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Receptor
PDB id Resolution Class Description Source Keywords
1VYP 1.27 Å EC: 1.6.99.1 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102F MU COMPLEXED WITH PICRIC ACID ENTEROBACTER CLOACAE OXIDOREDUCTASE FLAVOENZYME EXPLOSIVE DEGRADATION STEROID
Ref.: ATOMIC RESOLUTION STRUCTURES AND SOLUTION BEHAVIOR ENZYME-SUBSTRATE COMPLEXES OF ENTEROBACTER CLOACAE PENTAERYTHRITOL TETRANITRATE REDUCTASE: MULTIPLE CONFORMATIONAL STATES AND IMPLICATIONS FOR THE MECH NITROAROMATIC EXPLOSIVE DEGRADATION J.BIOL.CHEM
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN X:401;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
TNF X:500;
Valid;
none;
Kd = 0.07 uM
229.104 C6 H3 N3 O7 c1c(c...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VYP 1.27 Å EC: 1.6.99.1 STRUCTURE OF PENTAERYTHRITOL TETRANITRATE REDUCTASE W102F MU COMPLEXED WITH PICRIC ACID ENTEROBACTER CLOACAE OXIDOREDUCTASE FLAVOENZYME EXPLOSIVE DEGRADATION STEROID
Ref.: ATOMIC RESOLUTION STRUCTURES AND SOLUTION BEHAVIOR ENZYME-SUBSTRATE COMPLEXES OF ENTEROBACTER CLOACAE PENTAERYTHRITOL TETRANITRATE REDUCTASE: MULTIPLE CONFORMATIONAL STATES AND IMPLICATIONS FOR THE MECH NITROAROMATIC EXPLOSIVE DEGRADATION J.BIOL.CHEM
Members (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
12 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
14 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
15 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
18 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
20 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
21 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
22 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
23 2ABB - IPA C3 H8 O CC(C)O
24 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
25 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
12 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
14 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
15 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
18 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
20 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
21 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
22 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
23 2ABB - IPA C3 H8 O CC(C)O
24 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
25 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (63)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1H60 Kd = 20 uM STR C21 H30 O2 CC(=O)[C@H....
2 3P7Y - P7Y C8 H7 N O3 c1ccc(c(c1....
3 1H50 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 3P67 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
5 3KFT - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
6 1VYP Kd = 0.07 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
7 3P74 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
8 1GVQ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
9 5LGX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
10 2ABA Kd = 0.7 uM STR C21 H30 O2 CC(=O)[C@H....
11 1VYS Kd = 0.24 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
12 1GVO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
13 3P81 - P81 C8 H7 N O3 c1cc(ccc1/....
14 5LGZ - FNR C17 H23 N4 O9 P Cc1cc2c(cc....
15 3P62 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
16 3P82 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
17 1GVR - TNL C7 H5 N3 O6 Cc1c(cc(cc....
18 1H63 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
19 1H62 Kd = 17 uM ANB C19 H24 O2 C[C@]12CC[....
20 1GVS - TNF C6 H3 N3 O7 c1c(cc(c(c....
21 1H61 Kd = 13 uM PDN C21 H26 O5 C[C@]12CC(....
22 3P80 - P80 C8 H7 N O3 c1cc(cc(c1....
23 2ABB - IPA C3 H8 O CC(C)O
24 1VYR Kd = 5.4 uM TNF C6 H3 N3 O7 c1c(cc(c(c....
25 1H51 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
26 2GQ9 - HBA C7 H6 O2 c1cc(ccc1C....
27 2GQ8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
28 2GOU - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
29 2GQA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
30 2HS8 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
31 2HS6 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
32 3HGO - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
33 2HSA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
34 3HGS - PHB C7 H6 O3 c1cc(ccc1C....
35 1OYB - HBA C7 H6 O2 c1cc(ccc1C....
36 1OYC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
37 1BWK - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
38 1OYA - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
39 4M5P - MLA C3 H4 O4 C(C(=O)O)C....
40 4TMB - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
41 4TMC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
42 1ICS - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
43 3HGR - PHB C7 H6 O3 c1cc(ccc1C....
44 1ICP - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
45 1ICQ - OPD C18 H28 O3 CCC=CC[C@@....
46 3ATY - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
47 3ATZ - HBA C7 H6 O2 c1cc(ccc1C....
48 1Q45 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
49 2Q3O - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50 2R14 Kd = 0.63 mM TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
51 3GX9 - TXD C21 H31 N7 O14 P2 c1nc(c2c(n....
52 1GWJ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
53 1VJI - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
54 2Q3R - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
55 4JIQ Kd = 0.73 mM 1L5 C9 H9 N O2 C/C(=CN(=O....
56 4JIP - HBA C7 H6 O2 c1cc(ccc1C....
57 4JIC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
58 5N6G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
59 4QNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
60 4RNX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
61 4RNV - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
62 4RNW - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
63 4A3U - 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: TNF; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 TNF 1 1
2 DNC 0.677419 0.909091
3 6J1 0.53125 0.97561
4 TNL 0.5 0.804878
5 DNF 0.432432 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VYP; Ligand: FMN; Similar sites found with APoc: 130
This union binding pocket(no: 1) in the query (biounit: 1vyp.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 4ORM ORO 1.37363
2 4ORM 2V6 1.37363
3 4ORM FMN 1.37363
4 2RDT FMN 1.64835
5 2RDT 2RD 1.64835
6 4CW5 FMN 1.64835
7 2X1E X1E 1.68067
8 1VHN FMN 1.88679
9 1M3U KPL 1.89394
10 1FDJ 13P 1.92837
11 2ZRU FMN 2.1978
12 5A5W GUO 2.37154
13 4YMZ 13P 2.39044
14 1AL8 FMN 2.50696
15 1AL8 DHP 2.50696
16 3C3N FMN 2.5641
17 3TAO PGH 2.62172
18 4QEK GLC 2.65781
19 5LUB 3Y7 2.67176
20 3UWV 2PG 2.68199
21 4PL9 ADP 2.73224
22 1D8C GLV 2.74725
23 6H45 QEI 2.74725
24 2BTM PGA 2.77778
25 4Q4K FMN 2.80112
26 5EYW PGA 2.81124
27 5YRI GLC GLC 2.8169
28 5YRF GLC GLC 2.8169
29 5YRJ BGC GLC 2.8169
30 1TB3 FMN 2.84091
31 3MJY IJZ 2.89017
32 3MJY FMN 2.89017
33 3CL7 HYN 2.92208
34 5NBW 8SK 3.15315
35 1P4C FMN 3.15789
36 3QH2 3NM 3.16742
37 4XP7 FNR 3.17919
38 5GVH FMN 3.18471
39 1EP2 FMN 3.21543
40 1EP2 ORO 3.21543
41 1OFD AKG 3.2967
42 1OFD FMN 3.2967
43 3FU7 3DM 3.2967
44 2JE7 XMM 3.34728
45 2GJN NIS 3.35366
46 2GJN FMN 3.35366
47 3OIX FMN 3.47826
48 4UTU LRY 3.49345
49 4UTW RFW 3.49345
50 1RZM E4P 3.5503
51 1RZM PEP 3.5503
52 1F76 FMN 3.57143
53 2GMP NAG MAN 3.57143
54 4DS0 A2G GAL NAG FUC 3.68098
55 3JQ7 DX2 3.81944
56 5K6A 6QT 3.81944
57 3BMQ AX5 3.81944
58 3JQA DX4 3.81944
59 3JQG AX6 3.81944
60 6BFG FMN 3.84615
61 5TCI MLI 3.84615
62 4EWN 0VR 3.95257
63 1O68 KIV 4
64 4GNC ASO 4.01338
65 4WZH FMN 4.03458
66 2YPI PGA 4.04858
67 4N02 FNR 4.20168
68 3B0P FMN 4.28571
69 1PVN MZP 4.3956
70 1ME8 RVP 4.3956
71 1E5Q SHR 4.3956
72 2Y88 2ER 4.5082
73 4C1K PEP 4.58015
74 2VGK REZ 4.67033
75 4I9A NCN 4.86111
76 2NLI LAC 4.94506
77 2NLI FMN 4.94506
78 4IGH 1EA 4.94506
79 4IGH FMN 4.94506
80 4IGH ORO 4.94506
81 1U4J MAN 5.08475
82 1OVD ORO 5.14469
83 1OVD FMN 5.14469
84 4O4Z N2O 5.19481
85 2Z9V PXM 5.21978
86 4JEJ 1GP 5.32787
87 3BW2 FMN 5.42005
88 3EXS 5RP 5.42986
89 6DVH FMN 5.49451
90 1SW0 PGA 5.64516
91 1OX5 1PR 5.76923
92 1TV5 FMN 5.86907
93 1VHZ APR 6.06061
94 5AHN IMP 6.31868
95 1KBI PYR 6.31868
96 1KBI FMN 6.31868
97 1KBJ FMN 6.59341
98 2ATJ BHO 6.81818
99 4NAE 1GP 7.11111
100 6BKA FMN 7.14286
101 2F6U CIT 7.26496
102 3AXK NDP 7.41758
103 2Z6J FMN 7.53012
104 2Z6I FMN 7.53012
105 1TRD PGH 7.6
106 1GTE IUR 7.69231
107 1GTE FMN 7.69231
108 4HKP 16B 7.69231
109 2HK1 FUD 7.76699
110 5XFV FMN 7.78443
111 3NZ1 3NY 8.04598
112 1LYX PGA 8.46774
113 1QDS PGA 8.76494
114 1UUO FMN 9.06593
115 1UUO BRF 9.06593
116 1UUO ORO 9.06593
117 3VY6 BGC BGC 9.21986
118 2QCD U5P 9.23077
119 3W9Z FMN 9.31677
120 1Q6O LG6 9.72222
121 5T96 79J 9.94152
122 3QX9 ATP 10.8696
123 2FLI DX5 10.9091
124 1VKF CIT 13.2979
125 3QMN A3P 14.7287
126 4BI7 PGA 15.1751
127 6A46 DCM 16.4062
128 6BVE PGA 18.3673
129 1DJN FMN 42.8571
130 1PS9 FMN 44.7802
Pocket No.: 2; Query (leader) PDB : 1VYP; Ligand: TNF; Similar sites found with APoc: 143
This union binding pocket(no: 2) in the query (biounit: 1vyp.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4ORM ORO 1.37363
2 4ORM 2V6 1.37363
3 4ORM FMN 1.37363
4 2RDT FMN 1.64835
5 2RDT 2RD 1.64835
6 4CW5 FMN 1.64835
7 2X1E X1E 1.68067
8 5V2L ATP 1.79641
9 1VHN FMN 1.88679
10 1M3U KPL 1.89394
11 1FDJ 13P 1.92837
12 2ZRU FMN 2.1978
13 4Y30 49L 2.2792
14 4Y30 SAH 2.2792
15 5A5W GUO 2.37154
16 4YMZ 13P 2.39044
17 1AL8 FMN 2.50696
18 1AL8 DHP 2.50696
19 3C3N FMN 2.5641
20 3TAO PGH 2.62172
21 4QEK GLC 2.65781
22 5LUB 3Y7 2.67176
23 3UWV 2PG 2.68199
24 2WNF CG3 A2G GAL 2.68456
25 4PL9 ADP 2.73224
26 1D8C GLV 2.74725
27 2BTM PGA 2.77778
28 4Q4K FMN 2.80112
29 5EYW PGA 2.81124
30 5YRJ BGC GLC 2.8169
31 1TB3 FMN 2.84091
32 3MJY IJZ 2.89017
33 3MJY FMN 2.89017
34 3CL7 HYN 2.92208
35 3FXU TSU 2.95082
36 1NU4 MLA 3.09278
37 2G30 ALA ALA PHE 3.10078
38 1P4C FMN 3.15789
39 3QH2 3NM 3.16742
40 4XP7 FNR 3.17919
41 5GVH FMN 3.18471
42 1EP2 FMN 3.21543
43 1EP2 ORO 3.21543
44 1OFD AKG 3.2967
45 5A1S FLC 3.2967
46 1OFD FMN 3.2967
47 4TVD BGC 3.2967
48 3FU7 3DM 3.2967
49 2JE7 XMM 3.34728
50 2GJN NIS 3.35366
51 2GJN FMN 3.35366
52 3OIX FMN 3.47826
53 4UTU LRY 3.49345
54 4UTW RFW 3.49345
55 1RZM E4P 3.5503
56 1F76 FMN 3.57143
57 1U1J MET 3.57143
58 1GYM MYG 3.69128
59 3JQ7 DX2 3.81944
60 5K6A 6QT 3.81944
61 4CM4 4NR 3.81944
62 3BMO AX4 3.81944
63 3JQB DX6 3.81944
64 5JCJ 6JM 3.81944
65 3JQG AX6 3.81944
66 6BFG FMN 3.84615
67 5TCI MLI 3.84615
68 4EWN 0VR 3.95257
69 1O68 KIV 4
70 4GNC ASO 4.01338
71 4WZH FMN 4.03458
72 2YPI PGA 4.04858
73 2WD7 VGD 4.10448
74 3R4S SLB 4.12088
75 4N02 FNR 4.20168
76 3B0P FMN 4.28571
77 1PVN MZP 4.3956
78 1ME8 RVP 4.3956
79 1E5Q SHR 4.3956
80 2Y88 2ER 4.5082
81 4C1K PEP 4.58015
82 4I9A NCN 4.86111
83 2NLI LAC 4.94506
84 2NLI FMN 4.94506
85 4IGH 1EA 4.94506
86 4IGH ORO 4.94506
87 4IGH FMN 4.94506
88 4WQQ MAN 4.96454
89 4MLO PAM 5.07246
90 1U4J MAN 5.08475
91 1OVD ORO 5.14469
92 1OVD FMN 5.14469
93 4O4Z N2O 5.19481
94 2Z9V PXM 5.21978
95 4JEJ 1GP 5.32787
96 3BW2 FMN 5.42005
97 3EXS 5RP 5.42986
98 6DVH FMN 5.49451
99 1SW0 PGA 5.64516
100 1OX5 1PR 5.76923
101 4FFG LBS 5.76923
102 1TV5 FMN 5.86907
103 1VHZ APR 6.06061
104 5AHN IMP 6.31868
105 1KBI PYR 6.31868
106 1KBI FMN 6.31868
107 2C6Q NDP 6.55271
108 1KBJ FMN 6.59341
109 1FUT 2GP 6.60377
110 2YN4 39J 6.77966
111 2ATJ BHO 6.81818
112 4NAE 1GP 7.11111
113 6BKA FMN 7.14286
114 2F6U CIT 7.26496
115 3AXK NDP 7.41758
116 2Z6J FMN 7.53012
117 2Z6I FMN 7.53012
118 1TRD PGH 7.6
119 1GTE IUR 7.69231
120 1GTE FMN 7.69231
121 4HKP 16B 7.69231
122 2HK1 FUD 7.76699
123 5XFV FMN 7.78443
124 2A9W UMP 7.95455
125 1LYX PGA 8.46774
126 1KTG AMP 8.69565
127 1QDS PGA 8.76494
128 3P7G MAN 8.90411
129 1UUO BRF 9.06593
130 1UUO ORO 9.06593
131 1UUO FMN 9.06593
132 2QCD U5P 9.23077
133 3W9Z FMN 9.31677
134 1Q6O LG6 9.72222
135 1S4P GDP 10.0575
136 2FLI DX5 10.9091
137 1VKF CIT 13.2979
138 3QMN A3P 14.7287
139 4BI7 PGA 15.1751
140 6A46 DCM 16.4062
141 6BVE PGA 18.3673
142 1DJN FMN 42.8571
143 1PS9 FMN 44.7802
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