA;style chemicals stick;color identity;select .A:261 or .A:262 or .A:263 or .A:265 or .A:266 or .A:270 or .A:271 or .A:272 or .A:273 or .A:274 or .A:275 or .A:297 or .A:312 or .A:316 or .A:345 or .A:346 or .A:347 or .A:348 or .A:363 or .A:414 or .A:440 or .A:441 or .A:442 or .A:443 or .A:444 or .A:445 or .A:464 or .A:465 or .A:466 or .A:467 or .A:469 or .A:480 or .A:481 or .A:482 or .A:483 or .A:656; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY261
3.197
ALA262
2.816
GLY263
3.614
SER265
4.307
VAL266
3.433
ILE270
3.463
PRO271
3.288
ASP272
3.334
PHE273
3.163
ARG274
2.825
SER275
3.830
PHE297
3.418
PHE312
4.087
ILE316
3.558
GLN345
3.517
ASN346
3.040
ILE347
2.913
ASP348
3.014
|
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| Ligand Name: Nicotinamide-Adenine-Dinucleotide | Ligand Info | |||||
| Structure Description | Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog | PDB:4I5I | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
NTIEDAVKLL
250 QECKKIIVLT260 GAGVSVSCGI270 PDFRSRDGIY280 ARLAVDFPDL290 PDPQAMFDIE 300 YFRKDPRPFF310 KFAKEIYPGQ320 FQPSLCHKFI330 ALSDKEGKLL340 RNYTQNIDTL 350 EQVAGIQRII360 QCHGSFATAS370 CLICKYKVDC380 EAVRGDIFNQ390 VVPRCPRCPA 400 DEPLAIMKPE410 IVFFGENLPE420 QFHRAMKYDK430 DEVDLLIVIG440 SSLKVRPVAL 450 IPSSIPHEVP460 QILINREPLP470 HLHFDVELLG480 DCDVIINELC490 HRLGGEYAKL 500 CCNPVKLSEI510 TE
|
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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 .NAD or .NAD2 or .NAD3 or :3NAD;style chemicals stick;color identity;select .A:261 or .A:262 or .A:263 or .A:266 or .A:272 or .A:273 or .A:274 or .A:275 or .A:280 or .A:293 or .A:294 or .A:295 or .A:297 or .A:298 or .A:345 or .A:346 or .A:363 or .A:412 or .A:413 or .A:414 or .A:440 or .A:441 or .A:442 or .A:443 or .A:445 or .A:464 or .A:465 or .A:466 or .A:467 or .A:469 or .A:480 or .A:481 or .A:482; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY261
3.360
ALA262
2.807
GLY263
3.645
VAL266
3.531
ASP272
3.246
PHE273
2.794
ARG274
2.646
SER275
4.101
TYR280
2.295
PRO293
4.910
GLN294
2.673
ALA295
4.827
PHE297
3.145
ASP298
4.073
GLN345
3.236
ASN346
4.445
HIS363
2.702
|
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| Ligand Name: Adenosine-5-diphosphoribose | Ligand Info | |||||
| Structure Description | Structure of NAD-dependent protein deacetylase sirtuin-1 (closed state, 1.85 A) | PDB:4KXQ | ||||
| Method | X-ray diffraction | Resolution | 1.85 Å | Mutation | No | [4] |
| PDB Sequence |
> Chain A
HMRKKRKDIN 241 TIEDAVKLLQ251 ECKKIIVLTG261 AGVSVSCGIP271 DFRSRDGIYA281 RLAVDFPDLP 291 DPQAMFDIEY301 FRKDPRPFFK311 FAKEIYPGQF321 QPSLCHKFIA331 LSDKEGKLLR 341 NYTQNIDTLE351 QVAGIQRIIQ361 CHGSFATASC371 LICKYKVDCE381 AVRGDIFNQV 391 VPRCPRCPAD401 EPLAIMKPEI411 VFFGENLPEQ421 FHRAMKYDKD431 EVDLLIVIGS 441 SLKVRPVALI451 PSSIPHEVPQ461 ILINREPLPH471 LHFDVELLGD481 CDVIINELCH 491 RLGGEYAKLC501 CNPVKLSEI> Chain B GPHMGSQYLF 644 LPPNRYIFHG654 AEVYSD
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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 .APR or .APR2 or .APR3 or :3APR;style chemicals stick;color identity;select .A:261 or .A:262 or .A:263 or .A:266 or .A:267 or .A:272 or .A:273 or .A:274 or .A:275 or .A:280 or .A:294 or .A:297 or .A:345 or .A:346 or .A:347 or .A:363 or .A:412 or .A:414 or .A:439 or .A:440 or .A:441 or .A:442 or .A:443 or .A:444 or .A:445 or .A:464 or .A:465 or .A:466 or .A:467 or .A:469 or .A:480 or .A:481 or .A:482 or .A:483 or .A:485 or .B:656; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
GLY261[A]
2.762
ALA262[A]
2.024
GLY263[A]
2.786
VAL266[A]
2.594
SER267[A]
3.868
ASP272[A]
2.410
PHE273[A]
2.204
ARG274[A]
2.021
SER275[A]
3.019
TYR280[A]
1.873
GLN294[A]
4.931
PHE297[A]
4.235
GLN345[A]
2.658
ASN346[A]
4.293
ILE347[A]
4.643
HIS363[A]
2.059
VAL412[A]
4.454
PHE414[A]
2.438
ILE439[A]
4.655
GLY440[A]
2.878
SER441[A]
1.912
SER442[A]
2.380
LEU443[A]
3.455
LYS444[A]
4.138
VAL445[A]
2.225
ILE464[A]
3.840
ASN465[A]
2.164
ARG466[A]
1.959
GLU467[A]
2.157
LEU469[A]
4.061
GLY480[A]
2.784
ASP481[A]
2.622
CYS482[A]
2.047
ASP483[A]
3.961
ILE485[A]
4.638
GLU656[B]
4.436
|
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: N~6~-acetyl-N-(4-methyl-2-oxo-2H-chromen-7-yl)-L-lysinamide | Ligand Info | |||||
| Structure Description | Crystal structure of SIRT1 in complex with resveratrol and an AMC-containing peptide | PDB:5BTR | ||||
| Method | X-ray diffraction | Resolution | 3.20 Å | Mutation | Yes | [1] |
| PDB Sequence |
DNLLFGDEII
153 TNGSDWTPRP180 RIGPYTFVQQ190 HLMIGTDPRT200 ILKDLLPETI210 PPPELDDMTL 220 WQIVINILSE230 PPKRKKRKDI240 NTIEDAVKLL250 QESKKIIVLT260 GAGVSVSSGI 270 PDFRSRDGIY280 ARLAVDFPDL290 PDPQAMFDIE300 YFRKDPRPFF310 KFAKEIYPGQ 320 FQPSLCHKFI330 ALSDKEGKLL340 RNYTQNIDTL350 EQVAGIQRII360 QCHGSFATAS 370 CLICKYKVDC380 EAVRGDIFNQ390 VVPRCPRCPA400 DEPLAIMKPE410 IVFFGENLPE 420 QFHRAMKYDK430 DEVDLLIVIG440 SSLKVRPVAL450 IPSSIPHEVP460 QILINREPLP 470 HLHFDVELLG480 DCDVIINELC490 HRLGGEYAKL500 SSNPVKLSEI510 TEQYLFLPPN 648 RYIFHGAEVY658
|
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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 .FDL or .FDL2 or .FDL3 or :3FDL;style chemicals stick;color identity;select .A:206 or .A:209 or .A:210 or .A:211 or .A:212 or .A:274 or .A:297 or .A:347 or .A:363 or .A:412 or .A:413 or .A:414 or .A:415 or .A:416 or .A:417 or .A:418 or .A:444 or .A:445 or .A:446 or .A:447; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
LEU206
3.635
THR209
3.575
ILE210
4.131
PRO211
4.770
PRO212
4.116
ARG274
3.226
PHE297
3.466
ILE347
4.615
HIS363
3.394
VAL412
2.678
|
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| Ligand Name: (3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4-carboxamide | Ligand Info | |||||
| Structure Description | SIRT1/Activator/Inhibitor Complex | PDB:4ZZI | ||||
| Method | X-ray diffraction | Resolution | 2.73 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 QYLFLPPNRY650 IFHGA
|
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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 .4TQ or .4TQ2 or .4TQ3 or :34TQ;style chemicals stick;color identity;select .A:202 or .A:206 or .A:209 or .A:210 or .A:211 or .A:212 or .A:215 or .A:219 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| Click to View More Binding Site Information of This Target and Ligand Pair | ||||||
| Ligand Name: 4-(4-{2-[(Methylsulfonyl)amino]ethyl}piperidin-1-Yl)thieno[3,2-D]pyrimidine-6-Carboxamide | Ligand Info | |||||
| Structure Description | SIRT1/Activator/Inhibitor Complex | PDB:4ZZI | ||||
| Method | X-ray diffraction | Resolution | 2.73 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 QYLFLPPNRY650 IFHGA
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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 .1NS or .1NS2 or .1NS3 or :31NS;style chemicals stick;color identity;select .A:262 or .A:265 or .A:270 or .A:271 or .A:272 or .A:273 or .A:274 or .A:280 or .A:297 or .A:345 or .A:346 or .A:347 or .A:348 or .A:363 or .A:411 or .A:412 or .A:413 or .A:414 or .A:418 or .A:445; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
ALA262
3.453
SER265
3.704
ILE270
3.381
PRO271
4.421
ASP272
3.355
PHE273
3.065
ARG274
3.838
TYR280
3.971
PHE297
3.507
GLN345
3.404
|
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| Ligand Name: N6-Acetyl-L-lysine | Ligand Info | |||||
| Structure Description | SIRT1/Activator/Substrate Complex | PDB:4ZZJ | ||||
| Method | X-ray diffraction | Resolution | 2.74 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 NGGSQYLFLP646 PNRYIFHGAE656 VYSD
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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 .ALY or .ALY2 or .ALY3 or :3ALY;style chemicals stick;color identity;select .A:297 or .A:347 or .A:363 or .A:411 or .A:412 or .A:413 or .A:414 or .A:415 or .A:416 or .A:418 or .A:445 or .A:446 or .A:447; 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)-N-[3-(1,3-Oxazol-5-Yl)phenyl]-7-[3-(Trifluoromethyl)phenyl]-3,4-Dihydro-1,4-Methanopyrido[2,3-B][1,4]diazepine-5(2h)-Carboxamide | Ligand Info | |||||
| Structure Description | SIRT1/Activator Complex | PDB:4ZZH | ||||
| Method | X-ray diffraction | Resolution | 3.10 Å | Mutation | No | [2] |
| PDB Sequence |
GPYTFVQQHL
192 MIGTDPRTIL202 KDLLPETIPP212 PELDDMTLWQ222 IVINILSEPP232 KRKKRKDINT 242 IEDAVKLLQE252 CKKIIVLTGA262 GVSVSCGIPD272 FRSRDGIYAR282 LAVDFPDLPD 292 PQAMFDIEYF302 RKDPRPFFKF312 AKEIYPGQFQ322 PSLCHKFIAL332 SDKEGKLLRN 342 YTQNIDTLEQ352 VAGIQRIIQC362 HGSFATASCL372 ICKYKVDCEA382 VRGDIFNQVV 392 PRCPRCPADE402 PLAIMKPEIV412 FFGENLPEQF422 HRAMKYDKDE432 VDLLIVIGSS 442 LKVRPVALIP452 SSIPHEVPQI462 LINREPLPHL472 HFDVELLGDC482 DVIINELCHR 492 LGGEYAKLCC502 SQYLFLPPNR649 YIFHGAEVY
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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 .4TO or .4TO2 or .4TO3 or :34TO;style chemicals stick;color identity;select .A:206 or .A:209 or .A:211 or .A:212 or .A:215 or .A:219 or .A:222 or .A:223 or .A:226 or .A:227 or .A:230; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
|
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| Ligand Name: (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide | Ligand Info | |||||
| Structure Description | Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog | PDB:4I5I | ||||
| Method | X-ray diffraction | Resolution | 2.50 Å | Mutation | No | [3] |
| PDB Sequence |
NTIEDAVKLL
250 QECKKIIVLT260 GAGVSVSCGI270 PDFRSRDGIY280 ARLAVDFPDL290 PDPQAMFDIE 300 YFRKDPRPFF310 KFAKEIYPGQ320 FQPSLCHKFI330 ALSDKEGKLL340 RNYTQNIDTL 350 EQVAGIQRII360 QCHGSFATAS370 CLICKYKVDC380 EAVRGDIFNQ390 VVPRCPRCPA 400 DEPLAIMKPE410 IVFFGENLPE420 QFHRAMKYDK430 DEVDLLIVIG440 SSLKVRPVAL 450 IPSSIPHEVP460 QILINREPLP470 HLHFDVELLG480 DCDVIINELC490 HRLGGEYAKL 500 CCNPVKLSEI510 TE
|
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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 .4I5 or .4I52 or .4I53 or :34I5;style chemicals stick;color identity;select .A:262 or .A:265 or .A:270 or .A:271 or .A:273 or .A:279 or .A:297 or .A:316 or .A:345 or .A:346 or .A:347 or .A:348 or .A:363 or .A:411 or .A:412 or .A:413; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
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| References | Top | ||||
|---|---|---|---|---|---|
| REF 1 | Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol. Genes Dev. 2015 Jun 15;29(12):1316-25. | ||||
| REF 2 | Crystallographic structure of a small molecule SIRT1 activator-enzyme complex. Nat Commun. 2015 Jul 2;6:7645. | ||||
| REF 3 | The 2.5 ? crystal structure of the SIRT1 catalytic domain bound to nicotinamide adenine dinucleotide (NAD+) and an indole (EX527 analogue) reveals a novel mechanism of histone deacetylase inhibition. J Med Chem. 2013 Feb 14;56(3):963-9. | ||||
| REF 4 | Structural and functional analysis of human SIRT1. J Mol Biol. 2014 Feb 6;426(3):526-41. | ||||
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