Receptor
PDB id Resolution Class Description Source Keywords
3IR5 2.3 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF NARGHI MUTANT NARG-H49C ESCHERICHIA COLI K-12 OXIDOREDUCTASE NITRATE REDUCTASE ELECTRON TRANSFER MEMBRAPROTEIN 4FE-4S CELL MEMBRANE ELECTRON TRANSPORT IRON ISULFUR MEMBRANE METAL-BINDING MOLYBDENUM NITRATE ASSIMITRANSPORT 3FE-4S CELL INNER MEMBRANE FORMYLATION HEME TRANSMEMBRANE
Ref.: PROTEIN CRYSTALLOGRAPHY REVEALS A ROLE FOR THE FS0 OF ESCHERICHIA COLI NITRATE REDUCTASE A (NARGHI) IN MATURATION. J.BIOL.CHEM. V. 285 8801 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6MO A:1248;
Part of Protein;
none;
submit data
95.94 Mo [Mo+6...
AGA A:1250;
Invalid;
none;
submit data
455.457 C19 H36 O10 P CCCCC...
F3S B:805;
Part of Protein;
none;
submit data
295.795 Fe3 S4 S1[Fe...
HEM C:806;
C:807;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
MD1 A:1247;
A:1251;
Valid;
Valid;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
SF4 A:1249;
B:802;
B:803;
B:804;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
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
1Y4Z 2 Å EC: 1.7.99.4 THE CRYSTAL STRUCTURE OF NITRATE REDUCTASE A, NARGHI, IN COMPLEX WITH THE Q-SITE INHIBITOR PENTACHLOROPHENOL ESCHERICHIA COLI NITRATE REDUCTION ELECTRON TRANSFER MEMBRANE PROTEIN Q- SITE OXIDOREDUCTASE
Ref.: STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF A QUINOL BINDING SITE OF ESCHERICHIA COLI NITRATE REDUCTASE A J.BIOL.CHEM. V. 280 14836 2005
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3IR7 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3IR5 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 1Q16 - AGA C19 H36 O10 P CCCCCCCC(=....
4 1Y5N Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
5 1Y4Z Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
6 1SIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3IR7 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3IR5 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 1Q16 - AGA C19 H36 O10 P CCCCCCCC(=....
4 1Y5N Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
5 1Y4Z Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
6 1SIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3IR7 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
2 3IR5 - MD1 C20 H26 N10 O13 P2 S2 c1nc2c(n1[....
3 1Q16 - AGA C19 H36 O10 P CCCCCCCC(=....
4 1Y5N Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
5 1Y4Z Ki = 57 nM PCI C6 H Cl5 O c1(c(c(c(c....
6 1SIW - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MD1; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 MD1 1 1
2 GP3 0.612613 0.892857
3 GDP 0.607143 0.891566
4 G1R 0.6 0.880952
5 GTP 0.591304 0.891566
6 GNH 0.587719 0.880952
7 GSP 0.581197 0.894118
8 GMV 0.577586 0.870588
9 GCP 0.57265 0.892857
10 2MD 0.571429 0.97619
11 G2R 0.570248 0.882353
12 9GM 0.567797 0.870588
13 GNP 0.567797 0.870588
14 5GP 0.5625 0.879518
15 G 0.5625 0.879518
16 Y9Z 0.56 0.833333
17 MGD 0.547445 0.97619
18 GTG 0.543307 0.862069
19 CAG 0.536232 0.815217
20 GDC 0.535433 0.882353
21 GDD 0.535433 0.882353
22 GKE 0.535433 0.882353
23 GAV 0.532787 0.904762
24 GFB 0.53125 0.882353
25 GDR 0.53125 0.882353
26 6CK 0.527132 0.862069
27 G3A 0.527132 0.892857
28 GDX 0.526718 0.892857
29 GP2 0.525424 0.882353
30 G5P 0.523077 0.892857
31 GKD 0.519084 0.882353
32 JB2 0.519084 0.882353
33 G2P 0.516393 0.882353
34 GPG 0.515873 0.882353
35 YGP 0.515625 0.895349
36 GPD 0.515152 0.873563
37 NGD 0.514706 0.882353
38 ALF 5GP 0.512397 0.8
39 GDP AF3 0.512 0.8
40 JB3 0.507353 0.872093
41 GDP ALF 0.5 0.8
42 PGD 0.5 0.940476
43 ALF GDP 0.5 0.8
44 FEG 0.492754 0.833333
45 ZGP 0.489209 0.865169
46 DBG 0.482993 0.872093
47 G3D 0.48 0.879518
48 GDP 7MG 0.477612 0.83908
49 U2G 0.471429 0.905882
50 PGD O 0.469799 0.931818
51 CG2 0.464789 0.905882
52 TPG 0.463087 0.879121
53 G G 0.462687 0.870588
54 G4P 0.460938 0.879518
55 KB7 0.459677 0.744444
56 0O2 0.458015 0.879518
57 FE9 0.452703 0.833333
58 GMP 0.451327 0.785714
59 KBD 0.44697 0.764045
60 G4M 0.443038 0.815217
61 KBJ 0.433824 0.758242
62 GH3 0.430769 0.891566
63 BGO 0.430556 0.850575
64 3GP 0.429752 0.845238
65 G1R G1R 0.424837 0.850575
66 GPX 0.424242 0.845238
67 A G 0.418919 0.858824
68 DGI 0.417323 0.848837
69 U A G G 0.416107 0.858824
70 DGT 0.415385 0.848837
71 IDP 0.412698 0.86747
72 GGM 0.412162 0.831461
73 GCP G 0.411765 0.823529
74 R7I 0.410853 0.845238
75 R5I 0.410853 0.845238
76 G A A A 0.409396 0.848837
77 G1G 0.407895 0.852273
78 P2G 0.4 0.790698
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1Y4Z; Ligand: PCI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1y4z.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1Y4Z; Ligand: PCI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1y4z.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1Y4Z; Ligand: PCI; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1y4z.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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