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Receptor
PDB id Resolution Class Description Source Keywords
1YKI 1.7 Å EC: 1.5.1.34 THE STRUCTURE OF E. COLI NITROREDUCTASE BOUND WITH THE ANTIBIOTIC NITROFURAZONE ESCHERICHIA COLI OXIDOREDUCTASE OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
Ref.: STRUCTURAL AND MECHANISTIC STUDIES OF ESCHERICHIA COLI NITROREDUCTASE WITH THE ANTIBIOTIC NITROFURAZONE. REVERSED BINDING ORIENTATIONS IN DIFFERENT REDOX STATES OF THE ENZYME. J.BIOL.CHEM. V. 280 13256 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT C:4220;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
DMS B:1225;
C:1223;
C:1224;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
FMN A:1218;
B:2218;
C:3218;
D:4218;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
NFZ A:1219;
B:2219;
C:3219;
D:4219;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
198.136 C6 H6 N4 O4 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YKI 1.7 Å EC: 1.5.1.34 THE STRUCTURE OF E. COLI NITROREDUCTASE BOUND WITH THE ANTIBIOTIC NITROFURAZONE ESCHERICHIA COLI OXIDOREDUCTASE OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE
Ref.: STRUCTURAL AND MECHANISTIC STUDIES OF ESCHERICHIA COLI NITROREDUCTASE WITH THE ANTIBIOTIC NITROFURAZONE. REVERSED BINDING ORIENTATIONS IN DIFFERENT REDOX STATES OF THE ENZYME. J.BIOL.CHEM. V. 280 13256 2005
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1OO6 - SN2 C11 H12 Cl2 N4 O5 c1c(c(cc(c....
2 1OO5 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1YLU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1ICU - NIO C6 H5 N O2 c1cc(cnc1)....
5 1DS7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 1ICR - NIO C6 H5 N O2 c1cc(cnc1)....
7 1IDT - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1YKI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 1OON - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1YLR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 1OOQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1OO6 - SN2 C11 H12 Cl2 N4 O5 c1c(c(cc(c....
2 1OO5 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1YLU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1ICU - NIO C6 H5 N O2 c1cc(cnc1)....
5 1DS7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 1ICR - NIO C6 H5 N O2 c1cc(cnc1)....
7 1IDT - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1YKI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 1OON - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 1YLR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 1OOQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 1KQB Ki = 0.1 mM BEZ C7 H6 O2 c1ccc(cc1)....
13 1KQD - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 1KQC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 1NEC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1V5Z - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 1V5Y - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 1VFR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 1OO6 - SN2 C11 H12 Cl2 N4 O5 c1c(c(cc(c....
5 1OO5 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
6 1YLU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
7 1ICU - NIO C6 H5 N O2 c1cc(cnc1)....
8 1DS7 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 1ICR - NIO C6 H5 N O2 c1cc(cnc1)....
10 1IDT - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
11 1YKI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
12 1OON - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 1YLR - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
14 1OOQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
15 1KQB Ki = 0.1 mM BEZ C7 H6 O2 c1ccc(cc1)....
16 1KQD - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1KQC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
18 1NEC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FMN; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAD 0.543307 0.876543
5 FAS 0.543307 0.876543
6 FAE 0.539062 0.865854
7 LFN 0.475 0.643836
8 C3F 0.473684 0.74359
9 CF4 0.463918 0.734177
10 FAY 0.446043 0.864198
11 FNR 0.444444 0.909091
12 RFL 0.442857 0.845238
13 4LS 0.411215 0.875
14 1VY 0.406593 0.769231
15 DLZ 0.404494 0.782051
Ligand no: 2; Ligand: NFZ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NFZ 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found with APoc: 121
This union binding pocket(no: 1) in the query (biounit: 1yki.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4NB5 2JT None
2 4I67 G G G RPC None
3 3KO0 TFP None
4 4UA3 COA None
5 2JAQ DCP 1.46341
6 1M48 FRG 1.50376
7 2ZQO NGA 1.53846
8 4DDY DN6 1.84332
9 1PX8 XYP 1.84332
10 2OFD NGA 2.11268
11 2OFE NAG 2.11268
12 4Z2S NDG 2.11268
13 4Z2S NAG 2.11268
14 6BR8 6OU 2.30415
15 4G86 BNT 2.30415
16 6DIO CIT 2.30415
17 6BR8 PGV 2.30415
18 5V3Y 5V8 2.30415
19 1FX8 BOG 2.76498
20 1F5V FMN 2.76498
21 1TV5 N8E 2.76498
22 5AHS COA 2.76498
23 4RKK GLC GLC GLC GLC GLC GLC 2.76498
24 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.22581
25 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.22581
26 5M36 9SZ 3.22581
27 1VRP IOM 3.22581
28 5VLQ ANP 3.22581
29 5M37 9SZ 3.22581
30 5N1P 8GK 3.39806
31 3HYW DCQ 3.48837
32 5W7B MYR 3.5461
33 3TDC 0EU 3.68664
34 2BHW NEX 3.68664
35 1HFU NAG NDG 3.68664
36 3ROE THM 3.68664
37 4TV1 36M 3.68664
38 3W54 RNB 3.68664
39 5WA0 MSS 3.68664
40 2BCG GER 3.8835
41 3GUZ PAF 3.97727
42 5WHU SIA GAL 4.02685
43 2HHP FLC 4.14747
44 5EW0 3C7 4.14747
45 4C2G ALA ALA ALA ALA 4.14747
46 4XOQ F42 4.34783
47 1HBK MYR 4.49438
48 3FXU TSU 4.60829
49 4FMS BDP 4.60829
50 4BQO COA 4.60829
51 1Y2W NAG 4.92958
52 1ZED PNP 5.06912
53 5EY0 GTP 5.06912
54 2JHP GUN 5.06912
55 2OI2 DP6 5.06912
56 5CX6 CDP 5.52995
57 5MRH Q9Z 5.52995
58 4K6B GLU 5.59006
59 3KP6 SAL 5.96026
60 3B6C SDN 5.99078
61 5AZC PGT 5.99078
62 3N7S 3N7 6.08696
63 2GN2 C5P 6.45161
64 3VSV XYP 6.45161
65 5TI9 NFK 6.45161
66 5XJ7 87O 6.46766
67 1OYJ GSH 6.49351
68 3RMK BML 6.91244
69 4TR9 38D 6.91244
70 3LGG CFE 6.91244
71 3QDW NDG 6.99301
72 3QDY CBS 6.99301
73 3QDX CBS 6.99301
74 2O1V ADP 7.37327
75 5UNJ RJW 7.37327
76 1GPM AMP 7.37327
77 1PFK ADP 7.37327
78 1WLJ U5P 7.40741
79 4JLS 3ZE 7.89474
80 5UGW GSH 8
81 4LWU 20U 8.23529
82 3O01 DXC 8.29493
83 1WTC ACP 8.29493
84 3RV5 DXC 8.98876
85 5UC1 486 9.21659
86 3ZVS MLI 9.375
87 5J62 FMN 10.1382
88 2ISJ FMN 10.1382
89 4RW3 SHV 10.1382
90 3EYK EYK 10.4651
91 4LSJ LSJ 10.5991
92 3DAK ANP 11.5207
93 3KPE TM3 11.7647
94 1I0B PEL 11.9816
95 1M2Z BOG 12.4424
96 5LX9 OLB 12.9032
97 5LWY OLB 12.9032
98 4UDK BMA 12.9032
99 2WZV FMN 13.3641
100 1PVC ILE SER GLU VAL 13.3641
101 3N2S FMN 14.7465
102 5YAK FMN 14.7465
103 5YAK YOF 14.7465
104 4OAS 2SW 15.625
105 1KNM LAT 16.9231
106 5J6C FMN 20.8955
107 1ZCH FMN 21.1982
108 2WOR 2AN 22
109 2Y69 CHD 24.3243
110 5ZCO CHD 24.6575
111 5Z84 CHD 24.6575
112 5W97 CHD 24.6575
113 4EO3 FMN 25.8065
114 4OGQ 7PH 29.7297
115 4OGQ UMQ 29.7297
116 1BKJ FMN 35.4839
117 5HDJ FMN 35.9447
118 3QDL FMN 39.0476
119 4QLX KTC 39.6313
120 4QLX FMN 39.6313
121 1NOX FMN 46.8293
Pocket No.: 2; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found with APoc: 138
This union binding pocket(no: 2) in the query (biounit: 1yki.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 4NB5 2JT None
2 1SBR VIB None
3 4I67 G G G RPC None
4 3KO0 TFP None
5 4UA3 COA None
6 4PNG GSF 0.921659
7 1V2A GTS 0.952381
8 2JAQ DCP 1.46341
9 2ZQO NGA 1.53846
10 4DDY DN6 1.84332
11 2OFD NGA 2.11268
12 4Z2S NDG 2.11268
13 4Z2S NAG 2.11268
14 2OFE NAG 2.11268
15 6BR8 6OU 2.30415
16 4G86 BNT 2.30415
17 6DIO CIT 2.30415
18 6BR8 PGV 2.30415
19 5E9G GLV 2.30415
20 5V3Y 5V8 2.30415
21 1F5V FMN 2.76498
22 1TV5 N8E 2.76498
23 4RKK GLC GLC GLC GLC GLC GLC 2.76498
24 2W58 ADP 2.9703
25 1NU4 MLA 3.09278
26 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.22581
27 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.22581
28 1Q19 SSC 3.22581
29 1VRP IOM 3.22581
30 5VLQ ANP 3.22581
31 5M37 9SZ 3.22581
32 3HYW DCQ 3.48837
33 5W7B MYR 3.5461
34 3TDC 0EU 3.68664
35 2BHW NEX 3.68664
36 1HFU NAG NDG 3.68664
37 4TV1 36M 3.68664
38 3ROE THM 3.68664
39 3W54 RNB 3.68664
40 3SP6 IL2 3.68664
41 4QBK 3NZ 3.68664
42 5WA0 MSS 3.68664
43 3KIV ACA 3.79747
44 2BCG GER 3.8835
45 1XPJ TLA 3.96825
46 3GUZ PAF 3.97727
47 2HHP FLC 4.14747
48 5EW0 3C7 4.14747
49 4YH2 GSH 4.14747
50 5FJJ MAN 4.14747
51 2X1L ADN 4.14747
52 4C2G ALA ALA ALA ALA 4.14747
53 4XOQ F42 4.34783
54 1HBK MYR 4.49438
55 6C0B MLI 4.60829
56 3FXU TSU 4.60829
57 4FMS BDP 4.60829
58 3E70 GDP 4.60829
59 4BQO COA 4.60829
60 4X1Z FUC GAL NDG 4.60829
61 1S8G DAO 4.95868
62 5E5U MLI 5.02513
63 5EY0 GTP 5.06912
64 2JHP GUN 5.06912
65 1CT9 GLN 5.06912
66 5CX6 CDP 5.52995
67 1WUU GLA 5.52995
68 2PRG BRL 5.52995
69 1DTL BEP 5.59006
70 4K6B GLU 5.59006
71 3KP6 SAL 5.96026
72 3B6C SDN 5.99078
73 3N7S 3N7 6.08696
74 5URY PAM 6.16438
75 2GN2 C5P 6.45161
76 3VSV XYP 6.45161
77 5TI9 NFK 6.45161
78 1OYJ GSH 6.49351
79 1JGS SAL 6.52174
80 1FLM FMN 6.55738
81 3RMK BML 6.91244
82 3QDW NDG 6.99301
83 3QDY CBS 6.99301
84 3QDX CBS 6.99301
85 3HY2 ATP 7.27273
86 4LIK CIT 7.37327
87 2O1V ADP 7.37327
88 5UNJ RJW 7.37327
89 1GPM AMP 7.37327
90 1PFK ADP 7.37327
91 1WLJ U5P 7.40741
92 4JLS 3ZE 7.89474
93 5UGW GSH 8
94 4LWU 20U 8.23529
95 3O01 DXC 8.29493
96 1WTC ACP 8.29493
97 2VWA PTY 8.91089
98 5UC1 486 9.21659
99 3ZVS MLI 9.375
100 5J62 FMN 10.1382
101 4RW3 SHV 10.1382
102 2ISJ FMN 10.1382
103 1TMX HGX 10.1382
104 4XCP PLM 10.5882
105 4LSJ LSJ 10.5991
106 2JAC GSH 10.9091
107 1EYQ NAR 11.5207
108 3DAK ANP 11.5207
109 3KPE TM3 11.7647
110 1M2Z BOG 12.4424
111 5CQG 55C 12.4424
112 5LX9 OLB 12.9032
113 5LWY OLB 12.9032
114 4UDK BMA 12.9032
115 2CDC XYS 12.9032
116 3OF1 CMP 12.9032
117 2WZV FMN 13.3641
118 3N2S FMN 14.7465
119 5YAK FMN 14.7465
120 5YAK YOF 14.7465
121 4OAS 2SW 15.625
122 1KNM LAT 16.9231
123 5J6C FMN 20.8955
124 1ZCH FMN 21.1982
125 2WOR 2AN 22
126 5C2N NAG 22.9167
127 2Y69 CHD 24.3243
128 5W97 CHD 24.6575
129 5ZCO CHD 24.6575
130 4EO3 FMN 25.8065
131 1O5O U5P 26.2673
132 4OGQ 7PH 29.7297
133 1BKJ FMN 35.4839
134 5HDJ FMN 35.9447
135 3QDL FMN 39.0476
136 4QLX KTC 39.6313
137 4QLX FMN 39.6313
138 1NOX FMN 46.8293
Pocket No.: 3; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found with APoc: 12
This union binding pocket(no: 3) in the query (biounit: 1yki.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 6BMN PAP 1.38249
2 3A23 GAL 2.30415
3 1U6R IOM 2.76498
4 1TL2 NDG 2.76498
5 5NC9 8SZ 3.22581
6 5N1P 8GK 3.39806
7 5LOL GSH 3.72093
8 6GR0 F8W 4.02299
9 5MUA GAL 4.14747
10 5TED SKM 4.14747
11 1PVC ILE SER GLU VAL 13.3641
12 2QQC AG2 17.8571
Pocket No.: 4; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found with APoc: 9
This union binding pocket(no: 4) in the query (biounit: 1yki.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3ALT MLB None
2 6BMN PAP 1.38249
3 3A23 GAL 2.30415
4 1U6R IOM 2.76498
5 5NC9 8SZ 3.22581
6 5TED SKM 4.14747
7 4OKE AMP 6.54762
8 3N75 G4P 7.8341
9 2QQC AG2 17.8571
Pocket No.: 5; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found with APoc: 7
This union binding pocket(no: 5) in the query (biounit: 1yki.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 3ALT MLB None
2 4LO6 SIA GAL 3.68664
3 4V3I ASP LEU THR ARG PRO 4.14747
4 4ZGR NGA GAL 4.14747
5 4AGS GSH 5.06912
6 1JOC ITP 5.6
7 5J3R GSH 7.38916
Pocket No.: 6; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found with APoc: 5
This union binding pocket(no: 6) in the query (biounit: 1yki.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 5MUA GAL 4.14747
2 1CT9 GLN 5.06912
3 1JOC ITP 5.6
4 5M90 JIF 6.91244
5 3LMS GLY 10.8108
Pocket No.: 7; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found with APoc: 6
This union binding pocket(no: 7) in the query (biounit: 1yki.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4V36 LYN 4.14747
2 5MRH Q9Z 5.52995
3 5M90 JIF 6.91244
4 3L4N GSH 7.08661
5 3A3B RBF 7.36842
6 3LMS GLY 10.8108
Pocket No.: 8; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found with APoc: 4
This union binding pocket(no: 8) in the query (biounit: 1yki.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4LO6 SIA GAL 3.68664
2 4ZGR NGA GAL 4.14747
3 2CDC XYS 12.9032
4 1YNS HPO 16.129
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