Receptor
PDB id Resolution Class Description Source Keywords
4rmi 1.45 Å EC: 3.5.1.- HUMAN SIRT2 IN COMPLEX WITH SIRREAL1 AND AC-LYS-OTC PEPTIDE HOMO SAPIENS HYDROLASE-HYDROLASE INBITITOR COMPLEX
Ref.: SELECTIVE SIRT2 INHIBITION BY LIGAND-INDUCED REARRA OF THE ACTIVE SITE. NAT COMMUN V. 6 6263 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLU ALY ARG B:87;
 Valid;
 Atoms found LESS than expected: % Diff = 0.03;
 submit data
458.54 n/a O=C(N...
ZN A:401;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
3TK A:402;
 Valid;
 none;
 submit data
370.492 C18 H18 N4 O S2 Cc1cc...
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: GLU ALY ARG; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 GLU ALY ARG 1 1
2 GLU ARG GLY SER GLY ARG 0.55914 0.792453
3 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.488095 0.829787
4 ARG ARG ARG ARG ARG ARG ARG ARG 0.488095 0.829787
5 MET ARG THR GLY ASN ALA XSN 0.47561 0.76
6 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.472527 0.851064
7 ARG ALA ARG 0.46988 0.808511
8 ARG ASP ALA ALA 0.465116 0.893617
9 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.464286 0.77193
10 ARG GLU ALA ALA 0.455556 0.893617
11 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.448819 0.758621
12 LYS ARG LYS 0.448276 0.913043
13 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.446809 0.823529
14 VAL ARG MET 0.444444 0.75
15 ARG ARG ALA ALA 0.443182 0.854167
16 CYS ALA ARG ALA TYR 0.44186 0.791667
17 THR ARG SER GLY ALY VAL MET ARG ARG LEU 0.441441 0.814815
18 ALA ARG THR ALY GLN THR ALA 0.438095 0.849057
19 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.434343 0.773585
20 GLU ARG GLY MET THR 0.432692 0.781818
21 ALA ARG THR LYS GLN THR ALA ARG 0.431373 0.826923
22 ACE THR ARG GLU 0.428571 0.769231
23 ALA TYR ARG 0.427083 0.740741
24 ACE ALA ARG THR LYS GLN 0.425743 0.807692
25 GLY ASP GLU VAL LYS VAL PHE ARG 0.422764 0.830189
26 ALA ARG M3L SER 0.416667 0.733333
27 ACE GLN THR ALA ARG BTK SER THR 0.415929 0.8
28 GLY ALA ARG 0.411765 0.869565
29 ALA ARG THR LYS GLN THR ALA ARG LYS 0.410714 0.811321
30 GLU THR VAL ARG PHE GLN SER ASP 0.408 0.736842
31 GLU GLU GLU ASP GLY TPO MET LYS ARG ASN 0.406504 0.714286
32 ALA ILE ARG SER 0.40625 0.769231
33 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.40566 0.762712
34 ASN ARG LEU ILE LEU THR GLY 0.403846 0.754717
35 GLU ALA GLN THR ARG LEU 0.401786 0.777778
36 GLN THR ALA ARG M3L SER 0.4 0.714286
Ligand no: 2; Ligand: 3TK; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 3TK 1 1
2 3TE 0.647059 0.979167
3 5GR 0.598039 0.712121
4 5GN 0.586957 0.903846
5 A2X 0.440476 0.87234
6 A2I 0.433333 0.777778
Similar Ligands (3D)
Ligand no: 1; Ligand: GLU ALY ARG; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: 3TK; 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
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