Receptor
PDB id Resolution Class Description Source Keywords
3A3B 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LUMP COMPLEXED WITH FLAVIN MONONUCLEOTI PHOTOBACTERIUM KISHITANII LUMINOUS BACTERIA LUMAZINE PROTEIN FLAVIN MONONUCLEOTIDE LUMINESCENT PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE LUMAZINE PROTEIN FROM PHOTOBACTERIUM KISHITANII IN COMPLEXES WITH THE AUT CHROMOPHORE, 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE ANALOGUES, RIBOFLAVIN AND FMN, AT HIGH RESOLUTION J.BACTERIOL. V. 192 127 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN B:191;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
RBF A:191;
Valid;
none;
submit data
376.364 C17 H20 N4 O6 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A3B 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LUMP COMPLEXED WITH FLAVIN MONONUCLEOTI PHOTOBACTERIUM KISHITANII LUMINOUS BACTERIA LUMAZINE PROTEIN FLAVIN MONONUCLEOTIDE LUMINESCENT PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE LUMAZINE PROTEIN FROM PHOTOBACTERIUM KISHITANII IN COMPLEXES WITH THE AUT CHROMOPHORE, 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE ANALOGUES, RIBOFLAVIN AND FMN, AT HIGH RESOLUTION J.BACTERIOL. V. 192 127 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 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: RBF; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 RBF 1 1
2 FMN 0.75641 0.876712
3 RS3 0.74026 0.942029
4 DLZ 0.546667 0.885714
5 1VY 0.525641 0.871429
6 C3F 0.523256 0.816901
7 LFN 0.513889 0.712121
8 CF4 0.511364 0.805556
9 FAD 0.460938 0.790123
10 FAS 0.460938 0.790123
11 FAE 0.457364 0.780488
12 RLP 0.438202 0.833333
13 DAL FAD PER 0.42446 0.771084
14 FO1 0.423913 0.871429
15 HDF 0.423913 0.871429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A3B; Ligand: RBF; Similar sites found: 96
This union binding pocket(no: 1) in the query (biounit: 3a3b.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1FLM FMN 0.009066 0.41835 None
2 3R5W F42 0.001473 0.40345 None
3 4KXQ APR 0.01043 0.42055 1.57895
4 4I5I NAD 0.02349 0.40972 1.57895
5 5M58 SAH 0.0213 0.40162 1.57895
6 3CB0 FMN 0.003021 0.43308 1.7341
7 1QX4 FAD 0.001598 0.47806 2.10526
8 4WQM FAD 0.001113 0.47126 2.10526
9 2D37 FMN 0.00534 0.44148 2.84091
10 2D37 NAD 0.005693 0.44148 2.84091
11 1G79 PLP 0.01836 0.42444 3.15789
12 1G79 FMN 0.01607 0.4243 3.15789
13 1BKC INN 0.006357 0.41748 3.15789
14 3RJ5 NAD 0.04675 0.40458 3.15789
15 3IAE D7K 0.03456 0.40454 3.15789
16 4COQ SAN 0.01726 0.40121 3.15789
17 1I0S NAP 0.01409 0.4212 3.5503
18 1I0S FMN 0.01012 0.4212 3.5503
19 2PIA FMN 0.0005687 0.48003 3.68421
20 1F20 FAD 0.001366 0.46111 3.68421
21 1CSI OAA 0.02671 0.41863 3.68421
22 4D42 NAP 0.04875 0.41234 3.68421
23 4D42 W0I 0.04875 0.41234 3.68421
24 3K87 FAD 0.0004367 0.5048 3.78378
25 1USF NAP 0.005205 0.4475 3.93258
26 1USF FMN 0.004347 0.4475 3.93258
27 4F07 FAD 0.0009635 0.46865 4.21053
28 1TLL FAD 0.001272 0.46266 4.21053
29 2GU8 796 0.03812 0.41968 4.21053
30 5X8G S0N 0.04349 0.41438 4.21053
31 2WFG ZZB 0.01809 0.40343 4.21053
32 3RIY NAD 0.03989 0.40012 4.21053
33 3OZV FAD 0.001618 0.4878 4.73684
34 3OZV ECN 0.00266 0.47989 4.73684
35 3W2E NAD 0.003635 0.46595 4.73684
36 3W2E FAD 0.003635 0.46595 4.73684
37 3W9F I3P 0.01043 0.41575 4.73684
38 1ZK4 NAP 0.02773 0.41489 4.73684
39 4GJ3 0XP 0.0306 0.40617 4.73684
40 1V2G OCA 0.01251 0.40323 4.73684
41 4U9U FAD 0.0007877 0.47502 5.26316
42 3JQQ FAD 0.002631 0.47239 5.26316
43 3JQQ A2P 0.002243 0.47034 5.26316
44 5O0X FAD 0.0003981 0.45936 5.26316
45 1A8P FAD 0.001817 0.45495 5.26316
46 3KRR DQX 0.03408 0.42695 5.26316
47 2BGM NAJ 0.01406 0.41991 5.26316
48 3ZOK NAD 0.01827 0.41909 5.26316
49 2IMP NAI 0.02367 0.41856 5.26316
50 4X5S AZM 0.01077 0.41228 5.26316
51 1RZ0 FAD 0.008348 0.4301 5.59006
52 2BFR ADP 0.01547 0.41345 5.78947
53 4G1V FAD 0.0008221 0.48464 6.31579
54 5GXU FAD 0.005227 0.44339 6.31579
55 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.01556 0.42272 6.31579
56 3HRD MCN 0.04824 0.40003 6.31579
57 3CLH NAD 0.01457 0.41478 6.84211
58 1XHL NDP 0.0397 0.40246 6.84211
59 3HWW AKG 0.002676 0.44035 7.36842
60 1DDG FAD 0.004286 0.43824 7.36842
61 2QTZ NAP 0.01044 0.43638 7.36842
62 2QTZ FAD 0.003569 0.43638 7.36842
63 3QFS NAP 0.03311 0.41268 7.36842
64 3QFS FAD 0.03311 0.41268 7.36842
65 3FJO FAD 0.0125 0.40953 7.36842
66 3TN7 NJP 0.03402 0.40491 7.36842
67 3O2Q PRO THR SEP PRO SER TYR 0.0194 0.4019 7.36842
68 4KOT CE3 0.03215 0.41243 7.40741
69 1DJN FMN 0.02627 0.40174 7.89474
70 2YNC YNC 0.04652 0.40187 8.42105
71 1XKQ NDP 0.04361 0.40135 8.42105
72 5UIU 8CG 0.02562 0.40901 8.66873
73 2EIX FAD 0.02012 0.4132 9.47368
74 4CQM NAP 0.03436 0.40467 9.47368
75 4DQL NAP 0.00684 0.44928 10
76 4DQL FAD 0.003322 0.44893 10
77 2BSA NAP 0.01206 0.44655 10
78 2BSA FAD 0.01168 0.44655 10
79 1S4M LUM 0.02943 0.40335 10
80 3VO1 FAD 0.00155 0.45196 11.0526
81 3ZOD HQE 0.00146 0.47029 11.5789
82 2ED4 FAD 0.000989 0.48052 12.7517
83 1A27 NAP 0.02469 0.41106 13.1579
84 4NBT NAD 0.03158 0.40427 13.6842
85 5H5J FAD 0.001605 0.45559 15.2632
86 1KRH FAD 0.0004095 0.48712 16.3158
87 1FND FAD 0.01073 0.43465 20.0637
88 1FND A2P 0.01073 0.43465 20.0637
89 1SM4 FAD 0.001871 0.44796 20.9459
90 1EWY FAD 0.002503 0.43947 21.4286
91 1QFY FAD 0.00819 0.44303 22.4026
92 1QFY NAP 0.00819 0.44303 22.4026
93 3MHP FAD 0.002397 0.44698 23.3108
94 1GAW FAD 0.002438 0.44002 35.2632
95 1KZL CRM 0.0000000004898 0.75551 48.9474
96 4G6I RS3 0.00000001673 0.46043 49.4737
Pocket No.: 2; Query (leader) PDB : 3A3B; Ligand: FMN; Similar sites found: 93
This union binding pocket(no: 2) in the query (biounit: 3a3b.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1FLM FMN 0.01382 0.40926 None
2 3R5W F42 0.0009852 0.4014 None
3 1KUV CA5 0.03998 0.4012 None
4 4KXQ APR 0.01802 0.40855 1.57895
5 3CB0 FMN 0.004054 0.42692 1.7341
6 1QX4 FAD 0.001048 0.48767 2.10526
7 4WQM FAD 0.001118 0.47115 2.10526
8 2VL8 CTS 0.01612 0.40768 2.63158
9 2D37 FMN 0.006253 0.43797 2.84091
10 2D37 NAD 0.006663 0.43797 2.84091
11 1G79 PLP 0.01161 0.43501 3.15789
12 1G79 FMN 0.01007 0.43497 3.15789
13 2V3V MGD 0.0398 0.42874 3.15789
14 3RJ5 NAD 0.0299 0.41506 3.15789
15 1BKC INN 0.007157 0.41499 3.15789
16 1I0S FMN 0.01349 0.41491 3.5503
17 1I0S NAP 0.01868 0.41488 3.5503
18 2PIA FMN 0.0005753 0.47978 3.68421
19 1F20 FAD 0.001336 0.46159 3.68421
20 1N4W FAD 0.04044 0.4123 3.68421
21 4HMT NNV 0.03042 0.4026 3.68421
22 2E7Z MGD 0.04512 0.40258 3.68421
23 4HMT FMN 0.03024 0.40142 3.68421
24 3K87 FAD 0.0007634 0.49218 3.78378
25 1USF NAP 0.005294 0.44712 3.93258
26 1USF FMN 0.004422 0.44712 3.93258
27 4F07 FAD 0.0009917 0.46803 4.21053
28 1TLL FAD 0.001135 0.46512 4.21053
29 2WFG ZZB 0.01887 0.40251 4.21053
30 3OZV FAD 0.001281 0.49324 4.73684
31 3OZV ECN 0.002081 0.48567 4.73684
32 3W2E FAD 0.0031 0.46964 4.73684
33 3W2E NAD 0.0031 0.46964 4.73684
34 2Z9I GLY ALA THR VAL 0.007564 0.41653 4.73684
35 1ZK4 NAP 0.03037 0.41279 4.73684
36 1V2G OCA 0.01257 0.40313 4.73684
37 3W9F I3P 0.0147 0.40295 4.73684
38 1HV9 UD1 0.03415 0.40249 4.73684
39 3TE4 ACO 0.02626 0.40025 4.73684
40 4U9U FAD 0.0006153 0.48038 5.26316
41 3JQQ FAD 0.002747 0.47139 5.26316
42 3JQQ A2P 0.002502 0.46785 5.26316
43 5O0X FAD 0.0004522 0.45692 5.26316
44 1A8P FAD 0.002268 0.45016 5.26316
45 2BGM NAJ 0.01769 0.41477 5.26316
46 1WMA AB3 0.04068 0.41216 5.26316
47 3ZOK NAD 0.0248 0.41212 5.26316
48 2IMP NAI 0.03225 0.41139 5.26316
49 1RZ0 FAD 0.009341 0.4276 5.59006
50 2BFR ADP 0.01604 0.41265 5.78947
51 4G1V FAD 0.0008015 0.4852 6.31579
52 5GXU FAD 0.003284 0.45376 6.31579
53 1XHL NDP 0.03826 0.40331 6.84211
54 3HWW AKG 0.002422 0.44247 7.36842
55 2QTZ NAP 0.00861 0.44079 7.36842
56 2QTZ FAD 0.002903 0.44079 7.36842
57 1DDG FAD 0.003841 0.44063 7.36842
58 3QFS FAD 0.02654 0.41785 7.36842
59 3QFS NAP 0.02654 0.41785 7.36842
60 3FJO FAD 0.01103 0.41221 7.36842
61 2DKN NAI 0.03437 0.40234 7.36842
62 3TN7 NJP 0.0417 0.40023 7.36842
63 4KOT CE3 0.0271 0.4164 7.40741
64 4G87 UD1 0.02933 0.40714 7.89474
65 1DJN FMN 0.0272 0.40096 7.89474
66 1XKQ NDP 0.03749 0.40485 8.42105
67 2YNC YNC 0.04555 0.40236 8.42105
68 1QSR ACO 0.02473 0.40453 8.64198
69 5UIU 8CG 0.01847 0.4164 8.66873
70 2EIX FAD 0.01779 0.41597 9.47368
71 4CQM NAP 0.02407 0.41281 9.47368
72 2BSA NAP 0.008457 0.45501 10
73 2BSA FAD 0.008182 0.45501 10
74 4DQL NAP 0.005704 0.45347 10
75 4DQL FAD 0.002885 0.45203 10
76 5E5U MLI 0.004733 0.40323 10.5263
77 3VO1 FAD 0.001426 0.45371 11.0526
78 3ZOD HQE 0.00164 0.46771 11.5789
79 3AFN NAP 0.04512 0.40056 12.4031
80 2ED4 FAD 0.001116 0.47782 12.7517
81 1A27 NAP 0.01986 0.41599 13.1579
82 5H5J FAD 0.001201 0.46183 15.2632
83 1KRH FAD 0.0003287 0.49186 16.3158
84 1FND A2P 0.008093 0.44109 20.0637
85 1FND FAD 0.008093 0.44109 20.0637
86 1SM4 FAD 0.001223 0.45698 20.9459
87 1EWY FAD 0.001913 0.44514 21.4286
88 1QFY FAD 0.00573 0.45123 22.4026
89 1QFY NAP 0.00573 0.45123 22.4026
90 3MHP FAD 0.002088 0.44995 23.3108
91 1GAW FAD 0.001918 0.44509 35.2632
92 1KZL CRM 0.0000000008226 0.74474 48.9474
93 4G6I RS3 0.00000003267 0.45598 49.4737
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