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 1 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 1 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: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAS 0.543307 0.876543
5 FAD 0.543307 0.876543
6 FAE 0.539062 0.865854
7 DAL FAD PER 0.5 0.833333
8 LFN 0.475 0.643836
9 C3F 0.473684 0.74359
10 CF4 0.463918 0.734177
11 FAY 0.446043 0.864198
12 FNR 0.444444 0.909091
13 RFL 0.442857 0.845238
14 4LS 0.411215 0.875
15 1VY 0.406593 0.769231
16 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: 68
This union binding pocket(no: 1) in the query (biounit: 1yki.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NB5 2JT 0.005264 0.42267 None
2 3KO0 TFP 0.03876 0.41139 None
3 4I67 G G G RPC 0.02386 0.40912 None
4 4UA3 COA 0.0126 0.40235 None
5 1M48 FRG 0.04727 0.4011 1.50376
6 2ZQO NGA 0.04006 0.40872 1.53846
7 1PX8 XYP 0.02743 0.41415 1.84332
8 2OFD NGA 0.01737 0.43091 2.11268
9 4Z2S NAG 0.02134 0.42501 2.11268
10 4Z2S NDG 0.02134 0.42501 2.11268
11 5V3Y 5V8 0.03485 0.40067 2.30415
12 1F5V FMN 0.000001019 0.59106 2.76498
13 1TV5 N8E 0.02177 0.42819 2.76498
14 5AHS COA 0.01817 0.40779 2.76498
15 4RKK GLC GLC GLC GLC GLC GLC 0.02429 0.40164 2.76498
16 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.002986 0.48922 3.22581
17 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.001911 0.48647 3.22581
18 3HYW DCQ 0.03575 0.41066 3.48837
19 3TDC 0EU 0.0001416 0.58784 3.68664
20 1HFU NAG NDG 0.007023 0.43557 3.68664
21 3ROE THM 0.01373 0.42137 3.68664
22 2HHP FLC 0.0008064 0.51047 4.14747
23 5EW0 3C7 0.03991 0.40509 4.14747
24 4C2G ALA ALA ALA ALA 0.03962 0.40141 4.14747
25 5D8U 0N8 0.01015 0.42805 4.56853
26 4FMS BDP 0.02977 0.41198 4.60829
27 4BQO COA 0.02015 0.40226 4.60829
28 1Y2W NAG 0.04952 0.40385 4.92958
29 5EY0 GTP 0.01889 0.41431 5.06912
30 2JHP GUN 0.04546 0.40141 5.06912
31 5CX6 CDP 0.01522 0.43084 5.52995
32 5MRH Q9Z 0.03432 0.40471 5.52995
33 3KP6 SAL 0.02489 0.42209 5.96026
34 3B6C SDN 0.005785 0.4501 5.99078
35 3N7S 3N7 0.03253 0.41597 6.08696
36 2GN2 C5P 0.01044 0.43273 6.45161
37 4TR9 38D 0.03595 0.40554 6.91244
38 3QDW NDG 0.04244 0.40271 6.99301
39 3QDY CBS 0.04362 0.40149 6.99301
40 5UNJ RJW 0.008789 0.41942 7.37327
41 1GPM AMP 0.02823 0.41839 7.37327
42 1WLJ U5P 0.02896 0.41208 7.40741
43 5UGW GSH 0.002282 0.51628 8
44 4LWU 20U 0.01496 0.41191 8.23529
45 3O01 DXC 0.002715 0.47946 8.29493
46 1WTC ACP 0.004686 0.45956 8.29493
47 3ZVS MLI 0.02694 0.40292 9.375
48 5J62 FMN 0.000008892 0.5546 10.1382
49 2ISJ FMN 0.0001242 0.47827 10.1382
50 4RW3 SHV 0.03825 0.40868 10.1382
51 3EYK EYK 0.02257 0.43633 10.4651
52 1I0B PEL 0.0342 0.41966 11.9816
53 1M2Z BOG 0.0037 0.46853 12.4424
54 2WZV FMN 0.0000006444 0.50926 13.3641
55 3N2S FMN 0.0000002448 0.61185 14.7465
56 4TTB FMN 0.000009214 0.55388 14.7465
57 4OAS 2SW 0.01841 0.40751 15.625
58 1KNM LAT 0.01729 0.42565 16.9231
59 5J6C FMN 0.0000006265 0.60792 20.8955
60 1ZCH FMN 0.004728 0.41806 21.1982
61 2WOR 2AN 0.003398 0.46911 22
62 4EO3 FMN 0.00000009502 0.62279 25.8065
63 1BKJ FMN 0.000001457 0.54837 35.4839
64 5HDJ FMN 0.0000001674 0.61919 35.9447
65 3QDL FMN 0.00000000004208 0.75917 39.0476
66 4QLX FMN 0.0000003765 0.57795 39.6313
67 4QLX KTC 0.000001761 0.50793 39.6313
68 1NOX FMN 0.00006323 0.50466 46.8293
Pocket No.: 2; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found: 90
This union binding pocket(no: 2) in the query (biounit: 1yki.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NB5 2JT 0.00475 0.42838 None
2 3KO0 TFP 0.04371 0.41139 None
3 1SBR VIB 0.03634 0.41052 None
4 4I67 G G G RPC 0.02765 0.40912 None
5 4UA3 COA 0.01467 0.40283 None
6 4PNG GSF 0.0424 0.40303 0.921659
7 1V2A GTS 0.03617 0.41185 0.952381
8 2ZQO NGA 0.04533 0.40872 1.53846
9 2OFD NGA 0.0199 0.43091 2.11268
10 4Z2S NAG 0.0244 0.42501 2.11268
11 4Z2S NDG 0.0244 0.42501 2.11268
12 2OFE NAG 0.03178 0.41786 2.11268
13 5V3Y 5V8 0.03364 0.4047 2.30415
14 1F5V FMN 0.000001396 0.59038 2.76498
15 1TV5 N8E 0.0248 0.42819 2.76498
16 4RKK GLC GLC GLC GLC GLC GLC 0.02415 0.40507 2.76498
17 2W58 ADP 0.02223 0.42781 2.9703
18 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.00345 0.48922 3.22581
19 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.002238 0.48647 3.22581
20 1Q19 SSC 0.008244 0.44826 3.22581
21 3HYW DCQ 0.04065 0.41066 3.48837
22 3TDC 0EU 0.000164 0.58784 3.68664
23 1HFU NAG NDG 0.0079 0.43557 3.68664
24 3ROE THM 0.01602 0.42137 3.68664
25 3SP6 IL2 0.01534 0.40492 3.68664
26 4QBK 3NZ 0.03621 0.40303 3.68664
27 3KIV ACA 0.00996 0.41554 3.79747
28 1XPJ TLA 0.02625 0.42204 3.96825
29 2HHP FLC 0.0009219 0.51047 4.14747
30 5EW0 3C7 0.01876 0.42615 4.14747
31 4YH2 GSH 0.03479 0.41156 4.14747
32 5FJJ MAN 0.02118 0.40774 4.14747
33 2GKL PD2 0.02789 0.40535 4.14747
34 2X1L ADN 0.04203 0.40324 4.14747
35 4C2G ALA ALA ALA ALA 0.04547 0.40141 4.14747
36 5D8U 0N8 0.009828 0.43228 4.56853
37 4FMS BDP 0.03417 0.41198 4.60829
38 3E70 GDP 0.02181 0.41076 4.60829
39 4BQO COA 0.02365 0.40226 4.60829
40 4X1Z FUC GAL NDG 0.02822 0.40119 4.60829
41 5E5U MLI 0.02829 0.41409 5.02513
42 5EY0 GTP 0.02195 0.41431 5.06912
43 2JHP GUN 0.03093 0.41055 5.06912
44 5CX6 CDP 0.01663 0.43207 5.52995
45 2PRG BRL 0.02013 0.40248 5.52995
46 3KP6 SAL 0.0282 0.42209 5.96026
47 3B6C SDN 0.005514 0.45486 5.99078
48 3N7S 3N7 0.01229 0.43375 6.08696
49 5URY PAM 0.008207 0.45353 6.16438
50 2GN2 C5P 0.01193 0.43273 6.45161
51 1JGS SAL 0.03808 0.40496 6.52174
52 1FLM FMN 0.0134 0.40763 6.55738
53 3QDW NDG 0.04798 0.40271 6.99301
54 3QDY CBS 0.04931 0.40149 6.99301
55 3HY2 ATP 0.04216 0.40316 7.27273
56 5UNJ RJW 0.01042 0.41942 7.37327
57 1GPM AMP 0.03194 0.41839 7.37327
58 1WLJ U5P 0.03288 0.41208 7.40741
59 5UGW GSH 0.002604 0.51628 8
60 4LWU 20U 0.0139 0.41691 8.23529
61 3O01 DXC 0.003093 0.47946 8.29493
62 1WTC ACP 0.005417 0.45956 8.29493
63 2VWA PTY 0.04567 0.41389 8.91089
64 3ZVS MLI 0.03037 0.40292 9.375
65 5J62 FMN 0.00001142 0.5546 10.1382
66 2ISJ FMN 0.0001776 0.47616 10.1382
67 4RW3 SHV 0.03849 0.41028 10.1382
68 1TMX HGX 0.01277 0.40263 10.1382
69 4XCP PLM 0.03607 0.41307 10.5882
70 2JAC GSH 0.04389 0.40589 10.9091
71 1EYQ NAR 0.03627 0.40666 11.5207
72 1M2Z BOG 0.003176 0.47287 12.4424
73 5CQG 55C 0.03163 0.41325 12.4424
74 5G4R LF1 0.03658 0.4028 12.7119
75 3OF1 CMP 0.02881 0.40819 12.9032
76 2WZV FMN 0.000001659 0.50855 13.3641
77 3N2S FMN 0.0000003311 0.61185 14.7465
78 4TTB FMN 0.00001183 0.55388 14.7465
79 4OAS 2SW 0.01864 0.41063 15.625
80 1KNM LAT 0.01966 0.42565 16.9231
81 5J6C FMN 0.0000007116 0.61101 20.8955
82 1ZCH FMN 0.005417 0.41913 21.1982
83 2WOR 2AN 0.003503 0.47177 22
84 4EO3 FMN 0.0000001307 0.62279 25.8065
85 1BKJ FMN 0.0000009543 0.5614 35.4839
86 5HDJ FMN 0.0000002274 0.61919 35.9447
87 3QDL FMN 0.00000000006385 0.75917 39.0476
88 4QLX FMN 0.0000008041 0.56999 39.6313
89 4QLX KTC 0.000002676 0.51151 39.6313
90 1NOX FMN 0.00008023 0.50466 46.8293
Pocket No.: 3; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 1yki.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1YKI; Ligand: FMN; 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: 1yki.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found: 6
This union binding pocket(no: 5) in the query (biounit: 1yki.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U6R IOM 0.03613 0.40669 2.76498
2 4V3I ASP LEU THR ARG PRO 0.0303 0.40597 4.14747
3 4ZGR NGA GAL 0.04883 0.40009 4.14747
4 4K6B GLU 0.02218 0.41255 5.59006
5 3KPE TM3 0.01913 0.43494 11.7647
6 2QQC AG2 0.03925 0.40223 17.8571
Pocket No.: 6; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found: 2
This union binding pocket(no: 6) in the query (biounit: 1yki.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4K6B GLU 0.01837 0.41243 5.59006
2 3LMS GLY 0.02086 0.40799 10.8108
Pocket No.: 7; Query (leader) PDB : 1YKI; Ligand: NFZ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 1yki.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 1YKI; Ligand: FMN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 1yki.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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