Target Binding Site Detail

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Target General Information
Ligand General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T91959 Target Info
Target Name NAD-dependent deacetylase sirtuin-3 (SIRT3)
Synonyms hSIRT3; SIR2L3; SIR2-like protein 3; Regulatory protein SIR2 homolog 3
Target Type Literature-reported Target
Gene Name SIRT3
Biochemical Class Sirtuin family. Class I subfamily
UniProt ID
SIR3_HUMAN
Ligand General Information  Top
Ligand Name Adenosine-5-diphosphoribose Ligand Info
Canonical SMILES C1=NC(=C2C(=N1)N(C=N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
InChI 1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
InChIKey SRNWOUGRCWSEMX-ZQSHOCFMSA-N
PubChem Compound ID 447048
Drug Binding Sites of Target  Top
PDB ID: 4BN4      Structure of human SIRT3 in complex with ADP-ribose
Method X-ray diffraction Resolution 1.30 Å Mutation No [1]
PDB Sequence
GKLSLQDVAE
130
LIRARACQRV
140
VVMVGAGIST
150
PSGIPDFRSP
160
GSGLYSNLQQ
170

YDLPYPEAIF
180
ELPFFFHNPK
190
PFFTLAKELY
200
PGNYKPNVTH
210
YFLRLLHDKG
220

LLLRLYTQNI
230
DGLERVSGIP
240
ASKLVEAHGT
250
FASATCTVCQ
260
RPFPGEDIRA
270

DVMADRVPRC
280
PVCTGVVKPD
290
IVFFGEPLPQ
300
RFLLHVVDFP
310
MADLLLILGT
320

SLEVEPFASL
330
TEAVRSSVPR
340
LLINRDLVGP
350
LAWHPRSRDV
360
AQLGDVVHGV
370

ESLVELLGWT
380
EEMRDLVQRE
390
TG
Residue
Distance (Å)
GLY145
2.597
ALA146
2.041
GLY147
2.341
THR150
1.890
PRO151
3.367
ASP156
2.102
PHE157
2.166
ARG158
1.914
SER159
3.139
TYR165
2.267
GLU177
4.133
PHE180
3.448
GLN228
2.537
ASN229
3.676
ILE230
4.520
HIS248
2.158
Residue
Distance (Å)
PHE294
3.663
GLY319
3.002
THR320
2.483
SER321
2.191
LEU322
3.546
GLU323
4.216
VAL324
2.670
ILE343
4.586
ASN344
2.047
ARG345
2.369
ASP346
3.494
VAL348
3.442
GLY364
2.395
ASP365
2.138
VAL366
2.201
VAL367
3.980
PDB ID: 4BVB      CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH THE INHIBITOR EX-527 AND ADP-RIBOSE
Method X-ray diffraction Resolution 2.00 Å Mutation No [2]
PDB Sequence
KLSLQDVAEL
131
IRARACQRVV
141
VMVGAGISTP
151
SGIPDFRSPG
161
SGLYSNLQQY
171

DLPYPEAIFE
181
LPFFFHNPKP
191
FFTLAKELYP
201
GNYKPNVTHY
211
FLRLLHDKGL
221

LLRLYTQNID
231
GLERVSGIPA
241
SKLVEAHGTF
251
ASATCTVCQR
261
PFPGEDIRAD
271

VMADRVPRCP
281
VCTGVVKPDI
291
VFFGEPLPQR
301
FLLHVVDFPM
311
ADLLLILGTS
321

LEVEPFASLT
331
EAVRSSVPRL
341
LINRDLVGPL
351
AWHPRSRDVA
361
QLGDVVHGVE
371

SLVELLGWTE
381
EMRDLVQRET
391
GKL
Residue
Distance (Å)
GLY145
3.247
ALA146
2.716
GLY147
3.350
THR150
2.935
PRO151
4.279
ASP156
3.148
PHE157
2.804
ARG158
2.673
SER159
3.936
TYR165
4.458
GLN228
3.118
ASN229
4.266
HIS248
2.745
PHE294
2.895
Residue
Distance (Å)
GLY319
3.466
THR320
2.640
SER321
2.685
LEU322
4.127
GLU323
4.845
VAL324
3.404
ASN344
3.087
ARG345
2.903
ASP346
3.653
VAL348
4.567
GLY364
3.252
ASP365
3.329
VAL366
2.804
References  Top
REF 1 Structures of human sirtuin 3 complexes with ADP-ribose and with carba-NAD+ and SRT1720: binding details and inhibition mechanism. Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1423-32.
REF 2 Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):E2772-81.

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