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Receptor
PDB id Resolution Class Description Source Keywords
4JIQ 2.49 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF GLYCEROL TRINITRATE REDUCTASE NERA FROM AGROBACTERIUM RADIOBACTER IN COMPLEX WITH 1-NITRO-2-PHENYLP AGROBACTERIUM TUMEFACIENS TIM-BARREL ENE-REDUCTASE OXIDOREDUCTASE
Ref.: THE STRUCTURE OF GLYCEROL TRINITRATE REDUCTASE NERA AGROBACTERIUM RADIOBACTER REVEALS THE MOLECULAR REA NITRO- AND ENE-REDUCTASE ACTIVITY IN OYE HOMOLOGUES CHEMBIOCHEM V. 14 836 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMS A:404;
A:403;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
1L5 A:402;
Valid;
none;
Kd = 0.73 mM
163.173 C9 H9 N O2 C/C(=...
FMN A:401;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JIQ 2.49 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF GLYCEROL TRINITRATE REDUCTASE NERA FROM AGROBACTERIUM RADIOBACTER IN COMPLEX WITH 1-NITRO-2-PHENYLP AGROBACTERIUM TUMEFACIENS TIM-BARREL ENE-REDUCTASE OXIDOREDUCTASE
Ref.: THE STRUCTURE OF GLYCEROL TRINITRATE REDUCTASE NERA AGROBACTERIUM RADIOBACTER REVEALS THE MOLECULAR REA NITRO- AND ENE-REDUCTASE ACTIVITY IN OYE HOMOLOGUES CHEMBIOCHEM V. 14 836 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 4JIQ Kd = 0.73 mM 1L5 C9 H9 N O2 C/C(=CN(=O....
2 4JIP - HBA C7 H6 O2 c1cc(ccc1C....
3 4JIC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 5N6G - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 4JIQ Kd = 0.73 mM 1L5 C9 H9 N O2 C/C(=CN(=O....
2 4JIP - HBA C7 H6 O2 c1cc(ccc1C....
3 4JIC - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
4 5N6G - 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: 1L5; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1L5 1 1
Ligand no: 2; 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JIQ; Ligand: 1L5; Similar sites found with APoc: 151
This union binding pocket(no: 1) in the query (biounit: 4jiq.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1GXU 2HP None
2 1ZEI CRS None
3 6G1O GLV 1.32626
4 4IGH FMN 1.34409
5 4IGH ORO 1.34409
6 4IGH 1EA 1.34409
7 3EXS 5RP 1.35747
8 5EY0 ILE 1.45985
9 6DIO CIT 1.59151
10 4OUE IPT 1.59151
11 1FDJ 13P 1.65289
12 1FDJ 2FP 1.65289
13 3AJ6 NGA 1.74825
14 4XFR CIT 1.87354
15 4N02 FNR 1.96078
16 1LYX PGA 2.01613
17 5AHN IMP 2.12202
18 4ORM 2V6 2.12202
19 4ORM FMN 2.12202
20 4ORM ORO 2.12202
21 2Z6I FMN 2.12202
22 1TV5 FMN 2.12202
23 5AHM IMP 2.12202
24 3VKX T3 2.29885
25 1Q6O LG6 2.31481
26 4BI7 PGA 2.33463
27 3U6W KIV 2.38727
28 5EYW PGA 2.40964
29 2NLI FMN 2.44565
30 2NLI LAC 2.44565
31 3B0P FMN 2.57143
32 4PVR ASP 2.58065
33 4WZH FMN 2.59366
34 3MJY IJZ 2.60116
35 3MJY FMN 2.60116
36 2A9W UMP 2.65152
37 1OFD AKG 2.65252
38 1OFD FMN 2.65252
39 4ZWP M44 2.65252
40 1TZJ A3B 2.66272
41 5XFV FMN 2.69461
42 1AL8 FMN 2.78552
43 1AL8 DHP 2.78552
44 3C3N FMN 2.88462
45 5CXX FER 2.90909
46 2D24 XYS XYS 2.91777
47 4FFG LBS 2.91777
48 3BW2 FMN 2.98103
49 5CSS G3P 3.09735
50 1D1Q 4NP 3.10559
51 1TB3 FMN 3.125
52 2C6Q NDP 3.1339
53 3QH2 3NM 3.16742
54 1GTE IUR 3.18302
55 1GTE FMN 3.18302
56 3DRW AMP 3.18302
57 4Z87 5GP 3.18302
58 1TRD PGH 3.2
59 6BKA FMN 3.20856
60 1F76 FMN 3.27381
61 1M5W DXP 3.29218
62 3TAO PGH 3.37079
63 5LUB 3Y7 3.43511
64 2RDT FMN 3.44828
65 2RDT 2RD 3.44828
66 4TVD BGC 3.44828
67 1OX5 1PR 3.44828
68 2VGK REZ 3.44828
69 5A5W GUO 3.55731
70 4YMZ 13P 3.58566
71 4OWK NGA 3.62319
72 2FLI DX5 3.63636
73 2YPI PGA 3.64372
74 1KBJ FMN 3.97878
75 1KBI PYR 3.97878
76 1KBI FMN 3.97878
77 1P4C FMN 3.97878
78 1D8C GLV 3.97878
79 4XP7 FNR 4.04624
80 4JEJ 1GP 4.09836
81 2XSB GDL 4.24403
82 2GEK GDP 4.24403
83 1VKF CIT 4.25532
84 2GJN NIS 4.26829
85 2GJN FMN 4.26829
86 3WW2 SF9 4.29688
87 6A46 DCM 4.29688
88 1UUO FMN 4.30108
89 1UUO BRF 4.30108
90 1UUO ORO 4.30108
91 2ZRU FMN 4.34783
92 3OIX FMN 4.34783
93 1O68 KIV 4.36364
94 1SW0 PGA 4.43548
95 1OVD ORO 4.50161
96 1OVD FMN 4.50161
97 4I9A NCN 4.51389
98 5T96 79J 4.67836
99 4CS4 AXZ 4.74453
100 1ME8 RVP 4.77454
101 5GVH FMN 4.77707
102 6BVE PGA 4.89796
103 2Y88 2ER 4.91803
104 1M3U KPL 4.92424
105 2JE7 XMM 5.02092
106 4AF0 IMP 5.30504
107 2F6U CIT 5.55556
108 1APZ ASP 5.67376
109 5F90 GLA GAL BGC 5VQ 5.76923
110 5F90 GLA GAL 5.76923
111 2BTM PGA 5.95238
112 5ZA2 NXL 6.21469
113 5DYO FLU 6.42202
114 3W9Z FMN 6.52174
115 5NBW 8SK 6.54206
116 1VHZ APR 6.56566
117 4NAE 1GP 6.66667
118 4EWN 0VR 6.71937
119 2GN3 MMA 6.74603
120 2GMM MAN MAN 6.74603
121 2GN3 MAN 6.74603
122 1RZM E4P 6.80473
123 1QDS PGA 7.17131
124 1PVN MZP 7.18085
125 3QX9 ATP 7.24638
126 2Z6J FMN 7.42706
127 6BFG FMN 7.5188
128 5XG5 A2G 7.58621
129 4MJ0 BGC SIA SIA GAL 7.63636
130 4Q4K FMN 8.12325
131 3FIU POP 8.43373
132 4L9Z OXL 8.55457
133 4HKP 16B 8.65385
134 6DVH FMN 9.28382
135 2QCD U5P 10.3846
136 6FX2 FUC C4W NAG BMA MAN NAG GAL 11.6279
137 5YRV 5AD 11.6788
138 1EP2 FMN 13.41
139 1EP2 ORO 13.41
140 3N1S 5GP 14.2857
141 3NZ1 3NY 15.7088
142 4PU6 ASP 16.0305
143 4UTU LRY 25.7642
144 4UTW RFW 26.2009
145 1PS9 FMN 29.1777
146 5OCS FMN 30.7278
147 2H8Z 8CM 32.312
148 2H8Z FMN 32.312
149 3HF3 FMN 34.0974
150 3KRU FMN 35.277
151 1DJN FMN 36.6048
Pocket No.: 2; Query (leader) PDB : 4JIQ; Ligand: FMN; Similar sites found with APoc: 151
This union binding pocket(no: 2) in the query (biounit: 4jiq.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1GXU 2HP None
2 1ZEI CRS None
3 6G1O GLV 1.32626
4 4IGH FMN 1.34409
5 4IGH ORO 1.34409
6 4IGH 1EA 1.34409
7 3EXS 5RP 1.35747
8 5EY0 ILE 1.45985
9 6DIO CIT 1.59151
10 4OUE IPT 1.59151
11 1FDJ 13P 1.65289
12 1FDJ 2FP 1.65289
13 3AJ6 NGA 1.74825
14 4XFR CIT 1.87354
15 4N02 FNR 1.96078
16 1LYX PGA 2.01613
17 5AHN IMP 2.12202
18 4ORM 2V6 2.12202
19 4ORM FMN 2.12202
20 4ORM ORO 2.12202
21 2Z6I FMN 2.12202
22 1TV5 FMN 2.12202
23 5AHM IMP 2.12202
24 3VKX T3 2.29885
25 1Q6O LG6 2.31481
26 4BI7 PGA 2.33463
27 3U6W KIV 2.38727
28 5EYW PGA 2.40964
29 2NLI FMN 2.44565
30 2NLI LAC 2.44565
31 3B0P FMN 2.57143
32 4PVR ASP 2.58065
33 4WZH FMN 2.59366
34 3MJY IJZ 2.60116
35 3MJY FMN 2.60116
36 2A9W UMP 2.65152
37 1OFD AKG 2.65252
38 1OFD FMN 2.65252
39 4ZWP M44 2.65252
40 1TZJ A3B 2.66272
41 5XFV FMN 2.69461
42 1AL8 FMN 2.78552
43 1AL8 DHP 2.78552
44 3C3N FMN 2.88462
45 5CXX FER 2.90909
46 2D24 XYS XYS 2.91777
47 4FFG LBS 2.91777
48 3BW2 FMN 2.98103
49 5CSS G3P 3.09735
50 1D1Q 4NP 3.10559
51 1TB3 FMN 3.125
52 2C6Q NDP 3.1339
53 3QH2 3NM 3.16742
54 1GTE IUR 3.18302
55 1GTE FMN 3.18302
56 3DRW AMP 3.18302
57 4Z87 5GP 3.18302
58 1TRD PGH 3.2
59 6BKA FMN 3.20856
60 1F76 FMN 3.27381
61 1M5W DXP 3.29218
62 3TAO PGH 3.37079
63 5LUB 3Y7 3.43511
64 2RDT FMN 3.44828
65 2RDT 2RD 3.44828
66 4TVD BGC 3.44828
67 1OX5 1PR 3.44828
68 2VGK REZ 3.44828
69 5A5W GUO 3.55731
70 4YMZ 13P 3.58566
71 4OWK NGA 3.62319
72 2FLI DX5 3.63636
73 2YPI PGA 3.64372
74 1KBJ FMN 3.97878
75 1KBI PYR 3.97878
76 1KBI FMN 3.97878
77 1P4C FMN 3.97878
78 1D8C GLV 3.97878
79 4XP7 FNR 4.04624
80 4JEJ 1GP 4.09836
81 2XSB GDL 4.24403
82 2GEK GDP 4.24403
83 1VKF CIT 4.25532
84 2GJN NIS 4.26829
85 2GJN FMN 4.26829
86 3WW2 SF9 4.29688
87 6A46 DCM 4.29688
88 1UUO FMN 4.30108
89 1UUO BRF 4.30108
90 1UUO ORO 4.30108
91 2ZRU FMN 4.34783
92 3OIX FMN 4.34783
93 1O68 KIV 4.36364
94 1SW0 PGA 4.43548
95 1OVD ORO 4.50161
96 1OVD FMN 4.50161
97 4I9A NCN 4.51389
98 5T96 79J 4.67836
99 4CS4 AXZ 4.74453
100 1ME8 RVP 4.77454
101 5GVH FMN 4.77707
102 6BVE PGA 4.89796
103 2Y88 2ER 4.91803
104 1M3U KPL 4.92424
105 2JE7 XMM 5.02092
106 4AF0 IMP 5.30504
107 2F6U CIT 5.55556
108 1APZ ASP 5.67376
109 5F90 GLA GAL BGC 5VQ 5.76923
110 5F90 GLA GAL 5.76923
111 2BTM PGA 5.95238
112 5ZA2 NXL 6.21469
113 5DYO FLU 6.42202
114 3W9Z FMN 6.52174
115 5NBW 8SK 6.54206
116 1VHZ APR 6.56566
117 4NAE 1GP 6.66667
118 4EWN 0VR 6.71937
119 2GN3 MMA 6.74603
120 2GMM MAN MAN 6.74603
121 2GN3 MAN 6.74603
122 1RZM E4P 6.80473
123 1QDS PGA 7.17131
124 1PVN MZP 7.18085
125 3QX9 ATP 7.24638
126 2Z6J FMN 7.42706
127 6BFG FMN 7.5188
128 5XG5 A2G 7.58621
129 4MJ0 BGC SIA SIA GAL 7.63636
130 4Q4K FMN 8.12325
131 3FIU POP 8.43373
132 4L9Z OXL 8.55457
133 4HKP 16B 8.65385
134 6DVH FMN 9.28382
135 2QCD U5P 10.3846
136 6FX2 FUC C4W NAG BMA MAN NAG GAL 11.6279
137 5YRV 5AD 11.6788
138 1EP2 FMN 13.41
139 1EP2 ORO 13.41
140 3N1S 5GP 14.2857
141 3NZ1 3NY 15.7088
142 4PU6 ASP 16.0305
143 4UTU LRY 25.7642
144 4UTW RFW 26.2009
145 1PS9 FMN 29.1777
146 5OCS FMN 30.7278
147 2H8Z 8CM 32.312
148 2H8Z FMN 32.312
149 3HF3 FMN 34.0974
150 3KRU FMN 35.277
151 1DJN FMN 36.6048
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