Receptor
PDB id Resolution Class Description Source Keywords
1TMO 2.5 Å EC: 1.6.6.9 TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA SHEWANELLA MASSILIA OXIDOREDUCTASE TMAO REDUCTASE OXOTRANSFERASE MOLYBDOENZYME MO-COFACTOR MOLYBDENUM BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)
Ref.: CRYSTAL STRUCTURE OF OXIDIZED TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA AT 2.5 A RESOLUTION. J.MOL.BIOL. V. 284 435 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2MD A:799;
A:800;
Valid;
Valid;
none;
none;
submit data
742.573 C20 H28 N10 O13 P2 S2 c1nc2...
6351_ A:801;
Part of Protein;
none;
submit data n/a n/a n/a n/a
6352_6353_ A:801;
Invalid;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1TMO 2.5 Å EC: 1.6.6.9 TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA SHEWANELLA MASSILIA OXIDOREDUCTASE TMAO REDUCTASE OXOTRANSFERASE MOLYBDOENZYME MO-COFACTOR MOLYBDENUM BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)
Ref.: CRYSTAL STRUCTURE OF OXIDIZED TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA AT 2.5 A RESOLUTION. J.MOL.BIOL. V. 284 435 1998
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1TMO - 2MD C20 H28 N10 O13 P2 S2 c1nc2c(n1[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1TMO - 2MD C20 H28 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 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: 2MD; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 2MD 1 1
2 MGD 0.694215 1
3 G1R 0.654206 0.880952
4 GP3 0.653846 0.892857
5 GSP 0.633027 0.894118
6 GDP 0.632075 0.891566
7 GTP 0.62963 0.891566
8 GNH 0.626168 0.880952
9 GCP 0.609091 0.870588
10 G2R 0.605263 0.860465
11 GNP 0.603604 0.870588
12 Y9Z 0.59322 0.813187
13 GMV 0.585586 0.870588
14 G 0.584906 0.879518
15 5GP 0.584906 0.879518
16 GFB 0.575 0.882353
17 GDR 0.575 0.882353
18 MD1 0.571429 0.97619
19 PGD O 0.57037 0.954023
20 G3A 0.570248 0.892857
21 GDD 0.566667 0.882353
22 GDC 0.566667 0.882353
23 GKE 0.566667 0.882353
24 G5P 0.565574 0.892857
25 GAV 0.565217 0.904762
26 GTG 0.561983 0.862069
27 GPG 0.559322 0.882353
28 GP2 0.558559 0.860465
29 6CK 0.557377 0.862069
30 GDP MG 0.548673 0.827586
31 JB2 0.548387 0.882353
32 GKD 0.548387 0.882353
33 G2P 0.547826 0.860465
34 JB3 0.546875 0.872093
35 GDX 0.544 0.892857
36 GPD 0.544 0.852273
37 GDP BEF 0.54386 0.808989
38 NGD 0.542636 0.882353
39 PGD 0.536765 0.963855
40 YGP 0.532787 0.895349
41 ALF 5GP 0.530435 0.8
42 GTP MG 0.529915 0.827586
43 BEF GDP 0.529915 0.8
44 GDP AF3 0.529412 0.8
45 GCP G 0.525424 0.837209
46 GDP ALF 0.516667 0.8
47 G G 0.516393 0.858824
48 ZGP 0.515152 0.844444
49 G3D 0.508475 0.879518
50 U2G 0.507576 0.905882
51 CAG 0.507353 0.815217
52 FEG 0.496241 0.813187
53 0O2 0.495935 0.879518
54 G4P 0.487603 0.879518
55 TPG 0.485915 0.879121
56 GMP 0.481132 0.785714
57 GDP 7MG 0.48062 0.83908
58 CG2 0.477941 0.905882
59 DBG 0.475524 0.872093
60 G4M 0.473333 0.815217
61 3GP 0.469027 0.845238
62 G1R G1R 0.465278 0.850575
63 FE9 0.464789 0.852632
64 I2C FE2 CMO CMO 0.450704 0.827957
65 G A A A 0.45 0.848837
66 U A G G 0.446809 0.858824
67 G G U 0.443609 0.858824
68 GH3 0.443548 0.869048
69 GPX 0.436508 0.845238
70 2GP 0.431034 0.857143
71 G1G 0.427586 0.852273
72 DGT 0.427419 0.827586
73 DGI 0.418033 0.827586
74 IDP 0.413223 0.86747
75 P2G 0.411765 0.790698
76 BGO 0.411348 0.850575
77 G C 0.402778 0.872093
78 GGM 0.402778 0.831461
79 U G A 0.402516 0.862069
80 MGP 0.4 0.860465
81 G2Q 0.4 0.860465
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1TMO; Ligand: 2MD; 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: 1tmo.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1TMO; Ligand: 2MD; Similar sites found: 40
This union binding pocket(no: 2) in the query (biounit: 1tmo.bio1) has 38 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1T3D CYS 0.0482 0.40444 2.07612
2 4K28 NAD 0.01075 0.40094 2.60223
3 3LST SAH 0.01909 0.4132 2.87356
4 4WXJ GLU 0.03026 0.41786 2.97398
5 1P31 EPU 0.01018 0.41637 3.15789
6 3ALT MLB 0.03369 0.41609 3.18471
7 5GWE GWM 0.04043 0.40707 3.20988
8 3U31 NAD 0.003283 0.42892 3.7931
9 3EGI ADP 0.0449 0.4084 3.8835
10 1M2K APR 0.002053 0.42252 4.01606
11 2X2T GAL NGA 0.009834 0.43558 4.57516
12 1KQF MGD 0.00008907 0.45698 5.10204
13 5K3W PLP 0.01159 0.42039 5.11182
14 2QCX PF1 0.04503 0.40981 5.32319
15 2PHW MAN MAN 0.03911 0.41172 5.55556
16 2PHR MAN MAN 0.04568 0.40798 5.55556
17 5UXF 2BA 0.03016 0.40014 5.84795
18 3G89 SAM 0.02907 0.40409 6.0241
19 1R27 MGD 0.001674 0.40152 6.15199
20 5WSY 7UC 0.0304 0.41373 6.35838
21 4RL4 PPV 0.03271 0.40773 6.60377
22 1XDS SAM 0.02557 0.40688 7.21925
23 3FGZ BEF 0.03801 0.42079 7.8125
24 4LED XXR 0.02209 0.41987 7.83582
25 4A6D SAM 0.009921 0.41374 8.2153
26 5AHO TLA 0.04985 0.4093 11.0119
27 1H0H MGD 0.000009666 0.48513 11.8215
28 1G8K MGD 0.000002072 0.41344 12.782
29 3IT7 TLA 0.02055 0.41455 13.1868
30 1L5Y BEF 0.02418 0.41435 14.1935
31 3P9Y N7P THR SEP PRO SER TYR SET 0.01539 0.41112 19.697
32 4YDD MGD 0.0000002312 0.42379 22.6779
33 4YDD MD1 0.0000002312 0.42379 22.6779
34 2IVF MGD 0.000001053 0.51695 24.9698
35 2IVF MD1 0.0003064 0.42175 24.9698
36 2V3V MGD 0.000004206 0.52935 34.5781
37 2VPY MGD 0.00001263 0.50508 35.5556
38 2NYA MGD 0.001005 0.40504 36.1111
39 2E7Z MGD 0.00004556 0.46441 37.8267
40 2IV2 MGD 0.000001089 0.51158 40.5594
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