Receptor
PDB id Resolution Class Description Source Keywords
1SIW 2.2 Å EC: 1.7.99.4 CRYSTAL STRUCTURE OF THE APOMOLYBDO-NARGHI ESCHERICHIA COLI APOMOLYBDO-NARGHI; ELECTRON-TRANSFER; MEMBRANE PROTEIN OXIDOREDUCTASE
Ref.: THE CATALYTIC SUBUNIT OF ESCHERICHIA COLI NITRATE REDUCTASE A CONTAINS A NOVEL [4FE-4S] CLUSTER WITH A HIGH-SPIN GROUND STATE BIOCHEMISTRY V. 43 5324 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PH A:1309;
B:1310;
Valid;
Valid;
none;
none;
submit data
704.998 C39 H77 O8 P CCCCC...
F3S B:805;
Part of Protein;
none;
submit data
295.795 Fe3 S4 S1[Fe...
GDP A:1247;
Valid;
none;
submit data
443.201 C10 H15 N5 O11 P2 c1nc2...
HEM C:806;
C:807;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
SF4 A:1248;
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: 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: GDP; Similar ligands found: 168
No: Ligand ECFP6 Tc MDL keys Tc
1 GDP 1 1
2 GTP 0.909091 1
3 GP3 0.881579 0.973684
4 GNH 0.858974 0.986667
5 GNP 0.839506 0.973684
6 9GM 0.839506 0.973684
7 G 0.828947 0.986486
8 5GP 0.828947 0.986486
9 G1R 0.82716 0.986667
10 GCP 0.82716 0.973684
11 GSP 0.817073 0.948718
12 GAV 0.797619 0.961039
13 GMV 0.792683 0.973684
14 G2P 0.77381 0.961039
15 G2R 0.770115 0.961039
16 GP2 0.756098 0.961039
17 GKE 0.747253 0.961039
18 GDD 0.747253 0.961039
19 GDC 0.747253 0.961039
20 GPG 0.741573 0.961039
21 G3D 0.732558 0.986486
22 ALF 5GP 0.729412 0.888889
23 Y9Z 0.728261 0.902439
24 G5P 0.723404 0.973684
25 GDR 0.72043 0.961039
26 GFB 0.72043 0.961039
27 GTG 0.72043 0.936709
28 G4P 0.715909 0.986486
29 6CK 0.712766 0.936709
30 G3A 0.712766 0.973684
31 GDP AF3 0.7 0.888889
32 GDP ALF 0.7 0.888889
33 ALF GDP 0.7 0.888889
34 YGP 0.698925 0.901235
35 JB2 0.697917 0.961039
36 GKD 0.697917 0.961039
37 GPD 0.690722 0.925
38 GDX 0.690722 0.973684
39 GMP 0.684211 0.88
40 0O2 0.666667 0.986486
41 JB3 0.656863 0.948718
42 NGD 0.650485 0.961039
43 GDP 7MG 0.636364 0.911392
44 DGI 0.636364 0.923077
45 U2G 0.634615 0.936709
46 GPX 0.634409 0.946667
47 G G 0.632653 0.948052
48 IDP 0.632184 0.972973
49 2MD 0.632075 0.891566
50 CAG 0.62963 0.880952
51 KB7 0.629214 0.82716
52 CG2 0.622642 0.936709
53 FEG 0.619048 0.879518
54 MGD 0.614679 0.891566
55 ZGP 0.613208 0.869048
56 GH3 0.612903 0.973333
57 3GP 0.611765 0.946667
58 MD1 0.607143 0.891566
59 PGD 0.59292 0.925
60 DGT 0.591398 0.923077
61 BGO 0.588785 0.924051
62 TPG 0.582609 0.840909
63 DBG 0.582609 0.948718
64 KBD 0.581633 0.82716
65 2GP 0.574713 0.96
66 FE9 0.570175 0.776596
67 GCP G 0.56 0.921053
68 KBJ 0.558824 0.797619
69 G A A A 0.553571 0.923077
70 A G 0.553571 0.935065
71 MGP 0.553191 0.961039
72 U A G G 0.548673 0.935065
73 G4M 0.548387 0.880952
74 6G0 0.547368 0.961039
75 G1R G1R 0.542373 0.924051
76 P2G 0.527473 0.883117
77 PGD O 0.525 0.850575
78 ADP 0.522222 0.92
79 R5I 0.520833 0.946667
80 R7I 0.520833 0.946667
81 GGM 0.517544 0.901235
82 DGP 0.516484 0.910256
83 DG 0.516484 0.910256
84 P1G 0.516129 0.871795
85 G U 0.513274 0.9
86 G1G 0.508475 0.925
87 IMP 0.505495 0.959459
88 AKW 0.504425 0.890244
89 G C 0.504348 0.9
90 GPC 0.491525 0.879518
91 G7M 0.483871 0.948052
92 6AD 0.479592 0.841463
93 ATP 0.473684 0.92
94 HEJ 0.473684 0.92
95 G2Q 0.471154 0.961039
96 AQP 0.46875 0.92
97 5FA 0.46875 0.92
98 GTA 0.468468 0.936709
99 7DD 0.468085 0.906667
100 G G G RPC 0.466102 0.875
101 SGP 0.463158 0.82716
102 01G 0.462963 0.902439
103 JSQ 0.459184 0.873418
104 HFD 0.459184 0.873418
105 AP5 0.457447 0.894737
106 B4P 0.457447 0.894737
107 A2D 0.456522 0.894737
108 6YZ 0.455446 0.896104
109 G G G C 0.455285 0.9125
110 ANP 0.454545 0.896104
111 5GP 5GP 0.454545 0.883117
112 ACQ 0.454545 0.896104
113 AT4 0.452632 0.884615
114 A G C C 0.451613 0.911392
115 APC G U 0.45082 0.886076
116 PRT 0.449541 0.959459
117 G U34 0.449153 0.888889
118 DG DG 0.448598 0.865854
119 ITT 0.447917 0.868421
120 BA3 0.446809 0.894737
121 35G 0.444444 0.933333
122 PCG 0.444444 0.933333
123 C2E 0.444444 0.921053
124 MGO 0.441176 0.864198
125 AN2 0.4375 0.907895
126 G C C C 0.4375 0.924051
127 NO7 0.436893 0.860759
128 M33 0.43299 0.883117
129 UCG 0.429688 0.911392
130 A G U 0.42963 0.888889
131 ACP 0.428571 0.896104
132 MGQ 0.424528 0.935897
133 7DT 0.424242 0.906667
134 APR 0.424242 0.894737
135 AR6 0.424242 0.894737
136 93A 0.42268 0.833333
137 A4P 0.420168 0.869048
138 AGS 0.42 0.873418
139 AD9 0.42 0.896104
140 G8D 0.42 0.875
141 SAP 0.42 0.873418
142 CA0 0.418367 0.896104
143 ATF 0.417476 0.884615
144 AGO 0.414634 0.888889
145 A G U U 0.414286 0.888889
146 KG4 0.414141 0.896104
147 NIA 0.413043 0.82716
148 MGV 0.412844 0.890244
149 T99 0.411765 0.884615
150 TAT 0.411765 0.884615
151 A1R 0.411215 0.839506
152 ADQ 0.411215 0.871795
153 RGT 0.410714 0.909091
154 CGP 0.409836 0.86747
155 HQG 0.409524 0.907895
156 C1Z 0.409091 0.986486
157 AMP 0.408602 0.893333
158 A 0.408602 0.893333
159 UP5 0.40678 0.873418
160 C2R 0.406593 0.906667
161 AMZ 0.406593 0.918919
162 JBT 0.405882 0.778947
163 A22 0.40566 0.907895
164 25L 0.405405 0.907895
165 ADX 0.40404 0.809524
166 8OD 0.401961 0.946667
167 4TC 0.4 0.851852
168 50T 0.4 0.883117
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
APoc FAQ
Feedback