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 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....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 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: 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JIQ; Ligand: 1L5; Similar sites found: 86
This union binding pocket(no: 1) in the query (biounit: 4jiq.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GXU 2HP 0.03253 0.42299 None
2 4IGH ORO 0.0002364 0.49103 1.34409
3 4IGH FMN 0.0002364 0.49103 1.34409
4 4IGH 1EA 0.0002364 0.49103 1.34409
5 3EXS 5RP 0.0008048 0.47612 1.35747
6 3AJ6 NGA 0.04722 0.40208 1.74825
7 4XFR CIT 0.02372 0.40633 1.87354
8 4N02 FNR 0.00001572 0.49225 1.96078
9 4ORM 2V6 0.000265 0.48805 2.12202
10 4ORM ORO 0.000265 0.48805 2.12202
11 4ORM FMN 0.000265 0.48805 2.12202
12 2Z6I FMN 0.0001512 0.47044 2.12202
13 1TV5 FMN 0.0001484 0.45242 2.12202
14 5EYW PGA 0.02848 0.40276 2.40964
15 2NLI FMN 0.000001376 0.5273 2.44565
16 2NLI LAC 0.002251 0.4682 2.44565
17 3B0P FMN 0.000000002055 0.71979 2.57143
18 4WZH FMN 0.00003683 0.48255 2.59366
19 3MJY IJZ 0.00001651 0.5074 2.60116
20 3MJY FMN 0.00001651 0.5074 2.60116
21 1OFD AKG 0.000005388 0.5289 2.65252
22 1OFD FMN 0.000006487 0.5289 2.65252
23 4ZWP M44 0.02681 0.4082 2.65252
24 1TZJ A3B 0.03206 0.40483 2.66272
25 1AL8 FMN 0.0000003971 0.57202 2.78552
26 1AL8 DHP 0.000002435 0.49841 2.78552
27 2B4G FMN 0.00001483 0.50017 2.83912
28 3C3N FMN 0.00009334 0.48124 2.88462
29 5CXX FER 0.0261 0.40471 2.90909
30 2D24 XYS XYS 0.03504 0.40642 2.91777
31 4FFG LBS 0.02506 0.40055 2.91777
32 3BW2 FMN 0.00001761 0.46996 2.98103
33 5CSS G3P 0.01277 0.42065 3.09735
34 1D1Q 4NP 0.03597 0.40164 3.10559
35 1TB3 FMN 0.0000002626 0.57642 3.125
36 1GTE IUR 0.0000192 0.44541 3.18302
37 1GTE FMN 0.0000192 0.44541 3.18302
38 1F76 FMN 0.0001158 0.4629 3.27381
39 5LUB 3Y7 0.02512 0.4094 3.43511
40 2RDT 2RD 0.000002115 0.54182 3.44828
41 2RDT FMN 0.000001517 0.53727 3.44828
42 1OX5 1PR 0.0008883 0.41738 3.44828
43 2BLE 5GP 0.003023 0.40993 3.54223
44 5A5W GUO 0.007713 0.40647 3.55731
45 4YMZ 13P 0.01396 0.41867 3.58566
46 4OWK NGA 0.03164 0.41538 3.62319
47 2YPI PGA 0.01674 0.41055 3.64372
48 1KBJ FMN 0.0000003523 0.56231 3.97878
49 1KBI PYR 0.0000004366 0.56097 3.97878
50 1P4C FMN 0.000005466 0.52513 3.97878
51 1D8C GLV 0.02204 0.40633 3.97878
52 4XP7 FNR 0.00000001378 0.56948 4.04624
53 2GJN FMN 0.0000726 0.47091 4.26829
54 2GJN NIS 0.00008651 0.45544 4.26829
55 2ZRU FMN 0.000006779 0.45128 4.34783
56 3OIX FMN 0.0002173 0.44345 4.34783
57 1O68 KIV 0.008196 0.43529 4.36364
58 1OVD ORO 0.00001977 0.43667 4.50161
59 1OVD FMN 0.00001977 0.43667 4.50161
60 4I9A NCN 0.003335 0.4283 4.51389
61 5T96 79J 0.01527 0.41692 4.67836
62 4CS4 AXZ 0.008808 0.40781 4.74453
63 1ME8 RVP 0.003758 0.4163 4.77454
64 2Y88 2ER 0.004951 0.41022 4.91803
65 2F6U CIT 0.007153 0.43838 5.55556
66 3W9Z FMN 0.00000009496 0.54324 6.52174
67 5NBW 8SK 0.01287 0.41228 6.54206
68 4NAE 1GP 0.0005117 0.50361 6.66667
69 4EWN 0VR 0.004889 0.42454 6.71937
70 2GN3 MMA 0.006897 0.43083 6.74603
71 2GMM MAN MAN 0.02269 0.41257 6.74603
72 2GN3 MAN 0.01225 0.41149 6.74603
73 1RZM E4P 0.02434 0.40227 6.80473
74 2Z6J FMN 0.0000746 0.47586 7.42706
75 4Q4K FMN 0.00003401 0.48391 8.12325
76 1EP2 FMN 0.00002096 0.47836 13.41
77 1EP2 ORO 0.00002526 0.442 13.41
78 3NZ1 3NY 0.02241 0.4162 15.7088
79 4PU6 ASP 0.02506 0.40975 16.0305
80 4UTU LRY 0.005535 0.42596 25.7642
81 4UTW RFW 0.006889 0.41762 26.2009
82 1PS9 FMN 0.00000006105 0.56985 29.1777
83 5OCS FMN 0.000000001157 0.71115 30.7278
84 3HF3 FMN 0.000000001874 0.62506 34.0974
85 3KRU FMN 0.000000004922 0.65073 35.277
86 1DJN FMN 0.0000002864 0.55377 36.6048
Pocket No.: 2; Query (leader) PDB : 4JIQ; Ligand: FMN; Similar sites found: 82
This union binding pocket(no: 2) in the query (biounit: 4jiq.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4IGH ORO 0.0002364 0.49103 1.34409
2 4IGH 1EA 0.0002364 0.49103 1.34409
3 4IGH FMN 0.0002364 0.49103 1.34409
4 3EXS 5RP 0.0008048 0.47612 1.35747
5 4OUE IPT 0.0177 0.41788 1.59151
6 3AJ6 NGA 0.04722 0.40208 1.74825
7 4XFR CIT 0.02372 0.40633 1.87354
8 4N02 FNR 0.031 0.41575 1.96078
9 4ORM FMN 0.000265 0.48805 2.12202
10 4ORM 2V6 0.000265 0.48805 2.12202
11 4ORM ORO 0.000265 0.48805 2.12202
12 2Z6I FMN 0.0001512 0.47044 2.12202
13 1TV5 FMN 0.0001484 0.45242 2.12202
14 1Q6O LG6 0.001136 0.45392 2.31481
15 5EYW PGA 0.02848 0.40276 2.40964
16 2NLI LAC 0.002251 0.4682 2.44565
17 2NLI FMN 0.002251 0.4682 2.44565
18 3B0P FMN 0.000000002055 0.71979 2.57143
19 4WZH FMN 0.00003683 0.48255 2.59366
20 3MJY IJZ 0.00001651 0.5074 2.60116
21 3MJY FMN 0.00001651 0.5074 2.60116
22 1OFD AKG 0.000005388 0.4685 2.65252
23 1OFD FMN 0.000006487 0.45523 2.65252
24 4ZWP M44 0.02681 0.4082 2.65252
25 1TZJ A3B 0.03206 0.40483 2.66272
26 2B4G FMN 0.00001483 0.50017 2.83912
27 3C3N FMN 0.00009334 0.42118 2.88462
28 5CXX FER 0.0261 0.40471 2.90909
29 2D24 XYS XYS 0.03504 0.40642 2.91777
30 4FFG LBS 0.02506 0.40055 2.91777
31 5CSS G3P 0.01277 0.42065 3.09735
32 1D1Q 4NP 0.03597 0.40164 3.10559
33 1TB3 FMN 0.0000002626 0.53281 3.125
34 3QH2 3NM 0.002634 0.46109 3.16742
35 1GTE IUR 0.0000192 0.44541 3.18302
36 1GTE FMN 0.0000192 0.44541 3.18302
37 1F76 FMN 0.0001158 0.4629 3.27381
38 1M5W DXP 0.03327 0.40323 3.29218
39 3TAO PGH 0.009059 0.42386 3.37079
40 5LUB 3Y7 0.02512 0.4094 3.43511
41 1OX5 1PR 0.0008883 0.41738 3.44828
42 5A5W GUO 0.007713 0.40647 3.55731
43 4YMZ 13P 0.01396 0.41867 3.58566
44 4OWK NGA 0.03164 0.41538 3.62319
45 2FLI DX5 0.005464 0.4084 3.63636
46 2YPI PGA 0.01674 0.41055 3.64372
47 1KBJ FMN 0.001041 0.45633 3.97878
48 1D8C GLV 0.02204 0.40633 3.97878
49 4XP7 FNR 0.00000001378 0.56948 4.04624
50 2XSB GDL 0.02158 0.40896 4.24403
51 2GEK GDP 0.02003 0.4029 4.24403
52 2GJN FMN 0.0000726 0.47091 4.26829
53 2GJN NIS 0.00008651 0.45544 4.26829
54 2ZRU FMN 0.000006779 0.45128 4.34783
55 3OIX FMN 0.0002173 0.44345 4.34783
56 1O68 KIV 0.008196 0.43529 4.36364
57 1OVD FMN 0.00001977 0.43667 4.50161
58 1OVD ORO 0.00001977 0.43667 4.50161
59 5T96 79J 0.01527 0.41692 4.67836
60 1M3U KPL 0.006697 0.43498 4.92424
61 2F6U CIT 0.007153 0.43838 5.55556
62 2BTM PGA 0.02068 0.40992 5.95238
63 3W9Z FMN 0.00000009496 0.54324 6.52174
64 5NBW 8SK 0.01287 0.41228 6.54206
65 4NAE 1GP 0.0005117 0.50361 6.66667
66 4EWN 0VR 0.004889 0.42454 6.71937
67 2GN3 MMA 0.006897 0.43083 6.74603
68 2GMM MAN MAN 0.02269 0.41257 6.74603
69 2GN3 MAN 0.01225 0.41149 6.74603
70 2Z6J FMN 0.0000746 0.45134 7.42706
71 4MJ0 BGC SIA SIA GAL 0.03182 0.40738 7.63636
72 4Q4K FMN 0.00003401 0.48391 8.12325
73 2QCD U5P 0.009799 0.40057 10.3846
74 3NZ1 3NY 0.02241 0.4162 15.7088
75 4PU6 ASP 0.02506 0.40975 16.0305
76 4UTU LRY 0.005535 0.42596 25.7642
77 4UTW RFW 0.006889 0.41762 26.2009
78 1PS9 FMN 0.00000006105 0.56985 29.1777
79 5OCS FMN 0.000000001157 0.71115 30.7278
80 3HF3 FMN 0.0000000007306 0.70128 34.0974
81 3KRU FMN 0.000000004922 0.65073 35.277
82 1DJN FMN 0.0000002864 0.57783 36.6048
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