Receptor
PDB id Resolution Class Description Source Keywords
2VPY 2.5 Å EC: 1.-.-.- POLYSULFIDE REDUCTASE WITH BOUND QUINONE INHIBITOR, PENTACHLOROPHENOL (PCP) THERMUS THERMOPHILUS OXIDOREDUCTASE MOLYBDOPTERIN GUANINE DINUCLEOTIDE IRON-SULFUR METAL-BINDING MOLYBDOPTERIN INTEGRAL MEMBRANE PROTEIN MGD MPT IRON FE4S4 4FE-4S MOLYBDENUM IRON SULFUR CLUSTER
Ref.: MOLECULAR MECHANISM OF ENERGY CONSERVATION IN POLYSULFIDE RESPIRATION. NAT.STRUCT.MOL.BIOL. V. 15 730 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MGD A:1765;
A:1766;
E:1765;
E:1766;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
MO A:1767;
E:1767;
Part of Protein;
Part of Protein;
none;
none;
submit data
95.94 Mo [Mo]
PCI C:1252;
G:1251;
Valid;
Valid;
none;
none;
submit data
266.337 C6 H Cl5 O c1(c(...
SF4 A:1764;
B:1194;
B:1195;
B:1196;
B:1197;
E:1764;
F:1194;
F:1195;
F:1196;
F:1197;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VPY 2.5 Å EC: 1.-.-.- POLYSULFIDE REDUCTASE WITH BOUND QUINONE INHIBITOR, PENTACHLOROPHENOL (PCP) THERMUS THERMOPHILUS OXIDOREDUCTASE MOLYBDOPTERIN GUANINE DINUCLEOTIDE IRON-SULFUR METAL-BINDING MOLYBDOPTERIN INTEGRAL MEMBRANE PROTEIN MGD MPT IRON FE4S4 4FE-4S MOLYBDENUM IRON SULFUR CLUSTER
Ref.: MOLECULAR MECHANISM OF ENERGY CONSERVATION IN POLYSULFIDE RESPIRATION. NAT.STRUCT.MOL.BIOL. V. 15 730 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 2VPZ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2VPY - PCI C6 H Cl5 O c1(c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 2VPZ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2VPY - PCI C6 H Cl5 O c1(c(c(c(c....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 2VPZ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2VPY - PCI C6 H Cl5 O c1(c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MGD; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 MGD 1 1
2 PGD O 0.706349 0.954023
3 2MD 0.694215 1
4 G1R 0.636364 0.880952
5 GP3 0.635514 0.892857
6 GNH 0.623853 0.880952
7 GSP 0.616071 0.894118
8 GDP 0.614679 0.891566
9 GTP 0.612613 0.891566
10 PGD 0.606061 0.963855
11 GCP 0.59292 0.870588
12 G2R 0.589744 0.860465
13 GNP 0.587719 0.870588
14 GMV 0.584071 0.870588
15 Y9Z 0.578512 0.813187
16 G 0.568807 0.879518
17 5GP 0.568807 0.879518
18 GFB 0.560976 0.882353
19 GDR 0.560976 0.882353
20 G3A 0.556452 0.892857
21 GKE 0.552846 0.882353
22 GDC 0.552846 0.882353
23 GDD 0.552846 0.882353
24 G5P 0.552 0.892857
25 GAV 0.550847 0.904762
26 GTG 0.548387 0.862069
27 GKD 0.547619 0.882353
28 MD1 0.547445 0.97619
29 6CK 0.544 0.862069
30 GP2 0.54386 0.860465
31 NGD 0.541985 0.882353
32 MTE 0.541284 0.855422
33 JB2 0.535433 0.882353
34 GDP MG 0.534483 0.827586
35 G2P 0.533898 0.860465
36 GPG 0.532787 0.882353
37 YGP 0.532258 0.895349
38 GDX 0.53125 0.892857
39 GPD 0.53125 0.852273
40 GDP BEF 0.529915 0.808989
41 BEF GDP 0.529412 0.8
42 GCP G 0.525 0.837209
43 JB3 0.522727 0.872093
44 FEG 0.518797 0.813187
45 ALF 5GP 0.516949 0.8
46 GTP MG 0.516667 0.827586
47 ZGP 0.514925 0.844444
48 CAG 0.507246 0.815217
49 GDP ALF 0.504065 0.8
50 GDP AF3 0.504065 0.8
51 PTE 0.503937 0.827586
52 U2G 0.496296 0.905882
53 G3D 0.495868 0.879518
54 G G 0.492063 0.858824
55 0O2 0.484127 0.879518
56 CG2 0.478261 0.905882
57 TPG 0.475862 0.879121
58 G4P 0.475806 0.879518
59 GDP 7MG 0.469697 0.83908
60 GMP 0.46789 0.785714
61 DBG 0.465753 0.872093
62 3GP 0.456897 0.845238
63 FE9 0.455172 0.852632
64 G1R G1R 0.445946 0.850575
65 G1G 0.438356 0.852273
66 G4M 0.435897 0.815217
67 G G U 0.433824 0.858824
68 GH3 0.433071 0.869048
69 I2C FE2 CMO CMO 0.431507 0.827957
70 G A A A 0.430556 0.848837
71 U A G G 0.427586 0.858824
72 DGT 0.417323 0.827586
73 GPX 0.415385 0.845238
74 2GP 0.408333 0.857143
75 DGI 0.408 0.827586
76 IDP 0.403226 0.86747
77 BGO 0.402778 0.850575
78 P2G 0.401639 0.790698
Ligand no: 2; Ligand: PCI; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 PCI 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VPY; Ligand: MGD; 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: 2vpy.bio1) has 60 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2vpy.bio1) has 61 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found: 53
This union binding pocket(no: 3) in the query (biounit: 2vpy.bio1) has 62 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1KYQ NAD 0.01192 0.43538 3.64964
2 4AZT SAM 0.04987 0.40118 4.10256
3 1ZQ9 SAM 0.0232 0.41781 4.34783
4 2Q28 ADP 0.007382 0.43916 4.61538
5 3P2E SAH 0.01407 0.4227 5.12821
6 3EGI ADP 0.0341 0.43268 5.13834
7 4IF4 BEF 0.02346 0.44693 5.28846
8 4NZF ARB 0.02969 0.43213 5.35948
9 1JQD HSM 0.02205 0.40137 5.47945
10 1JQD SAH 0.0182 0.40073 5.47945
11 3OFK SAH 0.03071 0.40398 5.55556
12 4RDH AMP 0.003818 0.46411 5.64103
13 1Y8Q ATP 0.02539 0.4031 5.64103
14 3LST SAH 0.03906 0.41837 5.74713
15 1KPG SAH 0.007842 0.43182 6.15385
16 5MX4 HPA 0.04962 0.42503 6.15385
17 3G2O SAM 0.04195 0.40496 6.15385
18 1OBB NAD 0.02596 0.40266 6.15385
19 3FZG SAM 0.005826 0.45472 6.5
20 1JG3 ADN 0.04036 0.40581 7.11462
21 4OH4 ANP 0.04413 0.40386 7.11462
22 4II2 ATP 0.01059 0.42858 7.22892
23 2PXX SAH 0.03665 0.40527 7.44186
24 5X62 SAH 0.02652 0.41781 7.50988
25 1ZOS MTM 0.03217 0.41355 7.50988
26 1P31 EPU 0.04732 0.40233 7.69231
27 3FGZ BEF 0.01173 0.44767 7.8125
28 4M73 M72 0.003678 0.41222 7.90514
29 5N53 8NB 0.01696 0.45191 8.69565
30 1V6A TRE 0.02824 0.43856 8.71795
31 2FK8 SAM 0.008491 0.43315 8.71795
32 1A5Z NAD 0.03245 0.40285 9.09091
33 1L1E SAH 0.01016 0.42944 9.23077
34 3G89 SAM 0.04305 0.41291 9.23695
35 4NEC SAH 0.04363 0.4126 9.4697
36 5JE8 NAD 0.005675 0.42985 9.48617
37 1IYB 5GP 0.04722 0.4207 10.2564
38 3ML1 MGD 0.00000000001753 0.61801 14.2484
39 4R6W SAH 0.0133 0.40031 14.3411
40 1M2K APR 0.008665 0.41676 15.8974
41 4QTU SAM 0.01819 0.42014 16.2963
42 4A6D SAM 0.01913 0.41908 18.1818
43 2NYA MGD 0.000005295 0.51259 19.3464
44 1R27 MGD 0.0000009695 0.42088 32.8205
45 2IV2 MGD 0.00000002345 0.46015 32.8671
46 3U31 NAD 0.003764 0.44671 33.3333
47 1TMO 2MD 0.00001263 0.50508 35.5556
48 2V3V MGD 0.00000000004599 0.60724 37.621
49 1H0H MGD 0.0000001474 0.58221 38.4615
50 1H0H 2MD 0.000001628 0.56283 38.4615
51 2E7Z MGD 0.000001769 0.54483 41.6781
52 2IVF MGD 0.000001701 0.42409 42.5641
53 1KQF MGD 0.000001762 0.54885 48.7179
Pocket No.: 4; Query (leader) PDB : 2VPY; Ligand: PCI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2vpy.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2VPY; Ligand: PCI; Similar sites found: 22
This union binding pocket(no: 5) in the query (biounit: 2vpy.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2I0G I0G 0.04379 0.41802 3.58974
2 2BJ4 OHT 0.01905 0.40834 4.10256
3 1LSS NAD 0.02665 0.40245 4.28571
4 2R5C C6P 0.01977 0.40751 4.4289
5 3VC3 C6P 0.02719 0.40788 4.65116
6 1XX4 BAM 0.008505 0.42051 5.12821
7 4A0M NAD 0.03658 0.40933 5.5336
8 4Q5M ROC 0.03729 0.4067 5.64103
9 3EWC MCF 0.03253 0.40238 6.19946
10 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.03664 0.40357 6.57534
11 3ZNN FAD 0.02498 0.43674 6.62824
12 4POJ 2VP 0.03323 0.40048 6.92641
13 5K8B PDG 0.009152 0.42813 7.17949
14 1OE0 TTP 0.02317 0.41155 7.17949
15 1M13 HYF 0.03974 0.4052 7.27848
16 1TPY 16A 0.0115 0.41392 8.69565
17 1HG4 LPP 0.01378 0.42484 9.09091
18 5GVL GI8 0.01515 0.43628 9.23077
19 5GVL PLG 0.01515 0.43628 9.23077
20 5JKG 6LF 0.04751 0.4061 9.23077
21 3VRV YSD 0.04193 0.41761 11.0672
22 4HEE 14R 0.01983 0.40744 19.4872
Pocket No.: 6; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2vpy.bio1) has 62 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback