Receptor
PDB id Resolution Class Description Source Keywords
4Y6O 1.6 Å EC: 3.5.1.- HUMAN SIRT2 IN COMPLEX WITH MYRISTOYLATED PEPTIDE (TNF-ALPHA HOMO SAPIENS SIRTUIN SIRT NAD-DEPENDENT DEACETYLASE MYRISTOYLATED LYSIHYDROLASE-PEPTIDE COMPLEX
Ref.: KINETIC AND STRUCTURAL BASIS FOR ACYL-GROUP SELECTI NAD(+) DEPENDENCE IN SIRTUIN-CATALYZED DEACYLATION. BIOCHEMISTRY V. 54 3037 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA SER ILE ASP ALA GLN A:350;
 Invalid;
 none;
 submit data
n/a n/a
LEU PRO LYS MYK THR GLY GLY C:7;
D:3;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.016;
Atoms found LESS than expected: % Diff = 0.016;
 submit data
896.229 n/a O=C(N...
GLU HIS ALA SER ILE ASP ALA GLN B:348;
 Invalid;
 none;
 submit data
n/a n/a
ZN A:501;
B:501;
 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
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: LEU PRO LYS MYK THR GLY GLY; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU PRO LYS MYK THR GLY GLY 1 1
2 PRO LYS LYS THR GLY 3LX 0.517986 0.828125
3 THR ALA ARG MYK SER THR GLY 0.468966 0.705882
4 LYS PRO VAL LEU ARG THR ALA 0.463087 0.835821
5 ARG PRO LYS ARG ILE ALA 0.455172 0.75
6 SER PRO LYS ARG ILE ALA 0.453901 0.779412
7 LEU SER SER PRO VAL THR LYS SER PHE 0.448718 0.875
8 TYR PRO LYS ARG ILE ALA 0.448052 0.736111
9 PBE PRO LYS THR SER GLY LYS ALA ALA 0.4375 0.880597
10 LEU PRO PHE ASP LYS THR THR ILE MET 0.436364 0.880597
11 LEU PRO PHE GLU LYS SER THR VAL MET 0.42515 0.852941
12 5JP PRO LYS ARG ILE ALA 0.421769 0.782609
13 SER THR GLY GLY VAL M3L LYS PRO HIS ARG 0.421622 0.776316
14 LEU PRO PHE ASP LYS SER THR ILE MET 0.418605 0.867647
15 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.418182 0.880597
16 SER SER GLY LYS VAL PRO LEU 0.416667 0.903226
17 THR PRO ARG VAL THR GLY GLY GLY ALA MET 0.416149 0.830986
18 LEU PRO PRO VAL VAL ALA LYS GLU ILE 0.414013 0.84127
19 SER SER GLY LYS VAL PRO LEU SER 0.408163 0.888889
20 ARG PRO MET THR PHE LYS GLY ALA LEU 0.407821 0.819444
21 THR THR ALA PRO SER LEU SER GLY LYS 0.406452 0.920635
22 ARG PRO MET THR TYR LYS GLY ALA LEU 0.405556 0.786667
23 LEU PRO GLU THR GLY 0.404412 0.918033
Similar Ligands (3D)
Ligand no: 1; Ligand: LEU PRO LYS MYK THR GLY GLY; 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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