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 318 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 280 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 187 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
Ligand no: 1; Ligand: PGD; Similar ligands found: 73
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 GKE 0.535433 0.914634
22 GDD 0.535433 0.914634
23 GDC 0.535433 0.914634
24 GDR 0.53125 0.914634
25 GFB 0.53125 0.914634
26 GTG 0.53125 0.892857
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 JB3 0.507353 0.903614
38 MD1 0.5 0.940476
39 ALF 5GP 0.5 0.827586
40 FEG 0.492754 0.840909
41 ZGP 0.489209 0.873563
42 GDP AF3 0.488189 0.827586
43 GDP ALF 0.488189 0.827586
44 ALF GDP 0.488189 0.827586
45 CAG 0.482517 0.842697
46 CG2 0.475177 0.915663
47 TPG 0.472973 0.846154
48 FE9 0.472603 0.840426
49 U2G 0.471429 0.915663
50 PGD O 0.469799 0.91954
51 G3D 0.468254 0.9125
52 0O2 0.458015 0.9125
53 GDP 7MG 0.455882 0.869048
54 DBG 0.453333 0.903614
55 G G 0.451852 0.902439
56 GMP 0.451327 0.814815
57 G4P 0.449612 0.9125
58 GH3 0.44186 0.901235
59 G4M 0.433962 0.842697
60 3GP 0.429752 0.876543
61 GCP G 0.422222 0.853659
62 AKW 0.42069 0.894118
63 G1G 0.417219 0.882353
64 U A G G 0.416107 0.890244
65 DGT 0.415385 0.857143
66 GPX 0.413534 0.876543
67 GPC 0.413333 0.862069
68 A G 0.409396 0.890244
69 G A A A 0.409396 0.879518
70 2GP 0.406504 0.888889
71 DGI 0.40625 0.857143
72 R5I 0.4 0.876543
73 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 AF3 0.6 0.784946
4 GDP ALF 0.586777 0.784946
5 ALF GDP 0.586777 0.784946
6 2MD 0.57037 0.954023
7 ALF 5GP 0.55 0.784946
8 GDP 7MG 0.546154 0.822222
9 GNH 0.533333 0.840909
10 G G 0.530769 0.852273
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 GMV 0.5 0.831461
18 GP2 0.5 0.822222
19 GTP 0.5 0.850575
20 GAV 0.496063 0.885057
21 G1R 0.496 0.840909
22 GCP 0.496 0.831461
23 9GM 0.492063 0.831461
24 GNP 0.492063 0.831461
25 G2P 0.492063 0.822222
26 GCP G 0.477273 0.806818
27 GKD 0.474453 0.842697
28 GFB 0.474074 0.842697
29 GDR 0.474074 0.842697
30 G2R 0.473282 0.822222
31 PGD 0.469799 0.91954
32 MD1 0.469799 0.931818
33 Y9Z 0.466667 0.778947
34 GDD 0.466667 0.842697
35 GDC 0.466667 0.842697
36 GKE 0.466667 0.842697
37 6CK 0.459854 0.824176
38 G3A 0.459854 0.852273
39 G A A A 0.458904 0.831461
40 A G 0.458904 0.840909
41 GPG 0.458647 0.842697
42 G3D 0.457364 0.83908
43 G5P 0.456522 0.852273
44 U A G G 0.455782 0.840909
45 JB2 0.453237 0.842697
46 GTG 0.452555 0.844444
47 GPD 0.45 0.815217
48 GDX 0.45 0.852273
49 YGP 0.448529 0.855556
50 ZGP 0.448276 0.808511
51 JB3 0.444444 0.833333
52 3GP 0.442623 0.806818
53 FEG 0.441379 0.778947
54 GMP 0.439655 0.75
55 CAG 0.433333 0.8
56 NGD 0.431507 0.863636
57 U2G 0.431507 0.865169
58 G4P 0.428571 0.83908
59 G U 0.428571 0.853933
60 0O2 0.416058 0.83908
61 G C 0.413333 0.853933
62 MTE 0.41129 0.816092
63 DBG 0.407643 0.833333
64 CG2 0.406667 0.865169
65 G G G C 0.406452 0.865169
66 FE9 0.406452 0.85567
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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