Receptor
PDB id Resolution Class Description Source Keywords
5g4c 2.1 Å EC: 3.5.1.- HUMAN SIRT2 CATALYSE SHORT CHAIN FATTY ACYL LYSINE HOMO SAPIENS HYDROLASE SIRTUIN CLASS I HDACS NAD DEPENDENT ADPR ACYL
Ref.: SIRT2 REVERSES 4-OXONONANOYL LYSINE MODIFICATION ON HISTONES. J. AM. CHEM. SOC. V. 138 12304 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CNA B:1356;
A:1357;
 Valid;
Valid;
 none;
none;
 submit data
662.46 C22 H30 N7 O13 P2 c1cc(...
ARG ALA ALA 6G4 THR F:1;
E:1;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.02;
Atoms found LESS than expected: % Diff = 0.02;
 Kd = 13.7 uM
685.868 n/a O=C(N...
ZN A:1356;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DY5 1.95 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH A SIRREAL P FRAGMENT HOMO SAPIENS HYDROLASE HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE-BASED DEVELOPMENT OF AN AFFINITY PROBE FO 2. ANGEW.CHEM.INT.ED.ENGL. V. 55 2252 2016
Members (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 4RMG ic50 = 0.14 uM 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
2 4R8M - PRO LYS LYS THR GLY 3LX n/a n/a
3 4RMH - 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
4 5DY4 ic50 = 0.21 uM 5GN C22 H19 Br N4 O S2 Cc1cc(nc(n....
5 4Y6L - THR ALA ARG MYK SER THR GLY n/a n/a
6 5MAR ic50 = 41.2 uM 7KE C11 H11 Cl N2 O2 c1cc(ccc1c....
7 3ZGV - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
8 4Y6O - LEU PRO LYS MYK THR GLY GLY n/a n/a
9 4RMJ - NCA C6 H6 N2 O c1cc(cnc1)....
10 5DY5 ic50 = 0.163 uM 5GR C28 H27 N7 O2 S2 Cc1cc(nc(n....
11 5D7P ic50 = 20 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
12 4RMI - 3TK C18 H18 N4 O S2 Cc1cc(nc(n....
13 5Y0Z ic50 = 0.46 uM 8K9 C30 H44 N2 O3 CCC(C)(C)c....
14 5YQN ic50 = 93.7 uM L55 C26 H26 N6 O3 S Cc1cc(nc(n....
15 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
16 6QCN - QUE C15 H10 O7 c1cc(c(cc1....
17 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
18 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
19 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
20 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
21 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
22 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
23 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
70% Homology Family (23)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 4RMG ic50 = 0.14 uM 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
2 4R8M - PRO LYS LYS THR GLY 3LX n/a n/a
3 4RMH - 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
4 5DY4 ic50 = 0.21 uM 5GN C22 H19 Br N4 O S2 Cc1cc(nc(n....
5 4Y6L - THR ALA ARG MYK SER THR GLY n/a n/a
6 5MAR ic50 = 41.2 uM 7KE C11 H11 Cl N2 O2 c1cc(ccc1c....
7 3ZGV - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
8 4Y6O - LEU PRO LYS MYK THR GLY GLY n/a n/a
9 4RMJ - NCA C6 H6 N2 O c1cc(cnc1)....
10 5DY5 ic50 = 0.163 uM 5GR C28 H27 N7 O2 S2 Cc1cc(nc(n....
11 5D7P ic50 = 20 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
12 4RMI - 3TK C18 H18 N4 O S2 Cc1cc(nc(n....
13 5Y0Z ic50 = 0.46 uM 8K9 C30 H44 N2 O3 CCC(C)(C)c....
14 5YQN ic50 = 93.7 uM L55 C26 H26 N6 O3 S Cc1cc(nc(n....
15 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
16 6QCN - QUE C15 H10 O7 c1cc(c(cc1....
17 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
18 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
19 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
20 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
21 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
22 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
23 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1SZD Kd = 29.16 uM APR C15 H23 N5 O14 P2 c1nc(c2c(n....
2 1Q1A - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
3 1SZC - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
4 4RMG ic50 = 0.14 uM 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
5 4R8M - PRO LYS LYS THR GLY 3LX n/a n/a
6 4RMH - 3TE C22 H20 N4 O S2 Cc1cc(nc(n....
7 5DY4 ic50 = 0.21 uM 5GN C22 H19 Br N4 O S2 Cc1cc(nc(n....
8 4Y6L - THR ALA ARG MYK SER THR GLY n/a n/a
9 5MAR ic50 = 41.2 uM 7KE C11 H11 Cl N2 O2 c1cc(ccc1c....
10 3ZGV - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
11 4Y6O - LEU PRO LYS MYK THR GLY GLY n/a n/a
12 4RMJ - NCA C6 H6 N2 O c1cc(cnc1)....
13 5DY5 ic50 = 0.163 uM 5GR C28 H27 N7 O2 S2 Cc1cc(nc(n....
14 5D7P ic50 = 20 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
15 4RMI - 3TK C18 H18 N4 O S2 Cc1cc(nc(n....
16 5Y0Z ic50 = 0.46 uM 8K9 C30 H44 N2 O3 CCC(C)(C)c....
17 5YQN ic50 = 93.7 uM L55 C26 H26 N6 O3 S Cc1cc(nc(n....
18 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
19 6QCN - QUE C15 H10 O7 c1cc(c(cc1....
20 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
21 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
22 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
23 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
24 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
25 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
26 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
27 4FZ3 - ACE ARG HIS LYS ALY MCM n/a n/a
28 4JT9 ic50 = 0.0072 uM 1NS C15 H21 N5 O3 S2 CS(=O)(=O)....
29 5BWO - PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP n/a n/a
30 4JT8 ic50 = 0.033 uM 1NR C19 H27 N5 O2 S CC(C)(C)C(....
31 4BV3 Kd = 16.5 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
32 4BVH - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
33 4C7B - ARG HIS LYS FDL n/a n/a
34 4C78 - BVB C14 H11 Br O2 c1cc(ccc1/....
35 5BWN - GLN THR ALA ARG MYK SER THR GLY GLY TRP n/a n/a
36 4BN4 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
37 4JSR ic50 = 0.004 uM 1NQ C22 H26 N6 O3 S2 CCNC(=O)c1....
38 4BVE - THR ARG SER GLY FZN VAL MET ARG ARG LEU n/a n/a
39 4BVB - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
40 4FVT - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
41 4I5I - 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: CNA; Similar ligands found: 274
No: Ligand ECFP6 Tc MDL keys Tc
1 CNA 1 1
2 DND 0.644068 0.972973
3 NAD 0.642276 0.972603
4 A2D 0.62 0.958904
5 BA3 0.607843 0.958904
6 NAD IBO 0.606557 0.958904
7 NAD TDB 0.606557 0.958904
8 A3D 0.606299 0.959459
9 B4P 0.601942 0.958904
10 AP5 0.601942 0.958904
11 DQV 0.591667 0.972603
12 M33 0.590476 0.92
13 ATP 0.584906 0.932432
14 HEJ 0.584906 0.932432
15 5FA 0.579439 0.932432
16 AR6 0.579439 0.932432
17 APR 0.579439 0.932432
18 AQP 0.579439 0.932432
19 3OD 0.577586 0.933333
20 AGS 0.574074 0.884615
21 OAD 0.573913 0.933333
22 8LE 0.572727 0.884615
23 ADP 0.571429 0.932432
24 ACP 0.570093 0.907895
25 KG4 0.570093 0.933333
26 8LQ 0.566372 0.896104
27 AN2 0.566038 0.92
28 AT4 0.566038 0.896104
29 OOB 0.561404 0.945946
30 CA0 0.560748 0.933333
31 AD9 0.559633 0.907895
32 A1R 0.556522 0.897436
33 A3R 0.556522 0.897436
34 QA7 0.552632 0.884615
35 ACQ 0.54955 0.907895
36 9X8 0.547009 0.884615
37 5AL 0.544643 0.92
38 HQG 0.54386 0.92
39 45A 0.542857 0.881579
40 ABM 0.542857 0.881579
41 GTA 0.540323 0.9
42 NAX 0.539683 0.911392
43 A22 0.53913 0.945946
44 DLL 0.538462 0.945946
45 JNT 0.538462 0.907895
46 00A 0.538462 0.897436
47 1ZZ 0.537815 0.831325
48 PRX 0.536364 0.858974
49 ANP 0.535714 0.907895
50 6YZ 0.535088 0.907895
51 8LH 0.535088 0.896104
52 9JJ 0.532895 0.9
53 ADX 0.53211 0.841463
54 AMP NAD 0.530303 0.945946
55 WAQ 0.529412 0.873418
56 AMP 0.528846 0.905405
57 A 0.528846 0.905405
58 TXD 0.527559 0.922078
59 6V0 0.527559 0.910256
60 NAI 0.527559 0.922078
61 50T 0.527273 0.894737
62 ATF 0.526316 0.896104
63 B5M 0.52459 0.909091
64 OMR 0.523438 0.843373
65 TXE 0.523438 0.922078
66 NAP 0.521739 0.959459
67 SRP 0.521739 0.921053
68 8QN 0.521368 0.92
69 3UK 0.521008 0.933333
70 NHD 0.518797 0.945946
71 4AD 0.516949 0.96
72 PAJ 0.516949 0.875
73 ADQ 0.516949 0.933333
74 B5V 0.516667 0.921053
75 9SN 0.516393 0.886076
76 NAQ 0.514493 0.910256
77 AHX 0.512605 0.910256
78 KMQ 0.512195 0.896104
79 F2R 0.511278 0.855422
80 NFD 0.511111 0.922078
81 ZID 0.510791 0.959459
82 NAD BBN 0.510067 0.878049
83 AMP MG 0.509434 0.917808
84 SON 0.509091 0.896104
85 APC 0.508929 0.896104
86 5SV 0.508475 0.817073
87 25L 0.508197 0.945946
88 48N 0.507812 0.886076
89 NAE 0.507246 0.934211
90 A12 0.504587 0.896104
91 AP2 0.504587 0.896104
92 AMO 0.504202 0.946667
93 PR8 0.504132 0.864198
94 DZD 0.503704 0.898734
95 NAD CJ3 0.503311 0.847059
96 PTJ 0.5 0.8625
97 TXA 0.5 0.921053
98 FYA 0.5 0.92
99 BIS 0.5 0.873418
100 ME8 0.5 0.853659
101 B5Y 0.5 0.909091
102 FA5 0.5 0.946667
103 T5A 0.496241 0.878049
104 L3W 0.496183 0.921053
105 8ID 0.496183 0.923077
106 AP0 0.496183 0.886076
107 9ZA 0.495798 0.873418
108 9ZD 0.495798 0.873418
109 TAT 0.495652 0.896104
110 T99 0.495652 0.896104
111 GAP 0.495652 0.907895
112 ADP MG 0.495495 0.931507
113 ADP BEF 0.495495 0.931507
114 SRA 0.495327 0.858974
115 NA0 0.492958 0.946667
116 A4P 0.492424 0.857143
117 UP5 0.492308 0.934211
118 4UV 0.492063 0.909091
119 LAD 0.491803 0.875
120 V2G 0.491379 0.8625
121 APC MG 0.491228 0.906667
122 AU1 0.491071 0.907895
123 LAQ 0.488372 0.831325
124 G3A 0.488189 0.910256
125 NB8 0.487805 0.910256
126 DAL AMP 0.487395 0.92
127 N01 0.485507 0.945946
128 COD 0.485294 0.825581
129 G5P 0.484375 0.910256
130 4UU 0.484375 0.909091
131 AFH 0.484375 0.875
132 XAH 0.484127 0.853659
133 25A 0.483333 0.932432
134 OZV 0.483333 0.932432
135 NDC 0.482993 0.910256
136 EAD 0.482517 0.911392
137 4UW 0.480916 0.875
138 NDE 0.479452 0.946667
139 ADV 0.478261 0.896104
140 ADP PO3 0.478261 0.931507
141 80F 0.478261 0.878049
142 RBY 0.478261 0.896104
143 ATP MG 0.478261 0.931507
144 NJP 0.477941 0.96
145 IOT 0.477612 0.823529
146 NAD NDT 0.475 0.739583
147 VO4 ADP 0.474576 0.907895
148 BEF ADP 0.474138 0.906667
149 139 0.474074 0.911392
150 ADJ 0.474074 0.865854
151 4TC 0.473684 0.910256
152 MYR AMP 0.472 0.831325
153 P1H 0.469388 0.888889
154 NGD 0.466667 0.923077
155 TYM 0.466165 0.946667
156 MAP 0.46281 0.884615
157 ANP MG 0.462185 0.92
158 ALF ADP 0.462185 0.860759
159 YLP 0.462121 0.833333
160 BT5 0.460432 0.823529
161 NAJ 0.459854 0.945946
162 M24 0.457746 0.864198
163 TAP 0.455172 0.897436
164 YLC 0.451852 0.853659
165 YLB 0.451852 0.833333
166 7MD 0.450382 0.876543
167 GA7 0.450382 0.896104
168 JSQ 0.449153 0.884615
169 HFD 0.449153 0.884615
170 ADP BMA 0.448 0.933333
171 AMP DBH 0.446154 0.907895
172 LMS 0.445455 0.797619
173 D4F 0.444444 0.876543
174 FB0 0.443709 0.797753
175 NAJ PZO 0.443662 0.886076
176 AHZ 0.443609 0.831325
177 0WD 0.442857 0.910256
178 A2R 0.442623 0.92
179 VMS 0.442623 0.781609
180 54H 0.442623 0.781609
181 7MC 0.441176 0.855422
182 PAP 0.440678 0.918919
183 7D4 0.439655 0.846154
184 ITT 0.439655 0.88
185 ARG AMP 0.439394 0.843373
186 8X1 0.439024 0.766667
187 TSB 0.439024 0.811765
188 AYB 0.438849 0.823529
189 A5A 0.438017 0.8
190 YLY 0.4375 0.823529
191 AOC 0.4375 0.789474
192 G5A 0.436975 0.793103
193 TAD 0.43609 0.875
194 AVV 0.435484 0.8625
195 5AS 0.434783 0.752809
196 3AT 0.433333 0.906667
197 BTX 0.432624 0.833333
198 2A5 0.432203 0.858974
199 LSS 0.432 0.775281
200 DSZ 0.432 0.813953
201 YLA 0.431655 0.833333
202 NPW 0.431655 0.9
203 52H 0.430894 0.772727
204 ATP A 0.430769 0.945205
205 ATP A A A 0.430769 0.945205
206 UPA 0.430657 0.922078
207 6AD 0.429752 0.851852
208 9K8 0.429688 0.728261
209 LPA AMP 0.42963 0.831325
210 N0B 0.428571 0.855422
211 ATR 0.428571 0.905405
212 NVA LMS 0.428571 0.786517
213 53H 0.427419 0.772727
214 6FA 0.425806 0.855422
215 ODP 0.425532 0.923077
216 LEU LMS 0.425197 0.764045
217 NA7 0.425197 0.896104
218 ALF ADP 3PG 0.423358 0.851852
219 SSA 0.422764 0.813953
220 MTA 0.422018 0.74359
221 P5A 0.421875 0.758242
222 NDO 0.421769 0.933333
223 NDP 0.421429 0.910256
224 NSS 0.420635 0.835294
225 FAS 0.420382 0.865854
226 FAD 0.420382 0.865854
227 8PZ 0.419847 0.835294
228 5N5 0.419048 0.786667
229 JB6 0.418605 0.873418
230 TXP 0.41844 0.910256
231 NZQ 0.41844 0.898734
232 7D3 0.417391 0.846154
233 EP4 0.416667 0.725
234 B1U 0.416667 0.769231
235 5CA 0.416 0.813953
236 5CD 0.415094 0.773333
237 3DH 0.414414 0.74359
238 A3P 0.413793 0.905405
239 ADN 0.413462 0.810811
240 RAB 0.413462 0.810811
241 XYA 0.413462 0.810811
242 AF3 ADP 3PG 0.413043 0.851852
243 DTA 0.412844 0.779221
244 4TA 0.412587 0.865854
245 NAJ PYZ 0.412162 0.843373
246 CUU 0.411765 0.906667
247 SFD 0.411392 0.747368
248 3AM 0.410714 0.866667
249 F2N 0.410714 0.827586
250 FDA 0.410256 0.825581
251 62F 0.409938 0.853659
252 FNK 0.409938 0.818182
253 DTP 0.409836 0.87013
254 AR6 AR6 0.407407 0.932432
255 P5F 0.407186 0.837209
256 PPS 0.406504 0.819277
257 ARU 0.40625 0.807229
258 YSA 0.406015 0.813953
259 AV2 0.403226 0.857143
260 K3E 0.402985 0.78481
261 649 0.402878 0.777778
262 XNP 0.402778 0.8875
263 A4D 0.401869 0.786667
264 DCA 0.401361 0.816092
265 ETB 0.401361 0.825581
266 5X8 0.4 0.779221
267 KAA 0.4 0.766667
268 V47 0.4 0.8
269 GSU 0.4 0.793103
270 38V 0.4 0.876543
271 M2T 0.4 0.728395
272 SMM 0.4 0.72093
273 H1Q 0.4 0.893333
274 FA9 0.4 0.878049
Ligand no: 2; Ligand: ARG ALA ALA 6G4 THR; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG ALA ALA 6G4 THR 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: CNA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: ARG ALA ALA 6G4 THR; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DY5; Ligand: 5GR; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5dy5.bio2) has 61 residues
No: Leader PDB Ligand Sequence Similarity
1 5OCQ CIT 4.21053
Pocket No.: 2; Query (leader) PDB : 5DY5; Ligand: 5GR; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 5dy5.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 5OCQ CIT 4.21053
Pocket No.: 3; Query (leader) PDB : 5DY5; Ligand: 5GR; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dy5.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback