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
2VCX 2.1 Å EC: 5.3.99.2 COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.1A. HOMO SAPIENS PROSTAGLANDIN BIOSYNTHESIS FATTY ACID BIOSYNTHESIS PROSTAGLANDIN D2 SYNTHASE PGDS ASTHMA CYTOPLASM ISOMERASE LIPID SYNTHESIS
Ref.: NOVEL PROSTAGLANDIN D SYNTHASE INHIBITORS GENERATED BY FRAGMENT-BASED DRUG DESIGN. J.MED.CHEM. V. 51 2178 2008
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
2 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
3 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
4 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
5 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
6 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
7 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
8 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
9 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
10 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
11 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
12 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
13 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
14 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
15 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
16 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
17 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
18 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
19 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
20 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
2 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
3 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
4 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
5 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
6 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
7 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
8 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
9 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
10 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
11 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
12 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
13 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
14 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
15 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
16 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
17 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
18 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
19 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
20 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
21 1PD2 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 1M0U - GSH C10 H17 N3 O6 S C(CC(=O)N[....
2 1GSQ - GDN C16 H19 N5 O10 S c1cc(c(cc1....
3 5H5L - GSH C10 H17 N3 O6 S C(CC(=O)N[....
4 1ZL9 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
5 3W8S - GSH C10 H17 N3 O6 S C(CC(=O)N[....
6 2VD1 ic50 = 0.138 uM D28 C17 H13 F N2 O3 S Cc1cc(ccc1....
7 4EC0 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
8 5AIX Kd = 0.17 uM KRX C20 H22 F3 N3 O2 COc1cccc(c....
9 2CVD Kd = 0.8 uM HQL C22 H27 N5 O c1ccc(cc1)....
10 3VI7 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
11 4EDY - GSH C10 H17 N3 O6 S C(CC(=O)N[....
12 4EE0 - GSF C10 H17 N3 O8 S C(CC(=O)N[....
13 5AIS Kd = 0.57 uM CWC C19 H22 N4 O CN(C)CCCC(....
14 2VCX ic50 = 0.021 uM D26 C12 H9 N3 S c1ccc(cc1)....
15 3VI5 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
16 5AIV Kd = 0.65 uM M1W C15 H16 N4 O3 COCCCNC(=O....
17 1V40 - GSH C10 H17 N3 O6 S C(CC(=O)N[....
18 1IYI - GSH C10 H17 N3 O6 S C(CC(=O)N[....
19 2VCW ic50 = 890 uM ZZA C10 H8 N2 O2 c1ccc(cc1)....
20 2VCZ - VC3 C9 H7 N3 O2 c1cc(ccc1c....
21 4EDZ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
22 3EE2 ic50 ~ 65 uM NZO C14 H11 N3 O3 S COC(=O)Nc1....
23 1IYH - GSH C10 H17 N3 O6 S C(CC(=O)N[....
24 2VD0 ic50 = 11.6 uM D27 C18 H17 N O5 COc1ccc(cc....
25 2VCQ ic50 = 0.92 uM D25 C12 H9 N3 O c1ccc(cc1)....
26 3VPQ - GSH C10 H17 N3 O6 S C(CC(=O)N[....
27 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: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 GSF 1 1
2 GSH 0.660714 0.72549
3 GDS 0.616667 0.722222
4 GTS 0.616667 0.910714
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 0HH 0.513514 0.6
12 HGS 0.507937 0.75
13 HCG 0.5 0.711538
14 GSO 0.486842 0.642857
15 GBI 0.475 0.6
16 3GC 0.473684 0.666667
17 48T 0.452381 0.610169
18 GVX 0.430233 0.637931
19 GCG 0.415584 0.678571
20 TS5 0.4 0.660714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VCX; Ligand: GSH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2vcx.bio1) has 96 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2VCX; Ligand: GSH; Similar sites found: 47
This union binding pocket(no: 2) in the query (biounit: 2vcx.bio1) has 101 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UGW GSH 0.007412 0.43808 None
2 2YFB SIN 0.01114 0.4425 1.50754
3 1Q1Y BB2 0.02571 0.41759 1.57068
4 1G27 BB1 0.04249 0.40044 1.78571
5 2VO4 GTB 0.001889 0.44886 2.01005
6 4MGA 27L 0.04857 0.42008 3.51759
7 5V4R MGT 0.03425 0.42003 3.7037
8 5KQA GSH 0.0005997 0.52653 3.78788
9 1V2A GTS 0.00007135 0.58048 4.0201
10 5ECP GSH 0.005253 0.45717 4.0201
11 3L4N GSH 0.001139 0.51087 4.72441
12 2VWA PTY 0.01653 0.45374 5.94059
13 2OKL BB2 0.04324 0.40006 5.94595
14 2V6K TGG 0.003933 0.44778 6.03015
15 1JLV GSH 0.0001647 0.54838 8.0402
16 1AXD GGL CYW GLY 0.0001175 0.56361 8.54271
17 3F6D GTX 0.0001574 0.51995 8.54271
18 2C3Q GTX 0.01753 0.42977 8.54271
19 5LOL GSH 0.0000107 0.62812 10.0503
20 3TDC 0EU 0.02505 0.41813 10.0503
21 5F06 GSH 0.003079 0.47399 11.0553
22 4F0B GDS 0.001804 0.4566 11.5578
23 4V3I ASP LEU THR ARG PRO 0.04815 0.4218 11.5578
24 3WYW GSH 0.0001519 0.55739 12.0603
25 1PN9 GTX 0.0002231 0.50767 13.5678
26 1GWC GTX 0.001143 0.49695 13.5678
27 5JF2 SF7 0.02977 0.4053 13.5678
28 2WCI GSH 0.007834 0.45729 14.0741
29 5TME UDP 0.04995 0.40896 16.0804
30 2DSA HPX 0.003656 0.43305 27.6382
31 2DSA GSH 0.004417 0.42663 27.6382
32 3VWX GSH 0.00008867 0.57045 29.6482
33 4ZBA GDS 0.003901 0.42356 36.1809
34 4ZB6 GDS 0.0009306 0.46618 37.1859
35 5AN1 GSH 0.0000002339 0.72639 38.6935
36 1DUG GSH 0.0000006733 0.4588 39.3162
37 2C80 GTX 0.00002147 0.40659 41.206
38 5GZZ GSH 0.0003002 0.53527 42.2018
39 3GST GPR 0.00001633 0.53164 42.7136
40 2C4J GSO 0.000003923 0.57979 43.7186
41 3IE3 GSH 0.000001087 0.57212 45.2261
42 3IE3 N11 0.000001087 0.57212 45.2261
43 1XW6 GSH 0.00000002073 0.59595 45.7286
44 3O76 GTB 0.00000005622 0.68874 46.7337
45 1TU7 GSH 0.00000002043 0.72899 48.7437
46 1ML6 GBX 0.00000856 0.48464 48.7437
47 2AAW GTX 0.0000008518 0.61699 49.7487
Pocket No.: 3; Query (leader) PDB : 2VCX; Ligand: D26; Similar sites found: 47
This union binding pocket(no: 3) in the query (biounit: 2vcx.bio1) has 101 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UGW GSH 0.007412 0.43808 None
2 2YFB SIN 0.01114 0.4425 1.50754
3 1Q1Y BB2 0.02571 0.41759 1.57068
4 1G27 BB1 0.04249 0.40044 1.78571
5 2VO4 GTB 0.001889 0.44886 2.01005
6 4MGA 27L 0.04857 0.42008 3.51759
7 5V4R MGT 0.03425 0.42003 3.7037
8 5KQA GSH 0.0005997 0.52653 3.78788
9 1V2A GTS 0.00007135 0.58048 4.0201
10 5ECP GSH 0.005253 0.45717 4.0201
11 3L4N GSH 0.001139 0.51087 4.72441
12 2VWA PTY 0.01653 0.45374 5.94059
13 2OKL BB2 0.04324 0.40006 5.94595
14 2V6K TGG 0.003933 0.44778 6.03015
15 1JLV GSH 0.0001647 0.54838 8.0402
16 1AXD GGL CYW GLY 0.0001175 0.56361 8.54271
17 3F6D GTX 0.0001574 0.51995 8.54271
18 2C3Q GTX 0.01753 0.42977 8.54271
19 5LOL GSH 0.0000107 0.62812 10.0503
20 3TDC 0EU 0.02505 0.41813 10.0503
21 5F06 GSH 0.003079 0.47399 11.0553
22 4F0B GDS 0.001804 0.4566 11.5578
23 4V3I ASP LEU THR ARG PRO 0.04815 0.4218 11.5578
24 3WYW GSH 0.0001519 0.55739 12.0603
25 1PN9 GTX 0.0002231 0.50767 13.5678
26 1GWC GTX 0.001143 0.49695 13.5678
27 5JF2 SF7 0.02977 0.4053 13.5678
28 2WCI GSH 0.007834 0.45729 14.0741
29 5TME UDP 0.04995 0.40896 16.0804
30 2DSA HPX 0.003656 0.43305 27.6382
31 2DSA GSH 0.004417 0.42663 27.6382
32 3VWX GSH 0.00008867 0.57045 29.6482
33 4ZBA GDS 0.003901 0.42356 36.1809
34 4ZB6 GDS 0.0009306 0.46618 37.1859
35 5AN1 GSH 0.0000002339 0.72639 38.6935
36 1DUG GSH 0.0000006733 0.4588 39.3162
37 2C80 GTX 0.00002147 0.40659 41.206
38 5GZZ GSH 0.0003002 0.53527 42.2018
39 3GST GPR 0.00001633 0.53164 42.7136
40 2C4J GSO 0.000003923 0.57979 43.7186
41 3IE3 GSH 0.000001087 0.57212 45.2261
42 3IE3 N11 0.000001087 0.57212 45.2261
43 1XW6 GSH 0.00000002073 0.59595 45.7286
44 3O76 GTB 0.00000005622 0.68874 46.7337
45 1TU7 GSH 0.00000002043 0.72899 48.7437
46 1ML6 GBX 0.00000856 0.48464 48.7437
47 2AAW GTX 0.0000008518 0.61699 49.7487
Pocket No.: 4; Query (leader) PDB : 2VCX; Ligand: GSH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2vcx.bio2) has 101 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2VCX; Ligand: GSH; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2vcx.bio2) has 96 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2VCX; Ligand: D26; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2vcx.bio2) has 96 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2VCX; Ligand: D26; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 2vcx.bio2) has 101 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback