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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 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
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: 150
This union binding pocket(no: 1) in the query (biounit: 1dmr.bio1) has 66 residues
No: Leader PDB Ligand Sequence Similarity
1 3ERR AMP 1.1194
2 5DNK SAH 1.44404
3 4KIB SAH 1.68067
4 2ZWA SAH 1.72662
5 5KOK SAH 1.8226
6 4KRG SAH 1.93133
7 5YF1 SFG 1.9337
8 4R6W SAH 1.93798
9 1ZQ9 SAM 2.10526
10 1V6A TRE 2.10843
11 5W7K SAH 2.24359
12 3LST SAH 2.30863
13 2JHP SAH 2.32919
14 1XTP SAI 2.3622
15 3DMH SAM 2.3622
16 3FZG SAM 2.5
17 5MGZ SAH 2.54237
18 6EQS BV8 2.54545
19 3RIY NAD 2.5641
20 5BW4 SAM 2.62172
21 3H8V ATP 2.73973
22 5WP5 SAH 2.85132
23 1QAN SAH 2.86885
24 4K91 SIN 2.89017
25 2J0W ASP 2.89532
26 3EGI ADP 2.91262
27 3TLJ SAH 2.94906
28 1RJW ETF 2.94985
29 4M3P HCS 2.95567
30 5XNC MTA 2.96496
31 2C49 ADN 2.98013
32 2Z49 AMG 3.00926
33 1SQF SAM 3.0303
34 3O7W SAM 3.06122
35 4V3C C 3.09278
36 6ECU SAH 3.16456
37 5E72 SAM 3.17919
38 1KYQ NAD 3.28467
39 6HOY AR6 3.31126
40 5E1M SAH 3.3195
41 5E1M PRO PRO LYS ARG ILE ALA 3.3195
42 1ZGS XMM 3.3557
43 5GM1 SAH 3.367
44 3ZG6 APR 3.37838
45 5FTW SAH 3.51562
46 3QPB URA 3.5461
47 4M73 M72 3.56083
48 4M73 SAH 3.56083
49 2QQF A1R 3.57143
50 2OD9 A1R NCA 3.57143
51 3R4S SLB 3.61174
52 3NJQ NJQ 3.62694
53 2IRY DGT 3.63036
54 3F5A SIA GAL NAG 3.65854
55 1L7N ALF 3.79147
56 1TPY SAH 3.83275
57 2AOT SAH 4.10959
58 3U31 NAD 4.13793
59 1KPH SAH 4.18118
60 1KPG SAH 4.18118
61 4RL4 PPV 4.24528
62 3ZO7 K6H 4.25532
63 5AHN IMP 4.29448
64 2NXE SAM 4.33071
65 2CYB TYR 4.33437
66 3G2O SAM 4.34783
67 3G89 SAM 4.41767
68 1JZN BGC GAL 4.44444
69 2FK8 SAM 4.71698
70 1UKG MMA 4.7619
71 1Q8V MAN MAN 4.7619
72 2PHU MAN MAN 4.7619
73 2PHX MAN MAN 4.7619
74 1Q8O MAN MMA 4.7619
75 6GKV SAH 4.8433
76 5N5D SAM 4.86726
77 5WP4 SAH 4.88798
78 3P2E SAH 4.88889
79 2Q28 ADP 4.96454
80 4OBW SAM 5.05837
81 4KRI SAH 5.08083
82 5N53 8NB 5.12821
83 3GFB NAD 5.14286
84 3VSE SAH 5.27638
85 3GWZ SAH 5.42005
86 3MB5 SAM 5.4902
87 3OFK SAH 5.55556
88 1W55 GPP 5.66038
89 6FDF SAH 5.98802
90 1H0H 2MD 6.07533
91 1H0H MGD 6.07533
92 5E9W SAH 6.41026
93 5E8J SAH 6.41026
94 1LSS NAD 6.42857
95 1P1C SAH 6.53266
96 4RDH AMP 6.59722
97 4RDI ATP 6.59722
98 4I5I NAD 6.62021
99 6DUB SAH 6.75676
100 4KXQ APR 6.76157
101 4D79 ATP 6.88406
102 3FGZ BEF 7.03125
103 2J5B TYE 7.18391
104 5BSZ SAH 7.2
105 1YRO UDP 7.31707
106 1DCP HBI 7.69231
107 1L5Y BEF 7.74194
108 1WHT BZS 7.84314
109 3TKY SAH 7.88043
110 1RJD SAM 8.08383
111 4QTU SAM 8.17308
112 3T7S SAM 8.20895
113 1S7G NAD 8.3004
114 3LCC SAH 8.51064
115 1DJL NAP 8.69565
116 1VKF CIT 9.04255
117 1KJ1 MAN 9.17431
118 1M2K APR 9.23695
119 1D4O NAP 9.78261
120 1IM8 SAI 9.83607
121 1L1E SAH 10.1045
122 1P31 EPU 10.3158
123 1P3D UMA 10.3158
124 2ZIF SAM 10.4377
125 4IWN GEK 10.4803
126 2CYC TYR 10.6667
127 3BGD SAH 10.7692
128 6FTB M0E 10.9524
129 5X62 SAH 11.0837
130 1ZEI CRS 11.3208
131 3PNA CMP 11.6883
132 5A3B APR 12.8713
133 1R27 MGD 13.1227
134 6CZ7 MGD 13.8821
135 2VT3 ATP 13.9535
136 2IVF MD1 16.2819
137 2IVF MGD 16.2819
138 4IF4 BEF 18.2692
139 1KQF MGD 19.0765
140 5ZZ6 ADP 20.1923
141 4II2 ATP 20.4819
142 1PNO NAP 22.2222
143 2OOR TXP 22.9885
144 6F5Z SAH 24.5902
145 2NYA MGD 33.7121
146 3ML1 MGD 35.4115
147 2IV2 MGD 40.8392
148 2IV2 2MD 40.8392
149 2E7Z MGD 41.1279
150 2V3V MGD 42.8769
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