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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:401;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
BU3 A:405;
Invalid;
none;
submit data
90.121 C4 H10 O2 C[C@H...
EPE A:404;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
5GR A:402;
Valid;
none;
ic50 = 0.118 uM
557.69 C28 H27 N7 O2 S2 Cc1cc...
EDO A:403;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
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 (22)
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 = 0.118 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 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
17 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
18 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
19 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
20 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
21 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
22 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 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 = 0.118 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 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
17 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
18 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
19 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
20 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
21 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
22 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
50% Homology Family (40)
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 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 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
20 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
21 5YQM - A2X C20 H19 N3 O S2 Cc1cc(nc(n....
22 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
23 5YQL ic50 = 25.9 uM A2I C21 H21 N3 O2 S Cc1cc(nc(n....
24 5YQO ic50 = 0.815 uM L5C C26 H26 N6 O3 S Cc1cc(nc(n....
25 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
26 4FZ3 - ACE ARG HIS LYS ALY MCM n/a n/a
27 4JT9 ic50 = 0.0072 uM 1NS C15 H21 N5 O3 S2 CS(=O)(=O)....
28 5BWO - PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP n/a n/a
29 4JT8 ic50 = 0.033 uM 1NR C19 H27 N5 O2 S CC(C)(C)C(....
30 4BV3 Kd = 16.5 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
31 4BVH - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
32 4C7B - ARG HIS LYS FDL n/a n/a
33 4C78 - BVB C14 H11 Br O2 c1cc(ccc1/....
34 5BWN - GLN THR ALA ARG MYK SER THR GLY GLY TRP n/a n/a
35 4BN4 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
36 4JSR ic50 = 0.004 uM 1NQ C22 H26 N6 O3 S2 CCNC(=O)c1....
37 4BVE - THR ARG SER GLY FZN VAL MET ARG ARG LEU n/a n/a
38 4BVB - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
39 4FVT - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
40 4I5I - 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GR; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 5GR 1 1
2 3TK 0.598039 0.712121
3 3TE 0.466102 0.701493
4 5GN 0.432 0.661972
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: 163
This union binding pocket(no: 1) in the query (biounit: 5dy5.bio2) has 61 residues
No: Leader PDB Ligand Sequence Similarity
1 5CHR 4NC None
2 5Y02 HBX None
3 1UO5 PIH None
4 4WG0 CHD None
5 5Y02 MXN None
6 1UO4 PIH None
7 5H6S HDH 1.64474
8 5WA0 MSS 1.64474
9 3GDN MXN 1.64474
10 3B1F NAD 1.72414
11 4XCP PLM 1.76471
12 1RNT 2GP 1.92308
13 4NTO 1PW 2.41546
14 3GU3 SAH 2.46479
15 3K6V CIT 2.54237
16 3NJQ NJQ 2.59067
17 1YBH FAD 2.63158
18 4DMG SAM 2.63158
19 3VSE SAH 2.63158
20 4L2I FAD 2.6616
21 1ZX5 LFR 2.66667
22 6CB2 OLC 2.73038
23 2NXE SAM 2.75591
24 3DAK ANP 2.75862
25 1O9W NAG 2.82486
26 2Q28 ADP 2.96053
27 5W7B MYR 2.96053
28 3L9W AMP 2.96053
29 2OG2 MLI 2.96053
30 2CXG GLC GLC 2.96053
31 3EYA FAD 2.96053
32 3L9W GSH 2.96053
33 1XF1 CIT 2.96053
34 3I9U DTU 3.04183
35 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.04348
36 3ZV6 NAD 3.20285
37 5KVA SAM 3.23741
38 2ALG HP6 3.26087
39 2ALG DAO 3.26087
40 3KLL MAL 3.28947
41 2HZL PYR 3.28947
42 1YKD CMP 3.28947
43 3EGI ADP 3.39806
44 4DE3 DN8 3.42205
45 6AYH C3G 3.48259
46 3VYW SAM 3.57143
47 4URG C2E 3.59281
48 5OSW DIU 3.61842
49 3G58 988 3.61842
50 4EJN 0R4 3.61842
51 3G4G D71 3.61842
52 1R6N 434 3.79147
53 2FKA BEF 3.87597
54 4QO5 NAG 3.94737
55 4Z2B 4LC 3.94737
56 5JE8 NAD 3.94737
57 1YXM ADE 3.9604
58 5AZC PGT 4
59 1UAY ADN 4.13223
60 4P3H 25G 4.14508
61 5OCQ CIT 4.21053
62 5GVR LMR 4.2735
63 1TZJ A3B 4.27632
64 1HFU NAG NDG 4.27632
65 5X7Q GLC GLC GLC 4.27632
66 5X7Q GLC GLC GLC GLC 4.27632
67 3FSY SCA 4.27632
68 3GWZ SAH 4.27632
69 3GXO SAH 4.27632
70 1QXA GLY GLY GLY 4.27632
71 3ABI NAD 4.27632
72 5WKC FAD 4.60526
73 1T9D FAD 4.60526
74 4K91 SIN 4.60526
75 2AF6 BRU 4.65116
76 4RHP PEF 4.68085
77 1RDS GPC 4.7619
78 3CF6 SP1 4.79042
79 2XYQ SAH 4.91803
80 1Q7E MET 4.93421
81 5HCN DAO 4.93421
82 1PJS NAD 4.93421
83 2BHZ MAL 4.93421
84 5N26 CPT 4.94506
85 4NTM 2K8 4.95868
86 4NTK ZSP 4.95868
87 1PNO NAP 5
88 2OOR TXP 5.17241
89 1J78 VDY 5.26316
90 5YAS FAC 5.44747
91 4FGC PQ0 5.45455
92 1KYQ NAD 5.47445
93 1SQL GUN 5.47945
94 6AYI C3G 5.52764
95 5CQG 55C 5.59211
96 5H4S RAM 5.6338
97 1L3I SAH 5.72917
98 2XG5 EC5 5.78035
99 2XG5 EC2 5.78035
100 1DEK DGP 5.80913
101 4URX FK1 5.92105
102 6BVM EBV 5.92105
103 6BVK EAV 5.92105
104 6BVI EC4 5.92105
105 6BVL EBY 5.92105
106 6BVJ EAS 5.92105
107 1O9U ADZ 5.92105
108 6BR8 6OU 5.95238
109 6BR8 PGV 5.95238
110 3LL5 IP8 6.0241
111 6CI9 NAP 6.17761
112 4A59 AMP 6.25
113 1G7C 5GP 6.25
114 2PX6 DH9 6.25
115 4R29 SAM 6.25
116 2JBM SRT 6.35452
117 1JG3 ADN 6.38298
118 5OBY ANP 6.57895
119 1SQF SAM 6.57895
120 2BCG GER 6.79612
121 2PRG BRL 6.81818
122 1DJN FMN 6.90789
123 5O2D 9HH 7
124 2HNK SAH 7.11297
125 3RMK BML 7.22892
126 3DEF GDP 7.23684
127 3FXU TSU 7.23684
128 1ZQ9 SAM 7.36842
129 5E5U MLT 7.53769
130 2WH8 II2 7.56579
131 4O4Z N2O 7.79221
132 4CQM NAP 8.22368
133 2GWH PCI 8.72483
134 1LSS NAD 8.88158
135 4I4S LAT 8.90411
136 1DJL NAP 9.17874
137 1NBU PH2 9.2437
138 1NU4 MLA 9.27835
139 2VOH CIT 9.55414
140 5A3B APR 9.57096
141 5LX9 OLB 9.85915
142 2V5E SCR 9.90099
143 5W8X UDP 10.1974
144 1D4O NAP 10.3261
145 4PW9 MSS 10.3774
146 1P77 ATR 10.8553
147 5MWE TCE 11.1111
148 5C1M CLR 11.2
149 3ROE THM 11.3208
150 5KAX RHQ 11.4458
151 1L5J TRA 11.5132
152 4CS9 AMP 11.6402
153 3W9F I3P 11.8421
154 4V1T ADP 12.5
155 5DCH 1YO 13.0208
156 5KK4 44E 14.5833
157 1N8V BDD 17.8571
158 1DCP HBI 18.2692
159 5Z84 CHD 18.6441
160 5ZCO CHD 18.6441
161 1T0S BML 20.9302
162 3U31 NAD 35.5172
163 1M2K APR 39.759
Pocket No.: 2; Query (leader) PDB : 5DY5; Ligand: 5GR; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5dy5.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 6G3R ADP 1.64474
2 5F8F SFG 1.97368
3 1RV1 IMZ 9.41177
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
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