Receptor
PDB id Resolution Class Description Source Keywords
3B0P 1.7 Å EC: 7.-.-.- TRNA-DIHYDROURIDINE SYNTHASE FROM THERMUS THERMOPHILUS THERMUS THERMOPHILUS TIM BARREL OXIDOREDUCTASE
Ref.: MOLECULAR BASIS OF DIHYDROURIDINE FORMATION ON TRNA PROC.NATL.ACAD.SCI.USA V. 108 19593 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN A:351;
B:351;
Valid;
Valid;
none;
none;
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456.344 C17 H21 N4 O9 P Cc1cc...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B0P 1.7 Å EC: 7.-.-.- TRNA-DIHYDROURIDINE SYNTHASE FROM THERMUS THERMOPHILUS THERMUS THERMOPHILUS TIM BARREL OXIDOREDUCTASE
Ref.: MOLECULAR BASIS OF DIHYDROURIDINE FORMATION ON TRNA PROC.NATL.ACAD.SCI.USA V. 108 19593 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3B0U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3B0P - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 3B0U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3B0P - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 3B0U - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3B0P - 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
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B0P; Ligand: FMN; Similar sites found: 160
This union binding pocket(no: 1) in the query (biounit: 3b0p.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BTM PGA 0.0001015 0.45288 1.98413
2 2RDT 2RD 0.0000009824 0.60632 2
3 2RDT FMN 0.0000006476 0.60412 2
4 1TRD PGH 0.0001652 0.46024 2
5 2BP1 NDP 0.009337 0.4217 2
6 1LQA NDP 0.01847 0.40744 2.02312
7 2GJN FMN 0.0000006848 0.50089 2.13415
8 2GJN NIS 0.0000008555 0.48294 2.13415
9 2GOU FMN 0.00000009498 0.65842 2.28571
10 1P4C FMN 0.0000005895 0.61681 2.28571
11 2C6Q NDP 0.0009135 0.47934 2.28571
12 2C6Q IMP 0.0004279 0.47178 2.28571
13 2OO0 PLP 0.003576 0.41616 2.28571
14 4JIQ 1L5 0.000000002055 0.71979 2.57143
15 4JIQ FMN 0.000000002055 0.71979 2.57143
16 4A3U FMN 0.000000001743 0.71058 2.57143
17 2NLI FMN 0.000000143 0.62932 2.57143
18 1TB3 FMN 0.0000005179 0.61744 2.57143
19 2NLI LAC 0.002065 0.4984 2.57143
20 2BLE 5GP 0.0007223 0.4663 2.57143
21 2WMI A2G GAL FUC 0.008654 0.40677 2.57143
22 2Z6I FMN 0.0000001995 0.53933 2.71084
23 4Q4K FMN 0.00000005084 0.65528 2.85714
24 4IXH IMP 0.0002369 0.42265 2.85714
25 1ZFJ IMP 0.004813 0.41645 2.85714
26 5OCS FMN 0.0000000005221 0.68033 3.14286
27 1TV5 FMN 0.000004963 0.46412 3.14286
28 1NJJ ORX 0.00646 0.41246 3.14286
29 3TAO PGH 0.00006164 0.4702 3.37079
30 4BH1 SIA GAL NAG 0.004896 0.41221 3.37423
31 3EXS 5RP 0.000002093 0.58318 3.61991
32 1M5W DXP 0.0008243 0.47217 3.7037
33 1OYB HBA 0.00000001808 0.6787 3.71429
34 1OYB FMN 0.00000001249 0.67788 3.71429
35 1AL8 FMN 0.0000002354 0.6194 3.71429
36 1AL8 DHP 0.0000009287 0.6055 3.71429
37 4RNV FMN 0.001928 0.45921 3.71429
38 4RNV HBA 0.002174 0.45777 3.71429
39 4HKP TKW 0.001022 0.45077 3.71429
40 4HKP 16B 0.001255 0.44075 3.71429
41 1TUF AZ1 0.00894 0.41087 3.71429
42 1W8S FBP 0.003826 0.40889 3.80228
43 3UWV 2PG 0.002456 0.43156 3.83142
44 5CSS G3P 0.0003198 0.48544 3.9823
45 2Q3R FMN 0.000000001403 0.71136 4
46 4TMC FMN 0.00000003266 0.57099 4
47 4TMC HBA 0.00000004335 0.54525 4
48 5GJO PLP 0.004159 0.408 4
49 2HSA FMN 0.000000002135 0.72721 4.28571
50 2Q3O FMN 0.000000001162 0.72194 4.28571
51 1VYP FMN 0.000000003214 0.7108 4.28571
52 1VYP TNF 0.000000002782 0.7108 4.28571
53 1OFD FMN 0.0000001689 0.65032 4.28571
54 1OFD AKG 0.0000001405 0.65032 4.28571
55 2TPS TPS 0.009174 0.41184 4.28571
56 2PLK P3D 0.00787 0.40855 4.28571
57 3KRU FMN 0.000000000573 0.76171 4.37318
58 1QPR PPC 0.006633 0.41194 4.57143
59 4QNW FMN 0.0000000005017 0.73512 4.59184
60 1Q6O LG6 0.00005158 0.4977 4.62963
61 1JCM 137 0.001129 0.44064 4.6332
62 3MI2 PFU 0.004898 0.44809 4.6595
63 3OVR 5SP 0.0000213 0.52746 4.82456
64 2C91 NAP 0.009816 0.42066 4.85714
65 2FLI DX5 0.00002805 0.51971 5
66 2QCD U5P 0.0004397 0.46338 5
67 4ORM 2V6 0.0000212 0.57849 5.14286
68 4ORM FMN 0.0000212 0.57849 5.14286
69 4ORM ORO 0.0000212 0.57849 5.14286
70 2OEM 1AE 0.001963 0.41642 5.14286
71 5EYW PGA 0.0001951 0.49593 5.22088
72 1KBJ FMN 0.0000001774 0.63016 5.42857
73 1KBI PYR 0.0000002054 0.62962 5.42857
74 4IGH FMN 0.00001337 0.58959 5.42857
75 4IGH 1EA 0.00001337 0.58959 5.42857
76 4IGH ORO 0.00001337 0.58959 5.42857
77 5TCI MLI 0.00007814 0.53354 5.43478
78 3HF3 FMN 0.0000000005653 0.73621 5.44413
79 3OIX FMN 0.000009635 0.54548 5.50725
80 1LBF 137 0.001092 0.45634 5.66802
81 2R14 FMN 0.000000002963 0.56096 5.71429
82 2R14 TXD 0.000000004882 0.51841 5.71429
83 1EIX BMQ 0.002943 0.42208 5.71429
84 5XL4 SIA 0.01138 0.40956 5.8104
85 4BI7 PGA 0.000124 0.4486 5.83658
86 4I9A NCN 0.0007868 0.43721 5.90278
87 1F76 FMN 0.000001295 0.59019 5.95238
88 1UZD CAP 0.003455 0.42482 5.97015
89 1DQX BMP 0.00169 0.43893 5.99251
90 1UJP CIT 0.00183 0.4226 6
91 3NRR D16 0.02295 0.41383 6
92 3B9O FMN 0.008921 0.40056 6
93 4WZH FMN 0.00000115 0.49157 6.05187
94 3QMN COA 0.01108 0.40004 6.20155
95 1Z44 FMN 0.0000000005483 0.72914 6.21302
96 1Z42 FMN 0.000000001179 0.72561 6.21302
97 1Z48 FMN 0.0000000006298 0.71523 6.21302
98 1Z41 FMN 0.0000000006744 0.71391 6.21302
99 4M5P FMN 0.00000006635 0.63886 6.28571
100 3VKC FPQ 0.001189 0.40812 6.28571
101 2Z6J FMN 0.00000007002 0.65611 6.3253
102 1RBL CAP 0.002572 0.43246 6.42202
103 3GLC R5P 0.001748 0.4391 6.44068
104 2NVA PL2 0.01052 0.40907 6.57143
105 3C3N FMN 0.000004939 0.58003 6.73077
106 1QDS PGA 0.00009446 0.46262 6.77291
107 1LYX PGA 0.000113 0.47495 6.85484
108 1ICP FMN 0.0000000003647 0.7632 6.85714
109 3C8F MT2 0.01366 0.41444 6.93878
110 2B4G FMN 0.000003837 0.57049 7.25552
111 2F6U CIT 0.00005353 0.53107 7.26496
112 4CW5 FMN 0.000002003 0.56621 7.26872
113 3KDN CAP 0.001698 0.47002 7.42857
114 4YMZ 13P 0.0001345 0.50382 7.56972
115 1PS9 FMN 0.00000001459 0.6718 7.71429
116 3CTL S6P 0.0006363 0.45614 7.79221
117 2V63 CAP 0.002714 0.42958 7.85714
118 2VDH CAP 0.002863 0.42853 7.85714
119 2V6A CAP 0.002688 0.42788 7.85714
120 3BW2 FMN 0.0000000205 0.51073 8.28571
121 1OX5 1PR 0.00003346 0.42237 8.28571
122 3VRV YSD 0.02894 0.40878 8.85609
123 1RBO CAP 0.03343 0.43604 8.94309
124 1IR1 CAP 0.002551 0.42891 8.94309
125 1UZH CAP 0.003647 0.42375 9.01639
126 4EWN 0VR 0.0002381 0.46829 9.09091
127 3PJU C2E 0.01077 0.41002 9.23695
128 1PVN MZP 0.0008035 0.47878 9.71429
129 4NAE 1GP 0.000008155 0.58412 9.77778
130 3AXK NDP 0.005854 0.40666 10.0775
131 1WDD CAP 0.002672 0.428 10.1562
132 2Y88 2ER 0.0001269 0.51243 10.2459
133 1DJN FMN 0.00001193 0.54123 10.2857
134 1SW0 PGA 0.0001254 0.46516 10.4839
135 3MJY FMN 0.000001663 0.59739 10.9827
136 3MJY IJZ 0.000001663 0.59739 10.9827
137 1GVE NAP 0.02044 0.40424 11.0092
138 1DBT U5P 0.0008996 0.42657 11.2971
139 4N02 FNR 0.000001192 0.58953 11.4286
140 4AF0 IMP 0.0001088 0.49514 11.4286
141 3EAU PDN 0.01413 0.41519 11.4286
142 5A5W GUO 0.00003739 0.54348 11.4625
143 2YPI PGA 0.0001681 0.49251 12.1457
144 1ME8 RVP 0.0005769 0.48215 12.2857
145 1GTE FMN 0.0000011 0.44291 13.4286
146 1GTE IUR 0.0000011 0.44291 13.4286
147 1BWV CAP 0.002826 0.42493 13.4286
148 4UTU LRY 0.000009279 0.52049 14.4105
149 4UTW RFW 0.00001634 0.5198 14.4105
150 1OVD FMN 0.000001051 0.61395 14.4695
151 1OVD ORO 0.000001051 0.61395 14.4695
152 1X1Z BMP 0.001249 0.47757 15.0794
153 2Q8Z NUP 0.002165 0.43763 15.7895
154 3QH2 3NM 0.0002609 0.42845 16
155 2FFC U5P 0.009916 0.40041 16
156 2ZRU FMN 0.0000006575 0.43897 18
157 4XP7 FNR 0.000000000002285 0.83275 23.1214
158 1EP2 FMN 0.0000001103 0.50458 27.3312
159 1EP2 ORO 0.0000002038 0.4561 27.3312
160 1VHN FMN 0.0000000004303 0.6916 37.4214
Pocket No.: 2; Query (leader) PDB : 3B0P; Ligand: FMN; Similar sites found: 7
This union binding pocket(no: 2) in the query (biounit: 3b0p.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DV8 0LX 0.02527 0.40087 1.71429
2 2Z9C FMN 0.01052 0.40108 2
3 3GFZ C2E 0.005795 0.41958 2.85714
4 1EYE PMM 0.01163 0.40079 3.57143
5 4OPC PGT 0.01923 0.44449 4.57143
6 2WQP WQP 0.01636 0.40151 4.58453
7 4ZBY URA 0.01691 0.41456 11.8557
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