Receptor
PDB id Resolution Class Description Source Keywords
4G1C 1.94 Å EC: 3.5.1.- HUMAN SIRT5 BOUND TO SUCC-IDH2 AND CARBA-NAD HOMO SAPIENS SIRTUIN SUCCINYLATED PEPTIDE CARBANAD HYDROLASE
Ref.: SYNTHESIS OF CARBA-NAD AND THE STRUCTURES OF ITS TE COMPLEXES WITH SIRT3 AND SIRT5. J.ORG.CHEM. V. 77 7319 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACE ALA VAL SLL CYS ALA NH2 D:0;
E:0;
Valid;
Valid;
none;
none;
submit data
632.76 n/a SCC(N...
CNA A:402;
Valid;
none;
submit data
662.46 C22 H30 N7 O13 P2 c1cc(...
ZN A:401;
B:401;
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
2NYR 2.06 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRTUIN HOMOLOG 5 IN COMPLEX WITH HOMO SAPIENS HISTONE DEACETYLASE STRUCTURAL GENOMICS STRUCTURAL GENOMICCONSORTIUM SGC HYDROLASE
Ref.: STRUCTURAL BASIS OF INHIBITION OF THE HUMAN NAD+-DE DEACETYLASE SIRT5 BY SURAMIN. STRUCTURE V. 15 377 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
2 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4UTV Ki = 100 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
2 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
3 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4BUZ - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
2 3D4B - THR SER ARG HIS LYS ALY LEU MET ALA n/a n/a
3 3D81 - SER ARG HIS LYS FZN LEU MET PHE n/a n/a
4 1S5P Kd = 0.44 uM LYS GLY GLY ALA ALY ARG HIS ARG n/a n/a
5 4UTV Ki = 100 uM BEZ GLY VAL LEU LYS GLU TYR GLY VAL FSL n/a n/a
6 1M2K - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
7 1M2J - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
8 1M2G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
9 1ICI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
10 1M2H - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
11 2NYR - SVR C51 H40 N6 O23 S6 Cc1ccc(cc1....
12 4G1C - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
13 1S7G - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
14 1YC2 - APR C15 H23 N5 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ACE ALA VAL SLL CYS ALA NH2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ACE ALA VAL SLL CYS ALA NH2 1 1
Ligand no: 2; Ligand: CNA; Similar ligands found: 239
No: Ligand ECFP6 Tc MDL keys Tc
1 CNA 1 1
2 NXX 0.644068 0.972973
3 DND 0.644068 0.972973
4 NAD 0.642276 0.972603
5 A2D 0.62 0.958904
6 NAD IBO 0.608 0.909091
7 BA3 0.607843 0.958904
8 A3D 0.606299 0.959459
9 AP5 0.601942 0.958904
10 B4P 0.601942 0.958904
11 M33 0.590476 0.92
12 ATP 0.584906 0.932432
13 AQP 0.579439 0.932432
14 APR 0.579439 0.932432
15 AR6 0.579439 0.932432
16 5FA 0.579439 0.932432
17 3OD 0.577586 0.933333
18 SAP 0.574074 0.884615
19 AGS 0.574074 0.884615
20 OAD 0.573913 0.933333
21 ADP 0.571429 0.932432
22 ACP 0.570093 0.907895
23 AN2 0.566038 0.92
24 OOB 0.561404 0.945946
25 CA0 0.560748 0.933333
26 NAJ PYZ 0.559702 0.8875
27 AD9 0.559633 0.907895
28 A1R 0.556522 0.897436
29 ACQ 0.54955 0.907895
30 5AL 0.544643 0.92
31 ABM 0.542857 0.881579
32 GTA 0.540323 0.9
33 NAX 0.539683 0.911392
34 A22 0.53913 0.945946
35 00A 0.538462 0.897436
36 DLL 0.538462 0.945946
37 1ZZ 0.537815 0.831325
38 PRX 0.536364 0.858974
39 ANP 0.535714 0.907895
40 ADX 0.53211 0.841463
41 WAQ 0.529412 0.873418
42 AMP 0.528846 0.905405
43 A 0.528846 0.905405
44 TXD 0.527559 0.922078
45 6V0 0.527559 0.910256
46 NAI 0.527559 0.922078
47 50T 0.527273 0.894737
48 ATF 0.526316 0.896104
49 OMR 0.523438 0.843373
50 TXE 0.523438 0.922078
51 NAP 0.521739 0.959459
52 SRP 0.521739 0.921053
53 8QN 0.521368 0.92
54 3UK 0.521008 0.933333
55 NHD 0.518797 0.945946
56 4AD 0.516949 0.96
57 ADQ 0.516949 0.933333
58 PAJ 0.516949 0.875
59 9SN 0.516393 0.886076
60 NAQ 0.514493 0.910256
61 AHX 0.512605 0.910256
62 NFD 0.511111 0.922078
63 ZID 0.510791 0.959459
64 AMP NAD 0.510791 0.921053
65 NAD BBN 0.510067 0.878049
66 SON 0.509091 0.896104
67 APC 0.508929 0.896104
68 5SV 0.508475 0.817073
69 25L 0.508197 0.945946
70 48N 0.507812 0.886076
71 NAE 0.507246 0.934211
72 AMP MG 0.504673 0.881579
73 A12 0.504587 0.896104
74 AP2 0.504587 0.896104
75 AMO 0.504202 0.946667
76 PR8 0.504132 0.864198
77 DZD 0.503704 0.898734
78 NAD CJ3 0.503311 0.847059
79 FA5 0.5 0.946667
80 FYA 0.5 0.92
81 BIS 0.5 0.873418
82 TXA 0.5 0.921053
83 ME8 0.5 0.853659
84 PTJ 0.5 0.8625
85 T5A 0.496241 0.878049
86 8ID 0.496183 0.923077
87 AP0 0.496183 0.886076
88 TAT 0.495652 0.896104
89 GAP 0.495652 0.907895
90 SRA 0.495327 0.858974
91 NA0 0.492958 0.946667
92 A4P 0.492424 0.857143
93 UP5 0.492308 0.934211
94 4UV 0.492063 0.909091
95 LAD 0.491803 0.875
96 ADP MG 0.491071 0.894737
97 AU1 0.491071 0.907895
98 LAQ 0.488372 0.831325
99 G3A 0.488189 0.910256
100 YAP 0.488 0.934211
101 NB8 0.487805 0.910256
102 ADP BEF 0.486726 0.871795
103 BEF ADP 0.486726 0.871795
104 N01 0.485507 0.945946
105 COD 0.485294 0.825581
106 AFH 0.484375 0.875
107 4UU 0.484375 0.909091
108 G5P 0.484375 0.910256
109 XAH 0.484127 0.853659
110 25A 0.483333 0.932432
111 NDC 0.482993 0.910256
112 EAD 0.482517 0.911392
113 4UW 0.480916 0.875
114 NDE 0.479452 0.946667
115 ADP PO3 0.478261 0.931507
116 RBY 0.478261 0.896104
117 ADV 0.478261 0.896104
118 NJP 0.477941 0.96
119 IOT 0.477612 0.823529
120 DAL AMP 0.475 0.92
121 NAD NDT 0.475 0.739583
122 ATP MG 0.474138 0.894737
123 ADJ 0.474074 0.865854
124 139 0.474074 0.911392
125 4TC 0.473684 0.910256
126 MYR AMP 0.472 0.831325
127 P1H 0.469388 0.888889
128 NGD 0.466667 0.923077
129 NAD TDB 0.466258 0.705882
130 TYM 0.466165 0.946667
131 MAP 0.46281 0.884615
132 ADP ALF 0.462185 0.860759
133 ALF ADP 0.462185 0.860759
134 YLP 0.462121 0.833333
135 BT5 0.460432 0.823529
136 NAJ 0.459854 0.945946
137 ANP MG 0.458333 0.884615
138 ADP VO4 0.458333 0.92
139 VO4 ADP 0.458333 0.92
140 M24 0.457746 0.864198
141 TAP 0.455172 0.897436
142 YLC 0.451852 0.853659
143 YLB 0.451852 0.833333
144 7MD 0.450382 0.876543
145 ADP BMA 0.448 0.933333
146 AMP DBH 0.446154 0.907895
147 FB0 0.443709 0.797753
148 NAJ PZO 0.443662 0.886076
149 AHZ 0.443609 0.831325
150 0WD 0.442857 0.910256
151 54H 0.442623 0.781609
152 A2R 0.442623 0.92
153 VMS 0.442623 0.781609
154 7MC 0.441176 0.855422
155 PAP 0.440678 0.918919
156 7D4 0.439655 0.846154
157 ITT 0.439655 0.88
158 TSB 0.439024 0.811765
159 AYB 0.438849 0.823529
160 TYR AMP 0.438462 0.946667
161 A5A 0.438017 0.8
162 YLY 0.4375 0.823529
163 AOC 0.4375 0.789474
164 G5A 0.436975 0.793103
165 TAD 0.43609 0.875
166 AVV 0.435484 0.8625
167 5AS 0.434783 0.752809
168 3AT 0.433333 0.906667
169 A A 0.433071 0.932432
170 BTX 0.432624 0.833333
171 2A5 0.432203 0.858974
172 DSZ 0.432 0.813953
173 LSS 0.432 0.775281
174 NPW 0.431655 0.9
175 YLA 0.431655 0.833333
176 52H 0.430894 0.772727
177 ATP A A A 0.430769 0.945205
178 UPA 0.430657 0.922078
179 6AD 0.429752 0.851852
180 LPA AMP 0.42963 0.831325
181 N0B 0.428571 0.855422
182 ATR 0.428571 0.905405
183 53H 0.427419 0.772727
184 6FA 0.425806 0.855422
185 ODP 0.425532 0.923077
186 NA7 0.425197 0.896104
187 LEU LMS 0.425197 0.795455
188 ALF ADP 3PG 0.423358 0.851852
189 LA8 ALF 3PG 0.423358 0.851852
190 SSA 0.422764 0.813953
191 ARG AMP 0.422222 0.843373
192 MTA 0.422018 0.74359
193 P5A 0.421875 0.758242
194 NDO 0.421769 0.933333
195 NDP 0.421429 0.910256
196 NSS 0.420635 0.835294
197 FAD 0.420382 0.865854
198 FAS 0.420382 0.865854
199 5N5 0.419048 0.786667
200 JB6 0.418605 0.873418
201 TXP 0.41844 0.910256
202 NZQ 0.41844 0.898734
203 7D3 0.417391 0.846154
204 NVA LMS 0.417323 0.795455
205 EP4 0.416667 0.725
206 5CA 0.416 0.813953
207 5CD 0.415094 0.773333
208 3DH 0.414414 0.74359
209 A3P 0.413793 0.905405
210 XYA 0.413462 0.810811
211 ADN 0.413462 0.810811
212 RAB 0.413462 0.810811
213 AF3 ADP 3PG 0.413043 0.851852
214 DTA 0.412844 0.779221
215 4TA 0.412587 0.865854
216 SFD 0.411392 0.747368
217 3AM 0.410714 0.866667
218 F2N 0.410714 0.827586
219 FDA 0.410256 0.825581
220 FNK 0.409938 0.818182
221 62F 0.409938 0.853659
222 DTP 0.409836 0.87013
223 AR6 AR6 0.407407 0.932432
224 P5F 0.407186 0.837209
225 PPS 0.406504 0.819277
226 ARU 0.40625 0.807229
227 YSA 0.406015 0.813953
228 AV2 0.403226 0.857143
229 649 0.402878 0.777778
230 XNP 0.402778 0.8875
231 A4D 0.401869 0.786667
232 DCA 0.401361 0.816092
233 ETB 0.401361 0.825581
234 5X8 0.4 0.779221
235 GSU 0.4 0.793103
236 KAA 0.4 0.766667
237 M2T 0.4 0.728395
238 FA9 0.4 0.878049
239 SMM 0.4 0.72093
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NYR; Ligand: SVR; Similar sites found: 59
This union binding pocket(no: 1) in the query (biounit: 2nyr.bio1) has 78 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DCP HBI 0.01546 0.4489 None
2 5XG5 A2G 0.03591 0.42838 None
3 1YP0 PEF 0.04394 0.40428 0.83682
4 2OG2 MLI 0.03064 0.42284 2.21402
5 1KYQ NAD 0.03557 0.41913 2.21402
6 3VYW SAM 0.04007 0.40862 2.21402
7 1D8C SOR 0.01842 0.43801 2.58303
8 3GCZ SAM 0.03503 0.4167 2.58303
9 5X62 SAH 0.0494 0.41165 2.58303
10 5ULP KB1 0.03565 0.40416 2.61194
11 1GQ2 NAP 0.02219 0.40511 2.95203
12 2ZX2 RAM 0.03814 0.44235 3.07692
13 3TDC 0EU 0.003043 0.49621 3.32103
14 1TZD ADP 0.03927 0.43938 3.32103
15 2EG5 SAH 0.02586 0.43263 3.32103
16 3EYA FAD 0.005819 0.41739 3.32103
17 3BIB PSF 0.04418 0.43353 3.44828
18 2AF6 BRU 0.04883 0.43044 3.48837
19 3BP1 GUN 0.0005016 0.53682 3.69004
20 2CXG GLC GLC 0.001676 0.52013 3.69004
21 3VSV XYS 0.02683 0.4448 3.69004
22 5KVA SAM 0.02394 0.4171 3.69004
23 2DPM SAM 0.03199 0.411 3.69004
24 5F90 GLA GAL BGC 5VQ 0.02185 0.44493 3.84615
25 5F90 GLA GAL 0.0225 0.44239 3.84615
26 5GVR LMR 0.02722 0.4313 3.84615
27 4XBA GMP 0.006478 0.46902 4
28 4XBA 5GP 0.01328 0.44823 4
29 1ZQ9 SAM 0.01806 0.43138 4.05904
30 4JOB TLA 0.04533 0.40816 4.05904
31 1LSS NAD 0.02788 0.41903 4.28571
32 5LW0 AR6 0.02621 0.41044 4.329
33 3LL5 IP8 0.02185 0.44906 4.41767
34 4HXY NDP 0.02056 0.4026 4.42804
35 1Q8S MAN MMA 0.02891 0.44677 4.7619
36 1Q8Q MAN MMA 0.03026 0.44563 4.7619
37 1UKG MMA 0.03514 0.43322 4.7619
38 2PHX MAN MAN 0.0492 0.43068 4.7619
39 1QXA GLY GLY GLY 0.03153 0.42887 5.53191
40 2HHP FLC 0.03696 0.44552 5.90406
41 1T9D FAD 0.00437 0.41267 5.90406
42 3T7S SAM 0.04192 0.41269 7.46269
43 2XOD FMN 0.0464 0.40788 7.56302
44 5CDH TLA 0.005348 0.47909 7.74908
45 5UFQ GNP 0.03745 0.40315 8.19672
46 3EGI ADP 0.02574 0.44772 8.73786
47 4JGP PYR 0.02069 0.45491 8.75576
48 1EJ0 SAM 0.04097 0.4132 9.44444
49 1J78 OLA 0.04253 0.43744 10.3321
50 1L3I SAH 0.015 0.41934 10.4167
51 1DJL NAP 0.001653 0.444 10.628
52 1PNO NAP 0.001793 0.45013 11.6667
53 1NBU PH2 0.001861 0.49859 11.7647
54 1D4O NAP 0.0009314 0.47125 11.9565
55 2OOR TXP 0.002046 0.45308 12.069
56 1SQL GUN 0.0004521 0.55183 13.6986
57 5A3B APR 0.00001082 0.558 17.3432
58 2FKA BEF 0.04109 0.42267 27.907
59 3U31 NAD 0.00002077 0.56374 46.1255
Pocket No.: 2; Query (leader) PDB : 2NYR; Ligand: SVR; Similar sites found: 18
This union binding pocket(no: 2) in the query (biounit: 2nyr.bio3) has 74 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KP6 SAL 0.02171 0.41559 None
2 3ML5 AZM 0.01561 0.42351 0.743494
3 3WJO IPE 0.03474 0.40784 1.84502
4 3U1T MLI 0.01818 0.41634 2.58303
5 4XOE KGM 0.04119 0.40068 2.58303
6 5JBX MLI 0.03522 0.40323 3.06513
7 3ZJQ NCA 0.01766 0.42631 3.07692
8 4UXU MLK 0.01849 0.41298 3.21101
9 3P7G MAN 0.02171 0.41504 3.42466
10 1UYY BGC BGC 0.01773 0.41905 3.81679
11 4Y4V DAL 0.04329 0.40906 5.16605
12 4U5I BXP 0.02918 0.40903 5.16605
13 4ZSI GLP 0.01473 0.40365 5.26316
14 1H6H PIB 0.02047 0.40274 6.99301
15 4D1J DGJ 0.02605 0.41263 7.38007
16 2CHT TSA 0.02528 0.4109 7.87402
17 4RDN 6MD 0.005769 0.44475 11.976
18 3UNG ADP 0.03053 0.40547 12.9151
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