Receptor
PDB id Resolution Class Description Source Keywords
1Q16 1.9 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF NITRATE REDUCTASE A, NARGHI, FROM ESCHERICHIA COLI ESCHERICHIA COLI MEMBRANE PROTEIN ELECTRON-TRANSFER OXIDOREDUCTASE
Ref.: INSIGHTS INTO THE RESPIRATORY ELECTRON TRANSFER PATHWAY FROM THE STRUCTURE OF NITRATE REDUCTASE A NAT.STRUCT.BIOL. V. 10 681 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PH B:1310;
Valid;
none;
submit data
704.998 C39 H77 O8 P CCCCC...
6MO A:1302;
Part of Protein;
none;
submit data
95.94 Mo [Mo+6...
AGA A:1309;
Valid;
none;
submit data
455.457 C19 H36 O10 P CCCCC...
F3S B:1405;
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:1300;
A:1301;
Valid;
Valid;
none;
none;
submit data
740.557 C20 H26 N10 O13 P2 S2 c1nc2...
SF4 A:1401;
B:1402;
B:1403;
B:1404;
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: 3PH; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 6PH 1 1
2 3PH 1 1
3 F57 1 1
4 LPP 1 1
5 7PH 1 1
6 7P9 0.980392 1
7 PD7 0.921569 1
8 D21 0.847458 0.976744
9 M7U 0.847458 1
10 44E 0.846154 1
11 PX8 0.803571 0.930233
12 PX2 0.803571 0.930233
13 PA8 0.785714 0.930233
14 TGL 0.745098 0.690476
15 CD4 0.725806 0.953488
16 8PE 0.714286 0.788462
17 PEH 0.714286 0.788462
18 PEV 0.714286 0.788462
19 PTY 0.714286 0.788462
20 PEF 0.714286 0.788462
21 9PE 0.703125 0.788462
22 PEE 0.703125 0.773585
23 PGT 0.703125 0.911111
24 LHG 0.703125 0.911111
25 CDL 0.6875 0.863636
26 P5S 0.681818 0.803922
27 HGX 0.681818 0.727273
28 PX4 0.681818 0.727273
29 LIO 0.681818 0.727273
30 PLD 0.681818 0.727273
31 HGP 0.681818 0.727273
32 6PL 0.681818 0.727273
33 PC7 0.681818 0.727273
34 PII 0.661765 0.836735
35 PIF 0.642857 0.857143
36 CN3 0.642857 0.953488
37 3PE 0.641791 0.711538
38 L2C 0.631579 0.697674
39 1EM 0.631579 0.697674
40 FAW 0.631579 0.697674
41 DGA 0.631579 0.697674
42 DDR 0.631579 0.697674
43 PIZ 0.630137 0.875
44 XP5 0.626866 0.727273
45 LOP 0.625 0.773585
46 6OU 0.625 0.773585
47 L9Q 0.625 0.773585
48 PC1 0.623188 0.685185
49 PCF 0.623188 0.685185
50 MC3 0.623188 0.685185
51 IP9 0.616438 0.875
52 52N 0.616438 0.857143
53 PIO 0.616438 0.857143
54 D3D 0.616438 0.891304
55 PGW 0.616438 0.891304
56 CN6 0.614286 0.953488
57 NKN 0.610169 0.953488
58 NKO 0.610169 0.953488
59 AGA 0.608696 0.869565
60 PGV 0.608108 0.891304
61 DR9 0.608108 0.891304
62 PCW 0.6 0.714286
63 PGK 0.6 0.854167
64 P6L 0.6 0.891304
65 OZ2 0.592105 0.891304
66 P50 0.592105 0.803922
67 44G 0.590909 0.911111
68 ZPE 0.586667 0.773585
69 B7N 0.584416 0.82
70 PCK 0.584416 0.689655
71 DGG 0.576923 0.854167
72 HXG 0.573529 0.727273
73 PSF 0.573529 0.803922
74 LBR 0.5625 0.644444
75 GP7 0.5625 0.773585
76 PEK 0.556962 0.773585
77 PIE 0.556962 0.764706
78 P3A 0.556962 0.851064
79 L9R 0.551282 0.672727
80 POV 0.551282 0.672727
81 PSC 0.548781 0.714286
82 NKP 0.529412 0.931818
83 2JT 0.527273 0.659091
84 G2A 0.527273 0.659091
85 T7X 0.517647 0.82
86 PDK 0.505618 0.683333
87 SQD 0.5 0.609375
88 GYM 0.491525 0.644444
89 1QW 0.491525 0.644444
90 BQ9 0.486486 0.681818
91 DLP 0.482353 0.672727
92 EPH 0.466667 0.773585
93 LPC 0.465753 0.732143
94 LAP 0.465753 0.732143
95 LP3 0.465753 0.732143
96 PGM 0.457143 0.847826
97 87O 0.45614 0.813953
98 PC5 0.432432 0.603448
99 3PC 0.428571 0.666667
100 OLB 0.426471 0.630435
101 OLC 0.426471 0.630435
102 PVC 0.426471 0.625
103 CN5 0.421053 0.931818
104 42H 0.414634 0.719298
105 DB4 0.413333 0.795918
106 PBU 0.410256 0.795918
107 MVC 0.405797 0.630435
108 S12 0.402439 0.769231
Ligand no: 2; Ligand: AGA; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 AGA 1 1
2 CDL 0.80303 0.909091
3 P3A 0.763158 0.977778
4 PGT 0.666667 0.955556
5 LHG 0.666667 0.955556
6 3PE 0.657534 0.784314
7 PA8 0.656716 0.888889
8 PX8 0.647059 0.888889
9 PX2 0.647059 0.888889
10 PC1 0.64 0.690909
11 MC3 0.64 0.690909
12 PCF 0.64 0.690909
13 PGM 0.637681 0.977273
14 LPP 0.608696 0.869565
15 7PH 0.608696 0.869565
16 3PH 0.608696 0.869565
17 6PH 0.608696 0.869565
18 F57 0.608696 0.869565
19 7P9 0.6 0.869565
20 CD4 0.594595 0.911111
21 PGW 0.592593 0.934783
22 D3D 0.592593 0.934783
23 44G 0.589041 0.955556
24 DR9 0.585366 0.934783
25 PGV 0.585366 0.934783
26 PD7 0.57971 0.869565
27 P6L 0.578313 0.934783
28 PGK 0.578313 0.895833
29 OZ2 0.571429 0.934783
30 POV 0.571429 0.678571
31 L9R 0.571429 0.678571
32 PEV 0.565789 0.792453
33 8PE 0.565789 0.792453
34 PEH 0.565789 0.792453
35 PTY 0.565789 0.792453
36 PEF 0.565789 0.792453
37 TGL 0.5625 0.659091
38 9PE 0.558442 0.792453
39 DGG 0.55814 0.895833
40 HGP 0.544304 0.701754
41 6PL 0.544304 0.701754
42 LIO 0.544304 0.701754
43 PX4 0.544304 0.701754
44 PC7 0.544304 0.701754
45 P5S 0.544304 0.807692
46 PLD 0.544304 0.701754
47 HGX 0.544304 0.701754
48 PIE 0.54023 0.803922
49 D21 0.538462 0.851064
50 M7U 0.538462 0.869565
51 PEE 0.538462 0.811321
52 CN3 0.536585 0.911111
53 DDR 0.529412 0.704545
54 1EM 0.529412 0.704545
55 L2C 0.529412 0.704545
56 FAW 0.529412 0.704545
57 DGA 0.529412 0.704545
58 44E 0.528571 0.869565
59 XP5 0.518987 0.701754
60 PII 0.512195 0.803922
61 CN6 0.512195 0.911111
62 LOP 0.505882 0.777778
63 6OU 0.505882 0.777778
64 L9Q 0.505882 0.777778
65 DLP 0.505495 0.678571
66 PIF 0.5 0.788462
67 PCW 0.488636 0.689655
68 IP9 0.482759 0.769231
69 PIO 0.482759 0.788462
70 52N 0.482759 0.788462
71 LBR 0.48 0.652174
72 GP7 0.478261 0.777778
73 PCK 0.477778 0.666667
74 GYM 0.477612 0.727273
75 1QW 0.477612 0.727273
76 ZPE 0.477273 0.777778
77 PIZ 0.477273 0.769231
78 PSF 0.475 0.807692
79 HXG 0.475 0.701754
80 P50 0.466667 0.773585
81 2JT 0.461538 0.666667
82 G2A 0.461538 0.666667
83 B7N 0.461538 0.788462
84 PEK 0.456522 0.777778
85 PSC 0.452632 0.689655
86 PC5 0.444444 0.610169
87 NKN 0.432432 0.869565
88 NKO 0.432432 0.869565
89 SQD 0.423913 0.615385
90 BQ9 0.423529 0.688889
91 OLB 0.421053 0.711111
92 OLC 0.421053 0.711111
93 T7X 0.414141 0.788462
94 DGD 0.412371 0.618182
95 78M 0.407895 0.711111
96 78N 0.407895 0.711111
97 PDK 0.407767 0.688525
98 3PC 0.406977 0.672727
99 LPC 0.404762 0.736842
100 LP3 0.404762 0.736842
101 LAP 0.404762 0.736842
102 MVC 0.402597 0.711111
103 1O2 0.402062 0.6
104 EPH 0.401961 0.777778
105 PCJ 0.4 0.607143
Ligand no: 3; 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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