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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 318 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 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....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 187 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: 79
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 9GM 0.587719 0.870588
14 GNP 0.587719 0.870588
15 GMV 0.584071 0.870588
16 Y9Z 0.578512 0.813187
17 G 0.568807 0.879518
18 5GP 0.568807 0.879518
19 GFB 0.560976 0.882353
20 GDR 0.560976 0.882353
21 G3A 0.556452 0.892857
22 GDD 0.552846 0.882353
23 GKE 0.552846 0.882353
24 GDC 0.552846 0.882353
25 G5P 0.552 0.892857
26 GAV 0.550847 0.904762
27 GTG 0.548387 0.862069
28 GKD 0.547619 0.882353
29 MD1 0.547445 0.97619
30 6CK 0.544 0.862069
31 GP2 0.54386 0.860465
32 NGD 0.541985 0.882353
33 MTE 0.541284 0.855422
34 JB2 0.535433 0.882353
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 JB3 0.522727 0.872093
41 FEG 0.518797 0.813187
42 ALF 5GP 0.516949 0.8
43 ZGP 0.514925 0.844444
44 CAG 0.507246 0.815217
45 GDP AF3 0.504065 0.8
46 GDP ALF 0.504065 0.8
47 ALF GDP 0.504065 0.8
48 PTE 0.503937 0.827586
49 G G 0.5 0.870588
50 U2G 0.496296 0.905882
51 G3D 0.495868 0.879518
52 0O2 0.484127 0.879518
53 CG2 0.478261 0.905882
54 TPG 0.475862 0.879121
55 G4P 0.475806 0.879518
56 GDP 7MG 0.469697 0.83908
57 GMP 0.46789 0.785714
58 DBG 0.465753 0.872093
59 3GP 0.456897 0.845238
60 FE9 0.455172 0.852632
61 G1R G1R 0.445946 0.850575
62 G1G 0.438356 0.852273
63 G4M 0.435897 0.815217
64 GCP G 0.435115 0.823529
65 GH3 0.433071 0.869048
66 G A A A 0.430556 0.848837
67 A G 0.430556 0.858824
68 U A G G 0.427586 0.858824
69 R5I 0.424 0.845238
70 R7I 0.424 0.845238
71 DGT 0.417323 0.827586
72 GPX 0.415385 0.845238
73 2GP 0.408333 0.857143
74 DGI 0.408 0.827586
75 IDP 0.403226 0.86747
76 AKW 0.402778 0.863636
77 BGO 0.402778 0.850575
78 P2G 0.401639 0.790698
79 G U 0.4 0.872093
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 with APoc: 106
This union binding pocket(no: 1) in the query (biounit: 2vpy.bio1) has 60 residues
No: Leader PDB Ligand Sequence Similarity
1 2UYQ SAM 3.54839
2 1KYQ NAD 3.64964
3 4KRI SAH 3.9261
4 1LSS NAD 4.28571
5 3FRH SAH 4.34783
6 5MGZ SAH 4.34783
7 1ZQ9 SAM 4.34783
8 5XNC MTA 4.61538
9 2Q28 ADP 4.61538
10 5D4V SAH 4.85075
11 3P2E SAH 5.12821
12 5KOK SAH 5.12821
13 3EGI ADP 5.13834
14 3MCT SAH 5.13834
15 3MAG SAH 5.13834
16 4IF4 BEF 5.28846
17 6DUB SAH 5.40541
18 3OFK SAH 5.55556
19 4PIO SAH 5.57276
20 4PIO AVI 5.57276
21 4RDH AMP 5.64103
22 4RDI ATP 5.64103
23 4D79 ATP 5.64103
24 1Y8Q ATP 5.64103
25 4RL4 PPV 5.66038
26 5E1M PRO PRO LYS ARG ILE ALA 5.80913
27 5E1M SAH 5.80913
28 1RJW ETF 5.8997
29 3UIM ANP 5.92885
30 3IT7 TLA 6.04396
31 3GWZ SAH 6.15385
32 6GKV SAH 6.15385
33 1KPG SAH 6.15385
34 1KPH SAH 6.15385
35 1OBB NAD 6.15385
36 3G2O SAM 6.15385
37 5BW4 SAM 6.32411
38 2QQF A1R 6.49351
39 3FZG SAM 6.5
40 2VT3 ATP 6.51163
41 1BC5 SAH 6.66667
42 5G3L SIA GAL 6.71937
43 1XTP SAI 7.08661
44 3JWH SAH 7.11462
45 4OH4 ANP 7.11462
46 4II2 ATP 7.22892
47 3LCC SAH 7.23404
48 5X62 SAH 7.50988
49 4DI8 0GY 7.59076
50 4DI8 0GZ 7.59076
51 4PPF FLC 7.69231
52 1E5F PLP 7.69231
53 3FGZ BEF 7.8125
54 4KIB SAH 7.90514
55 4M73 SAH 7.90514
56 4M73 M72 7.90514
57 5M58 SAH 8.26087
58 2JHP SAH 8.3004
59 1FP2 SAH 8.3004
60 5N53 8NB 8.69565
61 5OFW 9TW 8.69565
62 1TPY SAH 8.69565
63 2FK8 SAM 8.71795
64 3I53 SAH 9.03614
65 1A5Z NAD 9.09091
66 5HJM MTA 9.09091
67 1L1E SAH 9.23077
68 5JE8 NAD 9.48617
69 2F7A BEZ 9.74359
70 5WP5 SAH 9.88142
71 6B92 SAH 9.88142
72 3QPB URA 10.2564
73 5Y8L NAD 10.7692
74 5MPT SAH 10.7692
75 1ZGA SAH 10.9244
76 5MZI FYK 11.7949
77 3Q3C NAD 11.8577
78 3T7S SAM 12.8205
79 6F5Z SAH 13.1148
80 2AOT SAH 13.3333
81 2HMT NAI 13.8889
82 5RHN 8BR 13.913
83 1JZN BGC GAL 14.0741
84 3ML1 MGD 14.2484
85 5WP4 SAH 14.359
86 3LCV SAM 14.6245
87 2OX9 GAL NAG FUC 15
88 3TKY SAH 15.3846
89 1M2K APR 15.8974
90 4QTU SAM 16.2963
91 6ECU SAH 17.7866
92 4A6D SAM 18.1818
93 2NYA MGD 19.3464
94 1R27 MGD 32.8205
95 2IV2 MGD 32.8671
96 2IV2 2MD 32.8671
97 3U31 NAD 33.3333
98 1TMO 2MD 35.5556
99 1EU1 MGD 36.2092
100 2V3V MGD 37.621
101 1H0H 2MD 38.4615
102 1H0H MGD 38.4615
103 2E7Z MGD 41.6781
104 2IVF MGD 42.5641
105 2IVF MD1 42.5641
106 1KQF MGD 48.7179
Pocket No.: 2; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 2vpy.bio1) has 61 residues
No: Leader PDB Ligand Sequence Similarity
1 1P31 EPU 7.69231
Pocket No.: 3; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found with APoc: 35
This union binding pocket(no: 3) in the query (biounit: 2vpy.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 6GFK SAH 2.78884
2 1V59 NAD 3.58974
3 1RJD SAM 3.95257
4 5DNK SAH 4.10256
5 4WKB TDI 4.34783
6 4AZW SAM 4.88323
7 4NZF ARB 5.35948
8 1JQD HSM 5.47945
9 1JQD SAH 5.47945
10 5ZI9 FLC 5.5336
11 3LST SAH 5.74713
12 6F4W FMC 6.15385
13 3GXO SAH 6.15385
14 2P3V SRT 6.25
15 3BJE URA 6.30372
16 2V2G BEZ 6.43777
17 5XLX SAH 6.73759
18 1JG3 ADN 7.11462
19 5F8F SFG 7.17949
20 2PXX SAH 7.44186
21 1ZOS MTM 7.50988
22 1X87 NAD 7.50988
23 2CDU ADP 7.69231
24 3U40 ADN 8.69565
25 1V6A TRE 8.71795
26 5LOG SAH 9.09091
27 4KRG SAH 9.23077
28 3G89 SAM 9.23695
29 4NEC SAH 9.4697
30 1IYB 5GP 10.2564
31 2HNK SAH 12.6482
32 3O7W SAM 13.8462
33 4R6W SAH 14.3411
34 4QAG F95 15.0376
35 4RDN 6MD 16.1677
Pocket No.: 4; Query (leader) PDB : 2VPY; Ligand: PCI; Similar sites found with APoc: 53
This union binding pocket(no: 4) in the query (biounit: 2vpy.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4MG8 27J 2.5641
2 3FQ8 PMP 3.55731
3 2I0G I0G 3.58974
4 1U3R 338 3.73444
5 3OLL EST 3.75
6 4MGB XDH 4.10256
7 4TUZ 36J 4.10256
8 2BJ4 OHT 4.10256
9 3KFL ME8 4.34783
10 4TTS 6DD 4.61538
11 1G2N EPH 4.61538
12 2ZHZ ATP 4.91803
13 4HWS 1B3 5.12821
14 3Q9O NAD 5.12821
15 2EV1 OLA 5.5336
16 4CJX NAP 5.5336
17 3FS1 MYR 5.64103
18 5UWA 8ND 5.91133
19 1QSM ACO 5.92105
20 1GKZ ADP 5.92885
21 4POJ 2VP 6.92641
22 4M8E 29V 6.92641
23 3TGE TGE 7.50988
24 9LDB NAD 7.69231
25 5L7G 6QE 7.86885
26 5MWY YNU 7.86885
27 1YB5 NAP 7.97721
28 2QX0 APC 8.1761
29 3D36 ADP 8.69565
30 1GUZ NAD 8.70968
31 6BWL NAD 8.71795
32 5HJM MTA 9.09091
33 1HG4 LPP 9.09091
34 5HCV 60R 9.23077
35 2V6A CAP 10
36 3D72 FAD 10.0671
37 1OKC CXT 10.101
38 5UNJ RJW 10.2564
39 2YX1 SFG 10.2564
40 3H0A 9RA 10.2941
41 1FMB HYB 10.5769
42 3VPH NAD 11.2821
43 3VPH OXM 11.2821
44 2UXI G50 11.2821
45 5CXI 5TW 11.4625
46 1ZDT PEF 11.6183
47 5LWY OLB 11.7647
48 1GTE IUR 11.8577
49 1GTE FMN 11.8577
50 2PR5 FMN 14.3939
51 4JGX PLM 19.3798
52 1QCI ADE 23.0769
53 2Z6D FMN 23.8462
Pocket No.: 5; Query (leader) PDB : 2VPY; Ligand: PCI; Similar sites found with APoc: 50
This union binding pocket(no: 5) in the query (biounit: 2vpy.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 5AAV GW5 2.5641
2 3H78 BE2 3.07692
3 3UC5 ATP 3.82166
4 4HE2 AMP 3.84615
5 5ZUN 9JX 3.95257
6 4LXH C1E 3.97112
7 2R5E QLP 4.1958
8 1LSS NAD 4.28571
9 1I1D 16G 4.34783
10 2R5C C6P 4.4289
11 2OBD PCW 4.61538
12 1DL5 SAH 4.61538
13 3VC3 C6P 4.65116
14 1XVB BHL 4.70588
15 4DDY DN6 4.94297
16 1XX4 BAM 5.12821
17 1IUP ALQ 5.12821
18 4A0M NAD 5.5336
19 1PZL MYR 5.64103
20 4Q5M ROC 5.64103
21 3EWC MCF 6.19946
22 3D9F FAD 6.32411
23 3VC1 SAH 6.32411
24 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 6.57534
25 3FAL LO2 6.61157
26 3ZNN 4WL 6.62824
27 3ZNN FAD 6.62824
28 2R40 20E 6.66667
29 5OC1 ANN 6.66667
30 5K8B PDG 7.17949
31 1OE0 TTP 7.17949
32 4ELG 52J 7.22892
33 1M13 HYF 7.27848
34 5IXK 6EW 7.89474
35 5W7B MYR 8.20513
36 5ZRR 9J3 8.3004
37 1TPY 16A 8.69565
38 5GVL PLG 9.23077
39 5GVL GI8 9.23077
40 5JKG 6LF 9.23077
41 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 9.52381
42 2VBQ BSJ 9.69697
43 4DK7 0KS 9.74359
44 3KFC 61X 9.74359
45 3NUB UD0 10.2767
46 4V1F BQ1 10.4651
47 3VRV YSD 11.0672
48 6GBV FMN 11.6438
49 3ABA FLI 19.3676
50 4HEE 14R 19.4872
Pocket No.: 6; Query (leader) PDB : 2VPY; Ligand: MGD; Similar sites found with APoc: 5
This union binding pocket(no: 6) in the query (biounit: 2vpy.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 3AB4 LYS 3.58974
2 5B2D SLT 4.74308
3 1Z45 GAL 6.15385
4 3VSE SAH 8.69565
5 1X14 NAD 12.3077
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