Receptor
PDB id Resolution Class Description Source Keywords
4EE0 1.75 Å EC: 5.3.99.2 CRYSTAL STRUCTURE OF HH-PGDS WITH WATER DISPLACING INHIBITOR HOMO SAPIENS INHIBITOR SOLVENT REPLACEMENT ISOMERASE-ISOMERASE INHIBITO
Ref.: INVESTIGATION OF THE BINDING POCKET OF HUMAN HEMATO PROSTAGLANDIN (PG) D2 SYNTHASE (HH-PGDS): A TALE OF WATERS. BIOORG.MED.CHEM.LETT. V. 22 3795 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0O4 A:202;
B:201;
Valid;
Valid;
none;
none;
submit data
361.437 C22 H23 N3 O2 c1ccc...
GSF A:203;
B:202;
Valid;
Valid;
none;
none;
submit data
339.322 C10 H17 N3 O8 S C(CC(...
MG A:201;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YWX 1.74 Å EC: 5.3.99.2 CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE WITH F092 HOMO SAPIENS PROSTAGLANDIN SYNTHASE INHIBITOR TRANSFERASE TRANSFERASETRANSFERASE INHIBITOR COMPLEX
Ref.: CHARACTERIZATION OF CRYSTAL WATER MOLECULES IN A HIGH-AFFINITY INHIBITOR AND HEMATOPOIETIC PROSTAGLA SYNTHASE COMPLEX BY INTERACTION ENERGY STUDIES. BIOORG. MED. CHEM. V. 26 4726 2018
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5YWX Kd = 0.14 nM 93C C20 H17 N5 O2 c1ccnc(c1)....
2 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
3 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
4 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
5 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
6 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
7 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
8 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
9 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
10 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
11 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
12 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
13 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
14 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
15 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
16 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
17 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
18 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
19 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
20 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
21 6N4E ic50 = 9.9 nM KCD C20 H24 F2 N2 O3 CC(C)(C1CC....
22 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5YWX Kd = 0.14 nM 93C C20 H17 N5 O2 c1ccnc(c1)....
2 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
3 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
4 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
5 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
6 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
7 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
8 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
9 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
10 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
11 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
12 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
13 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
14 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
15 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
16 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
17 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
18 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
19 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
20 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
21 6N4E ic50 = 9.9 nM KCD C20 H24 F2 N2 O3 CC(C)(C1CC....
22 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
23 6N69 ic50 = 220000 nM KDV C10 H6 N2 c1ccc2c(c1....
24 1PD2 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
50% Homology Family (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 1M0U - GSH C10 H17 N3 O6 S C(CC(=O)N[....
2 2ON5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
3 1OE7 Kd = 9 uM GSH C10 H17 N3 O6 S C(CC(=O)N[....
4 2CAQ Kd = 285 uM GSH C10 H17 N3 O6 S C(CC(=O)N[....
5 2C80 Kd = 4.7 uM GTX C16 H30 N3 O6 S CCCCCCSC[C....
6 2CA8 Kd = 22 uM GSH C10 H17 N3 O6 S C(CC(=O)N[....
7 2F8F Kd = 21 uM GSH C10 H17 N3 O6 S C(CC(=O)N[....
8 1OE8 Kd = 9 uM GSH C10 H17 N3 O6 S C(CC(=O)N[....
9 2GSQ - GBI C17 H22 I N3 O6 S c1cc(cc(c1....
10 1GSQ - GDN C16 H19 N5 O10 S c1cc(c(cc1....
11 5H5L - GSH C10 H17 N3 O6 S C(CC(=O)N[....
12 5YWX Kd = 0.14 nM 93C C20 H17 N5 O2 c1ccnc(c1)....
13 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
14 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
15 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
16 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
17 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
18 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
19 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
20 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
21 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
22 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
23 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
24 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
25 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
26 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
27 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
28 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
29 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
30 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
31 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
32 6N4E ic50 = 9.9 nM KCD C20 H24 F2 N2 O3 CC(C)(C1CC....
33 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
34 1Q4J - GTX C16 H30 N3 O6 S CCCCCCSC[C....
35 1ZL9 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
36 3W8S - GSH C10 H17 N3 O6 S C(CC(=O)N[....
37 6N69 ic50 = 220000 nM KDV C10 H6 N2 c1ccc2c(c1....
38 1PD2 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 0O4; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 0O4 1 1
2 0O5 0.632184 0.96
3 7PQ 0.62069 0.886792
4 9PQ 0.609195 0.87037
Ligand no: 2; Ligand: GSF; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 GSF 1 1
2 GSH 0.660714 0.72549
3 GTS 0.616667 0.910714
4 GDS 0.616667 0.722222
5 GS8 0.616667 0.862745
6 GSM 0.606557 0.654545
7 AHE 0.596774 0.666667
8 HGD 0.587302 0.722222
9 TGG 0.544118 0.698113
10 GSB 0.534247 0.654545
11 BWS 0.533333 0.641509
12 0HH 0.513514 0.6
13 HGS 0.507937 0.75
14 HCG 0.5 0.711538
15 GSO 0.486842 0.642857
16 GBI 0.475 0.6
17 3GC 0.473684 0.666667
18 48T 0.452381 0.610169
19 GVX 0.430233 0.637931
20 GCG 0.415584 0.678571
21 TS5 0.4 0.660714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YWX; Ligand: GSH; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 5ywx.bio2) has 104 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 3ISO GSH 44.4444
5 3O76 GTB 46.9697
6 2GSR GTS 47.4747
7 2GSR GTS 47.4747
8 1TU7 GSH 48.9899
9 3VPQ GSH 50
10 3VPQ GSH 50
11 1U3I GSH 50
Pocket No.: 2; Query (leader) PDB : 5YWX; Ligand: GSH; Similar sites found with APoc: 4
This union binding pocket(no: 2) in the query (biounit: 5ywx.bio2) has 96 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 3ISO GSH 44.4444
5 3VPQ GSH 50
6 3VPQ GSH 50
7 1U3I GSH 50
Pocket No.: 3; Query (leader) PDB : 5YWX; Ligand: 93C; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 5ywx.bio2) has 104 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 3ISO GSH 44.4444
5 3O76 GTB 46.9697
6 2GSR GTS 47.4747
7 2GSR GTS 47.4747
8 1TU7 GSH 48.9899
9 3VPQ GSH 50
10 3VPQ GSH 50
11 1U3I GSH 50
Pocket No.: 4; Query (leader) PDB : 5YWX; Ligand: 93C; Similar sites found with APoc: 4
This union binding pocket(no: 4) in the query (biounit: 5ywx.bio2) has 97 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 3ISO GSH 44.4444
5 3VPQ GSH 50
6 3VPQ GSH 50
7 1U3I GSH 50
Pocket No.: 5; Query (leader) PDB : 5YWX; Ligand: GSH; Similar sites found with APoc: 14
This union binding pocket(no: 5) in the query (biounit: 5ywx.bio1) has 96 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 5AN1 GSH 38.8889
5 5AN1 GSH 38.8889
6 5AN1 GSH 38.8889
7 5AN1 GSH 38.8889
8 5AN1 GSH 38.8889
9 3ISO GSH 44.4444
10 3O76 GTB 46.9697
11 2GSR GTS 47.4747
12 2GSR GTS 47.4747
13 1TU7 GSH 48.9899
14 1TU7 GSH 48.9899
15 3VPQ GSH 50
16 3VPQ GSH 50
17 1U3I GSH 50
Pocket No.: 6; Query (leader) PDB : 5YWX; Ligand: GSH; Similar sites found with APoc: 14
This union binding pocket(no: 6) in the query (biounit: 5ywx.bio1) has 104 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 5AN1 GSH 38.8889
5 5AN1 GSH 38.8889
6 5AN1 GSH 38.8889
7 5AN1 GSH 38.8889
8 5AN1 GSH 38.8889
9 3ISO GSH 44.4444
10 3O76 GTB 46.9697
11 2GSR GTS 47.4747
12 2GSR GTS 47.4747
13 1TU7 GSH 48.9899
14 1TU7 GSH 48.9899
15 3VPQ GSH 50
16 3VPQ GSH 50
17 1U3I GSH 50
Pocket No.: 7; Query (leader) PDB : 5YWX; Ligand: 93C; Similar sites found with APoc: 14
This union binding pocket(no: 7) in the query (biounit: 5ywx.bio1) has 96 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 5AN1 GSH 38.8889
5 5AN1 GSH 38.8889
6 5AN1 GSH 38.8889
7 5AN1 GSH 38.8889
8 5AN1 GSH 38.8889
9 3ISO GSH 44.4444
10 3O76 GTB 46.9697
11 2GSR GTS 47.4747
12 2GSR GTS 47.4747
13 1TU7 GSH 48.9899
14 1TU7 GSH 48.9899
15 3VPQ GSH 50
16 3VPQ GSH 50
17 1U3I GSH 50
Pocket No.: 8; Query (leader) PDB : 5YWX; Ligand: 93C; Similar sites found with APoc: 14
This union binding pocket(no: 8) in the query (biounit: 5ywx.bio1) has 104 residues
No: Leader PDB Ligand Sequence Similarity
1 5AN1 GSH 38.8889
2 5AN1 GSH 38.8889
3 5AN1 GSH 38.8889
4 5AN1 GSH 38.8889
5 5AN1 GSH 38.8889
6 5AN1 GSH 38.8889
7 5AN1 GSH 38.8889
8 5AN1 GSH 38.8889
9 3ISO GSH 44.4444
10 3O76 GTB 46.9697
11 2GSR GTS 47.4747
12 2GSR GTS 47.4747
13 1TU7 GSH 48.9899
14 1TU7 GSH 48.9899
15 3VPQ GSH 50
16 3VPQ GSH 50
17 1U3I GSH 50
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