Receptor
PDB id Resolution Class Description Source Keywords
2NYA 2.5 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF THE PERIPLASMIC NITRATE REDUCTASE (NAP) FROM ESCHERICHIA COLI ESCHERICHIA COLI K12 MOLYBDENUM NITRATE REDUCTASE OXIDOREDUCTASE
Ref.: SPECTROPOTENTIOMETRIC AND STRUCTURAL ANALYSIS OF THE PERIPLASMIC NITRATE REDUCTASE FROM ESCHERICHIA COLI J.BIOL.CHEM. V. 282 6425 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6MO A:2002;
F:5002;
Part of Protein;
Part of Protein;
none;
none;
submit data
95.94 Mo [Mo+6...
MGD A:3001;
A:4001;
F:6001;
F:7001;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
SF4 A:2001;
F:5001;
Part of Protein;
Part of Protein;
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
2NYA 2.5 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF THE PERIPLASMIC NITRATE REDUCTASE (NAP) FROM ESCHERICHIA COLI ESCHERICHIA COLI K12 MOLYBDENUM NITRATE REDUCTASE OXIDOREDUCTASE
Ref.: SPECTROPOTENTIOMETRIC AND STRUCTURAL ANALYSIS OF THE PERIPLASMIC NITRATE REDUCTASE FROM ESCHERICHIA COLI J.BIOL.CHEM. V. 282 6425 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2NYA - MGD C20 H26 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 5 families.
1 2NYA - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2JIR - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 2NAP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 2JIP - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
4 2JIQ - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
5 2V45 - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
6 2JIO - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
7 2JIM - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
8 2V3V - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
9 2NYA - MGD C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NYA; Ligand: MGD; Similar sites found: 24
This union binding pocket(no: 1) in the query (biounit: 2nya.bio2) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1M2W MTL 0.04713 0.41061 1.21704
2 5A7Y SAH 0.04975 0.404 3.84615
3 5EK3 5PK 0.004821 0.45839 4.4665
4 4NWJ 3PG 0.02324 0.42147 4.48343
5 5XKR BZE 0.04631 0.40218 5.03145
6 5GOE GDP 0.02781 0.40693 5.45024
7 3OFK SAH 0.01138 0.40722 5.55556
8 4RL4 PPV 0.02075 0.43001 6.13208
9 5AIG VPR 0.01766 0.42828 9.6
10 4YDD MD1 0.000001088 0.41412 14.0152
11 4YDD MGD 0.000001088 0.41412 14.0152
12 1EU1 MGD 0.0004394 0.41696 18.2051
13 2VPY MGD 0.000005295 0.51259 19.3464
14 3U31 NAD 0.009831 0.41003 21.0345
15 1KQF MGD 0.000000000077 0.62839 29.798
16 1DMR PGD 0.00000135 0.53726 33.7121
17 1G8K MGD 0.00000002123 0.60501 35.3535
18 1TMO 2MD 0.001005 0.40504 36.1111
19 2IVF MD1 0.000003137 0.48263 38.8889
20 2IVF MGD 0.0002038 0.43046 38.8889
21 1H0H 2MD 0.0000000009174 0.58171 40.6566
22 1H0H MGD 0.0001386 0.43053 40.6566
23 2IV2 2MD 0.000000482 0.49738 46.5734
24 2IV2 MGD 0.000663 0.40829 46.5734
Pocket No.: 2; Query (leader) PDB : 2NYA; 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: 2nya.bio2) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2NYA; Ligand: MGD; Similar sites found: 2
This union binding pocket(no: 3) in the query (biounit: 2nya.bio1) has 40 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5D3U TRP 0.03478 0.41638 3.51288
2 1NSA BEN 0.02518 0.40937 3.5443
Pocket No.: 4; Query (leader) PDB : 2NYA; Ligand: MGD; 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: 2nya.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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