Receptor
PDB id Resolution Class Description Source Keywords
5BWO 2.38 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH A PALMITOYL PEPTIDE SYNTHETIC CONSTRUCT HYDROLASE PEPTIDE-HYDROLASE COMPLEX
Ref.: CRYSTAL STRUCTURES OF SIRT3 REVEAL THAT THE ALPHA 2 LOOP AND ALPHA 3-HELIX AFFECT THE INTERACTION WITH LONG-CHAIN ACYL LYSINE. FEBS LETT. V. 590 3019 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...
PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP B:101;
Valid;
Atoms found LESS than expected: % Diff = 0.106;
submit data
1187.5 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JSR 1.7 Å EC: 3.5.1.- CRYSTAL STRUCTURE OF HUMAN SIRT3 WITH ELT INHIBITOR 11C [N-{ CARBAMOYLTHIENO[3,2-D]PYRIMIDIN-4-YL)PIPERIDIN-4-YL]ETHYL}-E THYLTHIOPHENE-2,5-DICARBOXAMIDE] HOMO SAPIENS DEACETYLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: DISCOVERY OF THIENO[3,2-D]PYRIMIDINE-6-CARBOXAMIDES POTENT INHIBITORS OF SIRT1, SIRT2, AND SIRT3. J.MED.CHEM. V. 56 3666 2013
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 4FZ3 - ACE ARG HIS LYS ALY MCM n/a n/a
2 4JT9 ic50 = 0.0072 uM 1NS C15 H21 N5 O3 S2 CS(=O)(=O)....
3 5BWO - PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP n/a n/a
4 4JT8 ic50 = 0.033 uM 1NR C19 H27 N5 O2 S CC(C)(C)C(....
5 4BV3 Kd = 16.5 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
6 4BVH - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
7 4C7B - ARG HIS LYS FDL n/a n/a
8 4C78 - BVB C14 H11 Br O2 c1cc(ccc1/....
9 5BWN - GLN THR ALA ARG MYK SER THR GLY GLY TRP n/a n/a
10 4BN4 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
11 4JSR ic50 = 0.004 uM 1NQ C22 H26 N6 O3 S2 CCNC(=O)c1....
12 4BVE - THR ARG SER GLY FZN VAL MET ARG ARG LEU n/a n/a
13 4BVB - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
14 4FVT - CNA C22 H30 N7 O13 P2 c1cc(c[n+]....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4FZ3 - ACE ARG HIS LYS ALY MCM n/a n/a
2 4JT9 ic50 = 0.0072 uM 1NS C15 H21 N5 O3 S2 CS(=O)(=O)....
3 5BWO - PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP n/a n/a
4 4JT8 ic50 = 0.033 uM 1NR C19 H27 N5 O2 S CC(C)(C)C(....
5 4BV3 Kd = 16.5 uM OCZ C13 H13 Cl N2 O c1cc2c(cc1....
6 4BVH - OAD C17 H25 N5 O15 P2 CC(=O)O[C@....
7 4C7B - ARG HIS LYS FDL n/a n/a
8 4C78 - BVB C14 H11 Br O2 c1cc(ccc1/....
9 5BWN - GLN THR ALA ARG MYK SER THR GLY GLY TRP n/a n/a
10 4BN4 - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
11 4JSR ic50 = 0.004 uM 1NQ C22 H26 N6 O3 S2 CCNC(=O)c1....
12 4BVE - THR ARG SER GLY FZN VAL MET ARG ARG LEU n/a n/a
13 4BVB - AR6 C15 H23 N5 O14 P2 c1nc(c2c(n....
14 4FVT - CNA C22 H30 N7 O13 P2 c1cc(c[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: PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 GLN THR ALA ARG MYK SER THR GLY GLY TRP 1 1
2 PLM GLN THR ALA ARG LYS SER THR GLY GLY TRP 1 1
3 THR ALA ARG MYK SER THR GLY 0.65493 0.835821
4 THR ALA ARG M3L SER THR GLY GLY LYS ALA 0.532051 0.72
5 ARG ARG ARG ARG SER TRP TYR 0.468354 0.828571
6 LYS GLN THR ALA ARG M3L SER THR GLY 0.467105 0.72
7 ALA ASN SER ARG TRP ALY THR SER ILE ILE 0.462857 0.941176
8 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.461111 0.913043
9 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.45614 0.911765
10 ILE SER PRO ARG THR LEU ASP ALA TRP 0.441026 0.866667
11 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.434066 0.855072
12 THR SER THR THR SER VAL ALA SER SER TRP 0.43038 0.710145
13 ALA ARG MLZ SER THR GLY GLY ALY 0.429448 0.785714
14 ALA ARG M3L SER THR GLY GLY ALY 0.426829 0.723684
15 ALA ARG MLY SER THR GLY GLY ALY 0.426829 0.743243
16 SER ARG TYR TRP ALA ILE ARG THR ARG 0.425414 0.873239
17 THR SER THR LEU GLN GLU GLN ILE GLY TRP 0.424581 0.826087
18 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.424242 0.869565
19 ARG GLY PHE ALA LEU M3L SER THR HIS GLY 0.420213 0.855263
20 ALA ARG LYS SEP THR GLY GLY LYS 0.417178 0.702703
21 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.416667 0.851351
22 ALA GLN THR ALA ARG ALY SER THR 0.416149 0.791045
23 ALA ASN SER ARG TRP PRO THR SER ALY ILE 0.407407 0.891892
24 ACE GLN THR ALA ARG KCR SER THR 0.407186 0.764706
25 LEU PRO LYS MYK THR GLY GLY 0.405714 0.702703
26 ALA ASN SER ARG TRP PRO THR SER FAK ILE 0.402985 0.822785
27 ILE ARG TYR PRO LYS THR PHE GLY TRP 0.40099 0.818182
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JSR; Ligand: 1NQ; Similar sites found: 30
This union binding pocket(no: 1) in the query (biounit: 4jsr.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OWK NGA 0.04047 0.43324 None
2 4XCP PLM 0.04637 0.41341 None
3 5HS2 CTP 0.04273 0.40174 1.72414
4 5L44 K26 0.01717 0.42171 2.45614
5 1Q8S MAN MMA 0.04446 0.41293 2.45614
6 1T9D FAD 0.001227 0.41325 2.80702
7 3VYW SAM 0.01816 0.40852 2.80702
8 2XG5 EC2 0.02126 0.44383 2.89017
9 2XG5 EC5 0.02126 0.44383 2.89017
10 5N53 8NB 0.0378 0.42338 3.07692
11 4I9B NAD 0.0292 0.40152 3.15789
12 3I9U DTU 0.01799 0.44141 3.42205
13 2ZX2 RAM 0.03601 0.42854 3.58974
14 5GVR LMR 0.02151 0.41236 3.84615
15 2XBL M7P 0.03556 0.40578 4.0404
16 3BFV ADP 0.04609 0.40614 4.05904
17 4JGT PYR 0.04551 0.4117 4.21053
18 3EGI ADP 0.04549 0.41708 4.36893
19 1RZU ADP 0.01481 0.43599 4.91228
20 4R08 URI 0.04614 0.40299 5.26316
21 2VOH CIT 0.02307 0.40753 5.73248
22 1SQL GUN 0.002618 0.48742 6.16438
23 1JG3 ADN 0.02839 0.40484 6.80851
24 5H6S HDH 0.03996 0.42611 7.36842
25 4ZM4 PLP 0.04602 0.40305 8.77193
26 3EYA FAD 0.003586 0.40693 11.2281
27 1QXA GLY GLY GLY 0.02595 0.41522 11.4894
28 5A3B APR 0.000001042 0.57548 24.5614
29 3U31 NAD 0.00001109 0.55134 36.8421
30 1M2K APR 0.000004036 0.41841 38.9558
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