Receptor
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
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...
PGD A:783;
 Valid;
 none;
 submit data
738.541 C20 H24 N10 O13 P2 S2 c1nc2...
PGD O O A:782;
 Part of Protein;
 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
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 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[....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 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 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: PGD; Similar ligands found: 72
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 5GP 0.5625 0.9125
14 G 0.5625 0.9125
15 GMV 0.550847 0.902439
16 GAV 0.545455 0.938272
17 YGP 0.539683 0.904762
18 6CK 0.539062 0.892857
19 2MD 0.536765 0.963855
20 GDC 0.535433 0.914634
21 GKE 0.535433 0.914634
22 GDD 0.535433 0.914634
23 GDR 0.53125 0.914634
24 GTG 0.53125 0.892857
25 GFB 0.53125 0.914634
26 GKD 0.530769 0.914634
27 JB2 0.530769 0.914634
28 GPG 0.528 0.914634
29 G3A 0.527132 0.925926
30 GPD 0.526718 0.882353
31 GP2 0.525424 0.891566
32 GDP BEF 0.525 0.837209
33 G5P 0.523077 0.925926
34 GDP MG 0.516667 0.857143
35 G2P 0.516393 0.891566
36 GDX 0.515152 0.925926
37 NGD 0.514706 0.914634
38 BEF GDP 0.512195 0.827586
39 GCP G 0.508065 0.86747
40 JB3 0.507353 0.903614
41 MD1 0.5 0.940476
42 GTP MG 0.5 0.857143
43 ALF 5GP 0.5 0.827586
44 FEG 0.492754 0.840909
45 ZGP 0.489209 0.873563
46 GDP AF3 0.488189 0.827586
47 GDP ALF 0.488189 0.827586
48 CAG 0.482517 0.842697
49 CG2 0.475177 0.915663
50 TPG 0.472973 0.846154
51 FE9 0.472603 0.840426
52 U2G 0.471429 0.915663
53 PGD O 0.469799 0.91954
54 G3D 0.468254 0.9125
55 G G 0.465649 0.890244
56 0O2 0.458015 0.9125
57 GDP 7MG 0.455882 0.869048
58 DBG 0.453333 0.903614
59 GMP 0.451327 0.814815
60 G4P 0.449612 0.9125
61 GH3 0.44186 0.901235
62 G4M 0.433962 0.842697
63 3GP 0.429752 0.876543
64 I2C FE2 CMO CMO 0.42953 0.815217
65 G1G 0.417219 0.882353
66 U A G G 0.416107 0.890244
67 DGT 0.415385 0.857143
68 GPX 0.413534 0.876543
69 GPC 0.413333 0.862069
70 G A A A 0.409396 0.879518
71 2GP 0.406504 0.888889
72 DGI 0.40625 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DMR; Ligand: PGD; Similar sites found: 94
This union binding pocket(no: 1) in the query (biounit: 1dmr.bio1) has 66 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZWA SAH 0.03337 0.40398 1.72662
2 4KRG SAH 0.04426 0.41097 1.93133
3 4R6W SAH 0.01167 0.40446 1.93798
4 1ZQ9 SAM 0.02314 0.41962 2.10526
5 1V6A TRE 0.04892 0.42675 2.10843
6 3LST SAH 0.04284 0.4147 2.30863
7 1XTP SAI 0.02292 0.41982 2.3622
8 3DMH SAM 0.03057 0.40827 2.3622
9 3FZG SAM 0.03475 0.41648 2.5
10 5MGZ SAH 0.02769 0.41297 2.54237
11 3H8V ATP 0.04731 0.404 2.73973
12 1QAN SAH 0.03403 0.40358 2.86885
13 4K91 SIN 0.04303 0.41531 2.89017
14 2J0W ASP 0.04626 0.42072 2.89532
15 3EGI ADP 0.02331 0.44398 2.91262
16 3TLJ SAH 0.02766 0.40545 2.94906
17 2Z49 AMG 0.01442 0.45169 3.00926
18 1SQF SAM 0.04028 0.40753 3.0303
19 1KYQ NAD 0.04086 0.40994 3.28467
20 5MF6 7M2 0.01266 0.40503 3.31126
21 5MF6 AR6 0.01266 0.40503 3.31126
22 1ZGS XMM 0.04004 0.42297 3.3557
23 5GM1 SAH 0.02148 0.41057 3.367
24 3ZG6 APR 0.004482 0.44828 3.37838
25 5FTW SAH 0.007283 0.43821 3.51562
26 3QPB URA 0.03469 0.43457 3.5461
27 4M73 M72 0.003374 0.41561 3.56083
28 3R4S SLB 0.03737 0.42664 3.61174
29 1TPY SAH 0.01376 0.42221 3.83275
30 3U31 NAD 0.003229 0.4518 4.13793
31 1KPG SAH 0.01387 0.42205 4.18118
32 4RL4 PPV 0.03559 0.4269 4.24528
33 2NXE SAM 0.02178 0.42093 4.33071
34 2CYB TYR 0.03005 0.43593 4.33437
35 3G2O SAM 0.02727 0.41605 4.34783
36 3G89 SAM 0.03381 0.42019 4.41767
37 1JZN BGC GAL 0.04844 0.4131 4.44444
38 2FK8 SAM 0.0167 0.42092 4.71698
39 1UKG MMA 0.02033 0.43877 4.7619
40 2PHU MAN MAN 0.02885 0.43383 4.7619
41 1Q8O MAN MMA 0.0449 0.42705 4.7619
42 3P2E SAH 0.02238 0.41481 4.88889
43 2Q28 ADP 0.002087 0.46772 4.96454
44 4OBW SAM 0.03502 0.4106 5.05837
45 4KRI SAH 0.03488 0.40549 5.08083
46 5N53 8NB 0.04104 0.4288 5.12821
47 3MB5 SAM 0.01263 0.42127 5.4902
48 3OFK SAH 0.01962 0.42622 5.55556
49 5GWX SAR 0.02569 0.40019 5.6338
50 5GWX SAM 0.02569 0.40019 5.6338
51 1W55 GPP 0.01589 0.43145 5.66038
52 1H0H MGD 0.000002214 0.54011 6.07533
53 1H0H 2MD 0.00002357 0.51781 6.07533
54 5E8J SAH 0.04603 0.41303 6.41026
55 1LSS NAD 0.0371 0.40419 6.42857
56 1P1C SAH 0.03593 0.40013 6.53266
57 4RDH AMP 0.03115 0.41895 6.59722
58 4I5I NAD 0.01023 0.41551 6.62021
59 4KXQ APR 0.005647 0.4404 6.76157
60 3FGZ BEF 0.02093 0.44813 7.03125
61 2J5B TYE 0.008787 0.46494 7.18391
62 1YRO UDP 0.01976 0.43579 7.31707
63 1L5Y BEF 0.02625 0.41791 7.74194
64 1WHT BZS 0.04037 0.43348 7.84314
65 1RJD SAM 0.03716 0.40416 8.08383
66 4QTU SAM 0.01831 0.42179 8.17308
67 3LCC SAH 0.03888 0.41104 8.51064
68 1DJL NAP 0.008512 0.40799 8.69565
69 1VKF CIT 0.03832 0.43235 9.04255
70 1KJ1 MAN 0.03177 0.41708 9.17431
71 1M2K APR 0.003299 0.43679 9.23695
72 2PP3 LGT 0.04463 0.41078 9.54774
73 1D4O NAP 0.003643 0.4376 9.78261
74 1IM8 SAI 0.0352 0.4053 9.83607
75 1L1E SAH 0.02598 0.41168 10.1045
76 1P31 EPU 0.01962 0.42319 10.3158
77 1P3D UMA 0.02355 0.40186 10.3158
78 2ZIF SAM 0.03969 0.40526 10.4377
79 2CYC TYR 0.02806 0.44022 10.6667
80 3BGD SAH 0.04571 0.40221 10.7692
81 5X62 SAH 0.01977 0.42606 11.0837
82 3PNA CMP 0.03284 0.43137 11.6883
83 1R27 MGD 0.00000001219 0.62701 13.1227
84 2IVF MD1 0.000003011 0.54253 16.2819
85 2IVF MGD 0.00000239 0.53159 16.2819
86 1KQF MGD 0.000001434 0.55526 19.0765
87 4II2 ATP 0.02163 0.41552 20.4819
88 2OOR TXP 0.00709 0.42241 22.9885
89 2NYA MGD 0.00000135 0.53726 33.7121
90 3ML1 MGD 0.00000001941 0.5221 35.4115
91 2IV2 MGD 0.000007548 0.51963 40.8392
92 2IV2 2MD 0.00007249 0.49767 40.8392
93 2E7Z MGD 0.0002759 0.46219 41.1279
94 2V3V MGD 0.00000001771 0.52427 42.8769
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