Receptor
PDB id Resolution Class Description Source Keywords
4I5I 2.5 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF THE SIRT1 CATALYTIC DOMAIN BOUND TO NAD EX527 ANALOG HOMO SAPIENS ROSSMANN FOLD HISTONE DEACETYLASE EPIGENETICS CANCER SIRACETYLATED LYSINE OF HISTONE HYDROLASE
Ref.: THE 2.5 ANGSTROM CRYSTAL STRUCTURE OF THE SIRT1 CAT DOMAIN BOUND TO NICOTINAMIDE ADENINE DINUCLEOTIDE ( AN INDOLE (EX527 ANALOGUE) REVEALS A NOVEL MECHANIS HISTONE DEACETYLASE INHIBITION. J.MED.CHEM. V. 56 963 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:603;
B:603;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
4I5 B:601;
A:601;
Valid;
Valid;
none;
none;
submit data
262.735 C14 H15 Cl N2 O c1cc2...
NAD B:602;
A:602;
Valid;
Valid;
none;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I5I 2.5 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF THE SIRT1 CATALYTIC DOMAIN BOUND TO NAD EX527 ANALOG HOMO SAPIENS ROSSMANN FOLD HISTONE DEACETYLASE EPIGENETICS CANCER SIRACETYLATED LYSINE OF HISTONE HYDROLASE
Ref.: THE 2.5 ANGSTROM CRYSTAL STRUCTURE OF THE SIRT1 CAT DOMAIN BOUND TO NICOTINAMIDE ADENINE DINUCLEOTIDE ( AN INDOLE (EX527 ANALOGUE) REVEALS A NOVEL MECHANIS HISTONE DEACETYLASE INHIBITION. J.MED.CHEM. V. 56 963 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 4I5I - 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
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 4I5I - 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
50% Homology Family (35)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 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 = 0.118 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 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
17 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
18 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
19 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
20 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
21 4FZ3 - ACE ARG HIS LYS ALY MCM n/a n/a
22 4JT9 ic50 = 0.0072 uM 1NS C15 H21 N5 O3 S2 CS(=O)(=O)....
23 5BWO - PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP n/a n/a
24 4JT8 ic50 = 0.033 uM 1NR C19 H27 N5 O2 S CC(C)(C)C(....
25 4BV3 Kd = 16.5 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
26 4BVH - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
27 4C7B - ARG HIS LYS FDL n/a n/a
28 4C78 - BVB C14 H11 Br O2 c1cc(ccc1/....
29 5BWN - GLN THR ALA ARG MYK SER THR GLY GLY TRP n/a n/a
30 4BN4 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
31 4JSR ic50 = 0.004 uM 1NQ C22 H26 N6 O3 S2 CCNC(=O)c1....
32 4BVE - THR ARG SER GLY FZN VAL MET ARG ARG LEU n/a n/a
33 4BVB - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
34 4FVT - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
35 4I5I - 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4I5; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 4I5 1 1
2 OCZ 0.821429 0.926829
3 2J2 0.645161 0.688889
Ligand no: 2; 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 : 4I5I; Ligand: NAD; Similar sites found: 77
This union binding pocket(no: 1) in the query (biounit: 4i5i.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4ONQ SFG 0.008833 0.40855 1.39373
2 4NBW NAD 0.002724 0.40612 1.55642
3 3A3B RBF 0.02349 0.40972 1.57895
4 3EF0 ALF 0.02617 0.41673 1.88172
5 1V6A TRE 0.04496 0.40027 2.09059
6 2BGM NAJ 0.003084 0.40085 2.15827
7 2IZ1 ATR 0.007181 0.4467 2.43902
8 4DCM SAM 0.005884 0.4237 2.43902
9 1YBH FAD 0.0001093 0.4092 2.43902
10 5LOG SAH 0.008473 0.40615 2.57511
11 1TDU DUR 0.02519 0.40815 2.64151
12 1DDU DDU 0.0271 0.40649 2.64151
13 3RKR NAP 0.02249 0.40677 2.67176
14 3VYW SAM 0.003482 0.41975 2.78746
15 3EYA FAD 0.0002101 0.41822 2.78746
16 2X8S AHR AHR AHR 0.026 0.41154 2.78746
17 2F5Z FAD 0.007776 0.40513 2.78746
18 3GU3 SAH 0.01799 0.41167 2.8169
19 2VDV SAM 0.008409 0.42017 2.84553
20 4FFG 0U8 0.0362 0.40157 3.13589
21 4L80 OXL 0.02757 0.40119 3.13589
22 4XH0 ADP 0.04181 0.40062 3.13589
23 3EGI ADP 0.003721 0.45622 3.39806
24 4NEC SAH 0.0214 0.40066 3.40909
25 2C31 ADP 0.0002067 0.49097 3.48432
26 2C31 TZD 0.0002147 0.49097 3.48432
27 2WSB NAD 0.00241 0.42298 3.54331
28 1UAY ADN 0.007081 0.42375 3.71901
29 3CBG SAH 0.01171 0.40628 3.87931
30 3I9U DTU 0.01215 0.424 4.18251
31 5JCM ISD 0.01619 0.40743 4.21286
32 5JCM FAD 0.01521 0.40743 4.21286
33 5JCM NAD 0.01521 0.40743 4.21286
34 4D42 NAP 0.01333 0.40042 4.25532
35 4D42 W0I 0.01333 0.40042 4.25532
36 1ZQ9 SAM 0.002243 0.43527 4.5614
37 3DXY SAM 0.005142 0.43459 4.58716
38 4URG C2E 0.04062 0.40202 4.79042
39 1P7T PYR 0.007134 0.42881 4.87805
40 1EJ0 SAM 0.0113 0.40374 5
41 2AE2 NAP 0.008054 0.4017 5
42 2Q28 ADP 0.000007611 0.5399 5.57491
43 1NFQ NAI 0.005002 0.40122 5.76923
44 4DMG SAM 0.01133 0.41775 5.92335
45 2GDZ NAD 0.0037 0.40376 5.99251
46 1YXM ADE 0.004218 0.45445 6.62021
47 1DMR PGD 0.01023 0.41551 6.62021
48 3R51 MMA 0.03693 0.40726 6.875
49 1V5F FAD 0.0007515 0.4624 7.31707
50 3OFK SAH 0.01283 0.40446 7.40741
51 1A5V Y3 0.03731 0.40584 7.59494
52 1I2B NAD 0.01127 0.40648 8.01394
53 1D4O NAP 0.0005664 0.43564 8.15217
54 5TVM PUT 0.02404 0.4061 8.23529
55 5TVF PUT 0.027 0.40244 8.23529
56 1LSS NAD 0.005184 0.4123 8.57143
57 1P77 ATR 0.009191 0.43549 8.82353
58 1NM5 NAP 0.001944 0.43622 9.05923
59 1NM5 NAD 0.002056 0.43604 9.05923
60 1O97 AMP 0.0006764 0.45885 9.09091
61 2XYQ SAH 0.003345 0.42749 9.83607
62 1DJL NAP 0.00062 0.40799 10.1449
63 2V3V MGD 0.00692 0.42526 10.8014
64 2IV2 MGD 0.00623 0.40209 10.8014
65 4P8O 883 0.02107 0.41217 11.7647
66 1XXR MAN 0.02403 0.41346 11.8012
67 5FA5 MTA 0.009811 0.41329 12.892
68 3AB4 LYS 0.02756 0.40612 12.892
69 1KYQ NAD 0.01577 0.40033 13.1387
70 1T9D FAD 0.00006363 0.41422 13.2404
71 2HNK SAH 0.005361 0.4149 13.8075
72 1NU4 MLA 0.01251 0.41915 14.433
73 1PNO NAP 0.0008023 0.42962 14.4444
74 4ISS TAR 0.02926 0.41073 14.6341
75 2OOR TXP 0.0006195 0.43092 14.9425
76 5A3B APR 0.000004254 0.51893 24.0418
77 3U31 NAD 0.00000009577 0.60893 35.5401
Pocket No.: 2; Query (leader) PDB : 4I5I; Ligand: 4I5; Similar sites found: 16
This union binding pocket(no: 2) in the query (biounit: 4i5i.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LCC SAH 0.008269 0.41393 1.70213
2 1XTP SAI 0.01478 0.40365 1.9685
3 3BP1 GUN 0.01146 0.42178 2.09059
4 2R4V GSH 0.01517 0.41105 2.42915
5 4LH7 1X8 0.01481 0.40167 2.43902
6 5X7Q GLC GLC GLC GLC 0.008937 0.44514 2.78746
7 5X7Q GLC GLC GLC 0.009527 0.44289 2.78746
8 3CIF NAD 0.02969 0.40189 3.13589
9 1SQL GUN 0.004488 0.42733 3.42466
10 4MCC 21X 0.02442 0.40232 4.47154
11 1WG8 SAM 0.01859 0.40684 4.87805
12 5B19 TLA 0.00776 0.41087 5.17241
13 1VL0 NAI 0.01159 0.41853 6.50685
14 4INI AMP 0.009714 0.40643 8.36237
15 3C6K SPD 0.03611 0.40309 12.336
16 3C6K MTA 0.03611 0.40309 12.336
Pocket No.: 3; Query (leader) PDB : 4I5I; Ligand: 4I5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4i5i.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4I5I; Ligand: NAD; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 4i5i.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VHZ APR 0.02605 0.41455 2.0202
2 4LH7 1X8 0.04673 0.4001 2.43902
3 4AG5 ADP 0.0225 0.41652 2.78746
4 4FC7 NAP 0.007724 0.40433 3.2491
5 4FC7 COA 0.007724 0.40433 3.2491
6 3ITJ CIT 0.01183 0.42637 4.18118
7 1ZGS XMM 0.03163 0.40163 4.18118
8 5GZZ JAA 0.03537 0.40439 13.7615
Pocket No.: 5; Query (leader) PDB : 4I5I; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4i5i.bio3) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4I5I; Ligand: 4I5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4i5i.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4I5I; Ligand: 4I5; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4i5i.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4I5I; Ligand: NAD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4i5i.bio3) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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