Receptor
PDB id Resolution Class Description Source Keywords
3RIY 1.55 Å EC: 3.5.1.- SIRT5 IS AN NAD-DEPENDENT PROTEIN LYSINE DEMALONYLASE AND DESUCCINYLASE HOMO SAPIENS DESUCCINYLASE DEMALONYLASE POSTTRANSLATIONAL MODIFICATIONBINDING DOMAIN ROSSMANN FOLD DOMAIN HYDROLASE
Ref.: SIRT5 IS A NAD-DEPENDENT PROTEIN LYSINE DEMALONYLAS DESUCCINYLASE SCIENCE V. 334 806 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAD A:2001;
B:2002;
Valid;
Valid;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
ZN A:1001;
B:1002;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RIY 1.55 Å EC: 3.5.1.- SIRT5 IS AN NAD-DEPENDENT PROTEIN LYSINE DEMALONYLASE AND DESUCCINYLASE HOMO SAPIENS DESUCCINYLASE DEMALONYLASE POSTTRANSLATIONAL MODIFICATIONBINDING DOMAIN ROSSMANN FOLD DOMAIN HYDROLASE
Ref.: SIRT5 IS A NAD-DEPENDENT PROTEIN LYSINE DEMALONYLAS DESUCCINYLASE SCIENCE V. 334 806 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 3RIY - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 3RIY - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 3RIY - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAD; Similar ligands found: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RIY; Ligand: NAD; Similar sites found: 146
This union binding pocket(no: 1) in the query (biounit: 3riy.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IF4 BEF 0.01871 0.41929 0.961538
2 3BRE C2E 0.02299 0.41337 1.0989
3 1IM8 SAI 0.01019 0.40223 1.22951
4 5U5G 7VD 0.04369 0.40183 1.4652
5 1P77 ATR 0.0332 0.40828 1.47059
6 2PW0 TRC 0.01425 0.42931 1.8315
7 1QPR PHT 0.02198 0.42086 1.8315
8 1N4K I3P 0.02732 0.41152 1.8315
9 2PT9 2MH 0.002981 0.40736 1.8315
10 3VC1 SAH 0.006161 0.40577 1.8315
11 2GJP MAL 0.008441 0.4032 1.8315
12 3DXY SAM 0.005911 0.43432 1.83486
13 1KYQ NAD 0.002131 0.44308 2.1978
14 4DMG SAM 0.004727 0.43912 2.1978
15 3VYW SAM 0.002504 0.42876 2.1978
16 2OBM ADP 0.04743 0.40092 2.1978
17 2OG2 MLI 0.04484 0.40038 2.1978
18 2P3V SRT 0.02322 0.41944 2.34375
19 2NXE SAM 0.01388 0.40228 2.3622
20 3GU3 SAH 0.007477 0.43353 2.46479
21 4K6B GLU 0.03097 0.40991 2.48447
22 1P1C SAH 0.003966 0.41379 2.51256
23 5X62 SAH 0.00304 0.43595 2.5641
24 3GGO NAI 0.002066 0.42134 2.5641
25 3GGO ENO 0.002066 0.42134 2.5641
26 1VPD TLA 0.028 0.41203 2.5641
27 1XDS SAM 0.01451 0.41134 2.5641
28 4AZT SAM 0.01015 0.40846 2.5641
29 2HK9 ATR 0.03003 0.40284 2.5641
30 2WPF WPF 0.03183 0.40196 2.5641
31 2G5C NAD 0.003169 0.40123 2.5641
32 2DVZ GLU 0.03277 0.4009 2.5641
33 1QZZ SAM 0.02483 0.4 2.5641
34 4YMH SAH 0.009029 0.40452 2.91667
35 5X7Q GLC GLC GLC 0.02844 0.43974 2.9304
36 5X7Q GLC GLC GLC GLC 0.02857 0.43919 2.9304
37 5H6S HDH 0.01149 0.43788 2.9304
38 2YX1 SFG 0.007467 0.4253 2.9304
39 3GWZ SAH 0.01227 0.41486 2.9304
40 3GXO SAH 0.01255 0.4144 2.9304
41 1D4D SIN 0.04296 0.40223 2.9304
42 2QZX IVA VAL VAL STA ALA STA 0.009283 0.40109 2.9304
43 2BOS GLA GAL GLC NBU 0.02604 0.41305 2.94118
44 2BOS GLA GAL GLC 0.02701 0.41205 2.94118
45 2V3V MGD 0.0008763 0.4585 3.2967
46 2EG5 SAH 0.00673 0.42748 3.2967
47 3EYA FAD 0.0002102 0.42201 3.2967
48 4JGT PYR 0.04164 0.405 3.2967
49 3DMH SAM 0.009767 0.40304 3.2967
50 1R6N 434 0.03072 0.41341 3.31754
51 1JG3 ADN 0.002675 0.43467 3.40426
52 5WSY 7UC 0.02124 0.41448 3.46821
53 1X87 NAD 0.001736 0.4288 3.62976
54 5DCH 1YO 0.04207 0.40309 3.64583
55 2VDV SAM 0.005569 0.43146 3.65854
56 5KVA SAM 0.001054 0.44139 3.663
57 2DPM SAM 0.00174 0.43212 3.663
58 3BP1 GUN 0.009244 0.42442 3.663
59 5FA5 MTA 0.01073 0.41407 3.663
60 3VSV XYS 0.02376 0.41268 3.663
61 2WET TRP 0.02095 0.41083 3.663
62 1Y8Q ATP 0.006098 0.40315 3.663
63 3LKZ SFG 0.01315 0.4003 3.663
64 1V84 GAL NDG 0.02669 0.41338 3.95257
65 1ZQ9 SAM 0.001014 0.45371 4.0293
66 3GRU AMP 0.004297 0.41233 4.0293
67 3WVR AMP 0.01938 0.40524 4.0293
68 5DUS APR 0.009652 0.40037 4.16667
69 2VT3 ATP 0.001935 0.45825 4.18605
70 3A3B RBF 0.03989 0.40012 4.21053
71 1LSS NAD 0.002911 0.42592 4.28571
72 5LW0 AR6 0.001119 0.4334 4.329
73 3GCM 5GP 0.02556 0.4295 4.3956
74 1L1E SAH 0.007219 0.41516 4.3956
75 1BW9 NAD 0.007962 0.40394 4.3956
76 1O94 ADP 0.006404 0.40227 4.3956
77 1R18 SAH 0.007777 0.40438 4.40529
78 4YSX E23 0.04314 0.40213 4.48718
79 3EWP APR 0.004329 0.40373 4.51977
80 2XVM SAH 0.02229 0.40229 4.52261
81 3K8D KDO 0.03371 0.40792 4.54545
82 2WHX ADP 0.03428 0.40796 4.7619
83 3FZG SAM 0.01201 0.41174 5
84 2HNK SAH 0.002089 0.43218 5.02092
85 4CVN ADP 0.04655 0.40034 5.10949
86 5MPT SAH 0.007479 0.41447 5.12821
87 1IXE CIT 0.03446 0.4074 5.12821
88 1N4W FAD 0.00549 0.40649 5.12821
89 2JJQ SAH 0.01877 0.40591 5.12821
90 2EJU SAH 0.0139 0.40224 5.12821
91 1L7N ALF 0.02274 0.41525 5.21327
92 3EGV SAH 0.0104 0.41126 5.44218
93 3MQ2 SAH 0.01249 0.40757 5.50459
94 3OFK SAH 0.008184 0.40343 5.55556
95 5LOG SAH 0.002647 0.43121 5.5794
96 1T9D FAD 0.0000229 0.42879 5.86081
97 5JE8 NAD 0.001815 0.42168 5.86081
98 4NEC SAH 0.02174 0.40281 6.06061
99 5L95 AMP 0.005193 0.41824 6.25
100 3FUU ADN 0.01237 0.40149 6.27306
101 2PHT MAN MAN MAN BMA MAN 0.01256 0.42212 6.34921
102 2GMM MAN MAN 0.01643 0.41933 6.34921
103 2PHU MAN MAN MAN BMA MAN 0.01448 0.41898 6.34921
104 2PHW MAN MAN MAN BMA MAN MAN MAN 0.01731 0.41504 6.34921
105 2GND MAN 0.02554 0.41154 6.34921
106 2AUY NAG MAN MMA 0.01791 0.41049 6.34921
107 1Q8P MAN MMA 0.03092 0.40994 6.34921
108 2PHF MAN MAN 0.03471 0.40724 6.34921
109 2AR6 NAG MAN 0.01789 0.40693 6.34921
110 2PHW MAN MAN 0.03598 0.40639 6.34921
111 2PHF MAN MAN BMA MAN 0.03438 0.40352 6.34921
112 2GNB MAN 0.03161 0.40222 6.34921
113 2XYQ SAH 0.00643 0.41744 6.55738
114 2BFR ADP 0.00114 0.43643 6.77083
115 3G89 SAM 0.005685 0.43102 6.82731
116 4N49 SAM 0.003048 0.42505 6.95971
117 1JT2 FER 0.02352 0.41459 7.08955
118 5HJM MTA 0.002881 0.42958 7.32601
119 3T7S SAM 0.00183 0.44213 7.46269
120 5E1M SAH 0.006889 0.40964 7.46888
121 4KRI SAH 0.01024 0.40514 7.69231
122 3PT9 SAH 0.006704 0.41662 8.05861
123 1V59 NAD 0.01136 0.42029 8.42491
124 3EGI ADP 0.0009473 0.49052 8.73786
125 2ZWS PLM 0.01817 0.4442 8.79121
126 1F3L SAH 0.006534 0.40761 9.15751
127 3G6N MET ALA SER 0.04462 0.40134 9.42408
128 2AOT SAH 0.004981 0.42982 9.89011
129 4NTX AMR 0.03759 0.41668 10.084
130 1L3I SAH 0.000391 0.44856 10.4167
131 1DJL NAP 0.0001174 0.43821 10.628
132 3VSE SAH 0.002614 0.45181 11.3553
133 1PNO NAP 0.000274 0.44126 11.6667
134 1D4O NAP 0.000086 0.47115 11.9565
135 2OOR TXP 0.0001884 0.45411 12.069
136 4II2 ATP 0.006893 0.40963 13.253
137 1QAN SAH 0.008254 0.40328 13.5246
138 1SQL GUN 0.01252 0.42966 13.6986
139 4QTU SAM 0.009998 0.40259 14.4231
140 5W3X ACO 0.04852 0.40077 16.25
141 5ITV NAI 0.002561 0.40084 17.2549
142 3CYQ AMU 0.01819 0.41891 17.3913
143 5A3B APR 0.000000002304 0.65216 19.4139
144 2QX0 PH2 0.02184 0.41564 19.4969
145 2FKA BEF 0.009221 0.45022 27.907
146 3FGZ BEF 0.01367 0.42816 28.125
Pocket No.: 2; Query (leader) PDB : 3RIY; Ligand: NAD; Similar sites found: 13
This union binding pocket(no: 2) in the query (biounit: 3riy.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GCZ SAM 0.01311 0.40341 2.5641
2 5LKC FUC GLA A2G 0.03217 0.40314 2.5641
3 4KRG SAH 0.01928 0.402 2.5641
4 3GL0 HXX 0.02835 0.40055 2.5641
5 4D79 ATP 0.01399 0.40212 2.9304
6 3K7S R52 0.03193 0.40147 3.35196
7 5T96 79J 0.0448 0.4021 4.3956
8 1DJN ADP 0.008381 0.40017 4.3956
9 1Z03 OCH 0.04697 0.40013 4.7619
10 4AFK FLC 0.031 0.40736 6.22711
11 2FAH MLA 0.02208 0.4187 6.59341
12 4NZ6 DLY 0.0414 0.40216 9.52381
13 1EU1 MGD 0.004919 0.40238 10.2564
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