Receptor
PDB id Resolution Class Description Source Keywords
3DMR 2.5 Å EC: 1.-.-.- STRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0 RHODOBACTER CAPSULATUS OXIDOREDUCTASE DMSO MOLYBDOPTERIN PH 7
Ref.: MOLYBDENUM ACTIVE CENTRE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS: CRYSTAL STRUCTURE OF THE OXIDISED ENZYME AT 1.82-A RESOLUTION AND THE DITHIONITE-REDUCED ENZYME AT 2.8-A RESOLUTION J.BIOL.INORG.CHEM. V. 2 690 1997
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6MO A:784;
 Part of Protein;
 none;
 submit data
95.94 Mo [Mo+6...
O A:786;
 Invalid;
 none;
 submit data
15.999 O O
PGD A:783;
 Valid;
 none;
 submit data
738.541 C20 H24 N10 O13 P2 S2 c1nc2...
PGD O A:782;
 Valid;
 none;
 submit data
754.548 n/a S(O)C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DMR 1.82 Å EC: 1.-.-.- OXIDIZED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS RHODOBACTER CAPSULATUS OXIDOREDUCTASE REDUCTASE DMSO MOLYBDOPTERIN
Ref.: MOLYBDENUM ACTIVE CENTRE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS: CRYSTAL STRUCTURE OF THE OXIDISED ENZYME AT 1.82-A RESOLUTION AND THE DITHIONITE-REDUCED ENZYME AT 2.8-A RESOLUTION J.BIOL.INORG.CHEM. V. 2 690 1997
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 383 families.
1 3DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
2 4DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
3 1DMS - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
4 1E5V - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
5 1E18 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
6 1H5N - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
7 1E61 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
8 1DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
9 1E60 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 337 families.
1 3DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
2 4DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
3 1DMS - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
4 1E5V - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
5 1E18 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
6 1H5N - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
7 1E61 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
8 1DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
9 1E60 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
10 1EU1 - GLC C6 H12 O6 C([C@@H]1[....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 225 families.
1 3DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
2 4DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
3 1DMS - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
4 1E5V - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
5 1E18 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
6 1H5N - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
7 1E61 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
8 1DMR - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
9 1E60 - PGD C20 H24 N10 O13 P2 S2 c1nc2c(n1[....
10 1TMO - 2MD C20 H28 N10 O13 P2 S2 c1nc2c(n1[....
11 1EU1 - GLC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PGD; Similar ligands found: 74
No: Ligand ECFP6 Tc MDL keys Tc
1 PGD 1 1
2 GP3 0.612613 0.925926
3 MGD 0.606061 0.963855
4 GNH 0.60177 0.91358
5 G1R 0.6 0.91358
6 GDP 0.59292 0.925
7 GTP 0.591304 0.925
8 GSP 0.581197 0.926829
9 GCP 0.57265 0.902439
10 Y9Z 0.572581 0.840909
11 G2R 0.570248 0.891566
12 GNP 0.567797 0.902439
13 9GM 0.567797 0.902439
14 5GP 0.5625 0.9125
15 G 0.5625 0.9125
16 GMV 0.550847 0.902439
17 GAV 0.545455 0.938272
18 YGP 0.539683 0.904762
19 6CK 0.539062 0.892857
20 2MD 0.536765 0.963855
21 GDC 0.535433 0.914634
22 GDD 0.535433 0.914634
23 GKE 0.535433 0.914634
24 GTG 0.53125 0.892857
25 GDR 0.53125 0.914634
26 GFB 0.53125 0.914634
27 GKD 0.530769 0.914634
28 JB2 0.530769 0.914634
29 GPG 0.528 0.914634
30 G3A 0.527132 0.925926
31 GPD 0.526718 0.882353
32 GP2 0.525424 0.891566
33 G5P 0.523077 0.925926
34 G2P 0.516393 0.891566
35 GDX 0.515152 0.925926
36 NGD 0.514706 0.914634
37 GDP BEF 0.508197 0.86747
38 JB3 0.507353 0.903614
39 GTP MG 0.504065 0.888889
40 MD1 0.5 0.940476
41 ALF 5GP 0.5 0.827586
42 FEG 0.492754 0.840909
43 ZGP 0.489209 0.873563
44 GDP ALF 0.488189 0.827586
45 GDP AF3 0.488189 0.827586
46 CAG 0.482517 0.842697
47 CG2 0.475177 0.915663
48 TPG 0.472973 0.846154
49 FE9 0.472603 0.840426
50 U2G 0.471429 0.915663
51 PGD O 0.469799 0.91954
52 G3D 0.468254 0.9125
53 0O2 0.458015 0.9125
54 GDP 7MG 0.455882 0.869048
55 DBG 0.453333 0.903614
56 GMP 0.451327 0.814815
57 G4P 0.449612 0.9125
58 KB7 0.448 0.770115
59 KBD 0.44697 0.790698
60 GH3 0.44186 0.901235
61 G4M 0.433962 0.842697
62 3GP 0.429752 0.876543
63 KBJ 0.423358 0.764045
64 AKW 0.42069 0.894118
65 G1G 0.417219 0.882353
66 DGT 0.415385 0.857143
67 I2C FE2 CMO CMO 0.414474 0.815217
68 QBQ 0.414062 0.9125
69 GPX 0.413534 0.876543
70 GPC 0.413333 0.862069
71 2GP 0.406504 0.888889
72 DGI 0.40625 0.857143
73 R5I 0.4 0.876543
74 R7I 0.4 0.876543
Ligand no: 2; Ligand: PGD O; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 PGD O 1 1
2 MGD 0.706349 0.954023
3 GDP BEF 0.626087 0.820225
4 GTP MG 0.606838 0.83908
5 GDP AF3 0.6 0.784946
6 GDP ALF 0.586777 0.784946
7 2MD 0.57037 0.954023
8 ALF 5GP 0.55 0.784946
9 GDP 7MG 0.546154 0.822222
10 GNH 0.533333 0.840909
11 GDP 0.525 0.850575
12 G1R G1R 0.524138 0.833333
13 5GP 0.521368 0.83908
14 G 0.521368 0.83908
15 GP3 0.516667 0.852273
16 GSP 0.504 0.875
17 GP2 0.5 0.822222
18 GMV 0.5 0.831461
19 GTP 0.5 0.850575
20 GAV 0.496063 0.885057
21 GCP 0.496 0.831461
22 G1R 0.496 0.840909
23 9GM 0.492063 0.831461
24 GNP 0.492063 0.831461
25 G2P 0.492063 0.822222
26 GKD 0.474453 0.842697
27 GDR 0.474074 0.842697
28 GFB 0.474074 0.842697
29 G2R 0.473282 0.822222
30 MD1 0.469799 0.931818
31 PGD 0.469799 0.91954
32 GKE 0.466667 0.842697
33 Y9Z 0.466667 0.778947
34 GDD 0.466667 0.842697
35 GDC 0.466667 0.842697
36 I2C FE2 CMO CMO 0.463087 0.8125
37 G3A 0.459854 0.852273
38 6CK 0.459854 0.824176
39 GPG 0.458647 0.842697
40 G3D 0.457364 0.83908
41 G5P 0.456522 0.852273
42 JB2 0.453237 0.842697
43 GTG 0.452555 0.844444
44 GPD 0.45 0.815217
45 GDX 0.45 0.852273
46 YGP 0.448529 0.855556
47 ZGP 0.448276 0.808511
48 JB3 0.444444 0.833333
49 3GP 0.442623 0.806818
50 FEG 0.441379 0.778947
51 GMP 0.439655 0.75
52 KB7 0.4375 0.712766
53 CAG 0.433333 0.8
54 NGD 0.431507 0.863636
55 U2G 0.431507 0.865169
56 G4P 0.428571 0.83908
57 PCD PEO 0.41875 0.851064
58 0O2 0.416058 0.83908
59 KBD 0.416058 0.731183
60 G C 0.413333 0.853933
61 MTE 0.41129 0.816092
62 DBG 0.407643 0.833333
63 CG2 0.406667 0.865169
64 FE9 0.406452 0.85567
65 KBJ 0.404255 0.708333
66 M7G A2M G 0.402235 0.831579
Similar Ligands (3D)
Ligand no: 1; Ligand: PGD; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: PGD O; 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 : 1DMR; Ligand: PGD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1dmr.bio1) has 66 residues
No: Leader PDB Ligand Sequence Similarity
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