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 (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 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 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
14 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
15 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
16 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
17 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 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 5MAT ic50 = 0.58 uM 7KJ C28 H28 N4 O3 S Cc1c(c(on1....
14 4Y6Q - OMR C29 H49 N5 O15 P2 CCCCCCCCCC....
15 5D7Q ic50 = 2.8 uM 4I5 C14 H15 Cl N2 O c1cc2c(cc1....
16 5G4C Kd = 13.7 uM ARG ALA ALA 6G4 THR n/a n/a
17 5D7O - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
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: 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: 49
This union binding pocket(no: 1) in the query (biounit: 5dy5.bio2) has 61 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5H6S HDH 0.0296 0.43758 1.64474
2 4GNI ATP 0.01376 0.43365 1.64474
3 4PW3 MSS 0.03008 0.40767 1.64474
4 4XCP PLM 0.007443 0.4677 1.76471
5 3GU3 SAH 0.0341 0.42325 2.46479
6 3NJQ NJQ 0.03662 0.4118 2.59067
7 4DMG SAM 0.02174 0.43027 2.63158
8 1EB1 ASP TYR GLU PRO ILE PRO GLU GLU ALA PHE 0.04819 0.41166 2.63158
9 3EGV SAH 0.04068 0.40658 2.75591
10 2CXG GLC GLC 0.01168 0.46236 2.96053
11 3L9W GSH 0.01635 0.40082 2.96053
12 3VYW SAM 0.03158 0.40407 3.57143
13 3G58 988 0.03462 0.42288 3.61842
14 2FKA BEF 0.03873 0.42722 3.87597
15 1YXM ADE 0.03398 0.42537 3.9604
16 1TZJ A3B 0.01933 0.44683 4.27632
17 1HFU NAG NDG 0.01527 0.44599 4.27632
18 1QXA GLY GLY GLY 0.04802 0.41148 4.27632
19 1T9D FAD 0.0002419 0.44685 4.60526
20 4K91 SIN 0.04634 0.4135 4.60526
21 2AF6 BRU 0.03579 0.43136 4.65116
22 5HCN DAO 0.0273 0.43644 4.93421
23 4NTM 2K8 0.0231 0.43253 4.95868
24 1PNO NAP 0.00217 0.43512 5
25 2OOR TXP 0.001603 0.4461 5.17241
26 1KYQ NAD 0.0173 0.42534 5.47445
27 1SQL GUN 0.001408 0.51355 5.47945
28 5CQG 55C 0.02601 0.43913 5.59211
29 1L3I SAH 0.007707 0.42197 5.72917
30 2XG5 EC2 0.04528 0.42655 5.78035
31 2XG5 EC5 0.04528 0.42655 5.78035
32 1DEK DGP 0.03641 0.40627 5.80913
33 3LL5 IP8 0.03276 0.43105 6.0241
34 1G7C 5GP 0.03693 0.42133 6.25
35 2JBM SRT 0.04697 0.41578 6.35452
36 4ONQ SFG 0.03189 0.40913 6.57895
37 2PRG BRL 0.03465 0.41012 6.81818
38 2WH8 II2 0.01346 0.44954 7.56579
39 1LSS NAD 0.03495 0.40196 8.88158
40 1NU4 MLA 0.0193 0.4605 9.27835
41 5A3B APR 0.000000491 0.40018 9.57096
42 1P77 ATR 0.03286 0.43181 10.8553
43 5KAX RHQ 0.04887 0.42183 11.4458
44 4CS9 AMP 0.01855 0.4396 11.6402
45 4V1T ADP 0.03521 0.40977 12.5
46 5DCH 1YO 0.03829 0.42919 13.0208
47 1N8V BDD 0.04646 0.41252 17.8571
48 3U31 NAD 0.0000002204 0.64055 35.5172
49 1M2K APR 0.0000000672 0.42181 39.759
Pocket No.: 2; Query (leader) PDB : 5DY5; Ligand: 5GR; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5dy5.bio1) has 64 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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