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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4tmb FMN Old yellow enzyme

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4tmb FMNOld yellow enzyme / 1.234
4tmc FMNOld yellow enzyme / 1.135
4rnx FMNNADPH dehydrogenase 1 1.6.99.1 1.087
4h6k FMNNADPH dehydrogenase 1 1.6.99.1 1.073
4k7y FMNNADPH dehydrogenase 1 1.6.99.1 1.068
1oya FMNNADPH dehydrogenase 1 1.6.99.1 1.036
1gwj FMNMorphinone reductase / 1.005
1icq FMN12-oxophytodienoate reductase 1 1.3.1.42 0.981
1h63 FMNPentaerythritol tetranitrate reductase / 0.980
4b5n FMNNAD(P)H:flavin oxidoreductase Sye4 / 0.980
3hgr FMN12-oxophytodienoate reductase 1 1.3.1.42 0.979
1ics FMN12-oxophytodienoate reductase 1 1.3.1.42 0.978
4jic FMNGTN Reductase / 0.970
1bwk FMNNADPH dehydrogenase 1 1.6.99.1 0.968
1h50 FMNPentaerythritol tetranitrate reductase / 0.965
3tjl FMNNADPH dehydrogenase / 0.965
4aws FMNNADH:flavin oxidoreductase Sye1 / 0.964
3p8i FMNPentaerythritol tetranitrate reductase / 0.961
4df2 FMNNADPH dehydrogenase / 0.959
1oyc FMNNADPH dehydrogenase 1 1.6.99.1 0.955
1icp FMN12-oxophytodienoate reductase 1 1.3.1.42 0.951
1vji FMN12-oxophytodienoate reductase 1 1.3.1.42 0.949
4rnv FMNNADPH dehydrogenase 1 1.6.99.1 0.949
2abb FMNPentaerythritol tetranitrate reductase / 0.943
3atz FMNProstaglandin F2a synthase / 0.940
3p62 FMNPentaerythritol tetranitrate reductase / 0.938
3gka FMNN-ethylmaleimide reductase / 0.937
1h51 FMNPentaerythritol tetranitrate reductase / 0.935
2h8x FMNXenA / 0.934
3aty FMNProstaglandin F2a synthase / 0.929
4rnw FMNNADPH dehydrogenase 1 1.6.99.1 0.929
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.924
4e2b FMNDehydrogenase / 0.924
1vyr FMNPentaerythritol tetranitrate reductase / 0.919
3f03 FMNPentaerythritol tetranitrate reductase / 0.911
3p74 FMNPentaerythritol tetranitrate reductase / 0.909
3p67 FMNPentaerythritol tetranitrate reductase / 0.907
3l67 FMNXenobiotic reductase / 0.904
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.896
4awt FMNNADH:flavin oxidoreductase Sye1 / 0.891
2hsa FMN12-oxophytodienoate reductase 3 1.3.1.42 0.878
4e2d FMNDehydrogenase / 0.876
2hs6 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.865
1z48 FMNNADPH dehydrogenase / 0.857
4qai FMNNADPH dehydrogenase / 0.853
5cpm FNRNADH:flavin oxidoreductase / 0.850
1vhn FMNtRNA-dihydrouridine synthase / 0.847
4utl FNRXenobiotic reductase / 0.846
1k02 FMNNADPH dehydrogenase 1 1.6.99.1 0.845
1z44 FMNNADPH dehydrogenase / 0.844
4ef9 FMNDihydroorotate dehydrogenase (fumarate) / 0.844
4m5p FMNNADPH dehydrogenase / 0.843
3l5l FMNXenobiotic reductase / 0.842
4utm FNRXenobiotic reductase / 0.842
4yco FMNtRNA-dihydrouridine(16) synthase / 0.841
3hgo FMN12-oxophytodienoate reductase 3 1.3.1.42 0.839
4uth FMNXenobiotic reductase / 0.837
1z41 FMNNADPH dehydrogenase / 0.835
2djx FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.834
3hgs FMN12-oxophytodienoate reductase 3 1.3.1.42 0.834
3n19 FNRXenobiotic reductase / 0.834
4ef8 FMNDihydroorotate dehydrogenase (fumarate) / 0.833
1q45 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.830
4ycp FMNtRNA-dihydrouridine(16) synthase / 0.830
4qnw FMNChanoclavine-I aldehyde reductase easA / 0.822
2q3r FMN12-oxophytodienoate reductase 1 1.3.1.42 0.821
2zfa FMNLactate oxidase / 0.818
1jue FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.807
3c3n FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.807
1jub FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.806
4rnu FMNNADPH dehydrogenase 1 1.6.99.1 0.802
3gye FMNDihydroorotate dehydrogenase (fumarate) / 0.801
2nli FMNLactate oxidase / 0.799
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.797
2hs8 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.790
2bsl FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.778
2djl FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.777
2j6x FMNLactate oxidase / 0.777
2zru FMNIsopentenyl-diphosphate delta-isomerase / 0.776
3kru FMNNADH:flavin oxidoreductase/NADH oxidase / 0.773
4xq6 FMNDihydroorotate dehydrogenase (quinone) / 0.757
1kbi FMNCytochrome b2, mitochondrial 1.1.2.3 0.753
2gou FMNNADH:flavin oxidoreductase Sye1 / 0.740
2e77 FMNLactate oxidase / 0.735
4bf9 FMNtRNA-dihydrouridine(16) synthase / 0.734
3p84 FMNPentaerythritol tetranitrate reductase / 0.731
3p8j FMNPentaerythritol tetranitrate reductase / 0.731
1ofd FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.729
2q3o FMN12-oxophytodienoate reductase 3 1.3.1.42 0.729
3b05 FNRIsopentenyl-diphosphate delta-isomerase / 0.725
3vkj FNRIsopentenyl-diphosphate delta-isomerase / 0.719
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 0.712
2zry FNRIsopentenyl-diphosphate delta-isomerase / 0.712
1uum FMNDihydroorotate dehydrogenase (quinone), mitochondrial 1.3.5.2 0.709
4hnb FMNLOV protein / 0.707
4utk FNRXenobiotic reductase / 0.704
4rje FNRLactate oxidase / 0.703
2gjl FMNNitronate monooxygenase 1.13.12.16 0.701
1gox FMNPeroxisomal (S)-2-hydroxy-acid oxidase 1.1.3.15 0.700
2a1t FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.697
4j8p FMNFlavodoxin / 0.695
2gqa FMNNADH:flavin oxidoreductase Sye1 / 0.692
3g5m FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.692
2qmy FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.690
2zrz FNRIsopentenyl-diphosphate delta-isomerase / 0.690
4qoe FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.690
4cw5 FMNDfnA / 0.689
1dxo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.688
3w77 FMNFMN-dependent NADH-azoreductase / 0.688
4yx6 FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.686
5a4k FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.684
2vyx FMNDodecin / 0.683
1qr2 FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.682
2b3d FADModulator of drug activity B / 0.682
1jqi FADShort-chain specific acyl-CoA dehydrogenase, mitochondrial / 0.680
3gr8 FMNNADPH dehydrogenase / 0.680
1x0p FADTll0078 protein / 0.679
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.678
3klb FMNUncharacterized protein / 0.678
3n14 FMNXenobiotic reductase / 0.677
4yl2 FMNLactate oxidase / 0.677
1nb9 RBFRiboflavin kinase 2.7.1.26 0.676
2z9d FMNFMN-dependent NADH-azoreductase / 0.676
3esz FMNFlavodoxin / 0.676
4iv6 FDAIsovaleryl-CoA dehydrogenase / 0.676
4kuk RBFPutative blue-light photoreceptor / 0.676
4m0c FMNFMN-dependent NADH-azoreductase 1 / 0.675
1siq FADGlutaryl-CoA dehydrogenase, mitochondrial 1.3.8.6 0.674
4qof FMNRibosyldihydronicotinamide dehydrogenase [quinone] / 0.674
1h69 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.673
1i0s FMNFerric-chelate reductase (NAD(P)H) / 0.673
4opt FDAConserved Archaeal protein / 0.673
2ohj FMNType A flavoprotein FprA 1 0.672
2hpv FMNFMN-dependent NADH-azoreductase 1.7 0.671
2eba FADPutative glutaryl-CoA dehydrogenase / 0.670
4zoh FADPutative oxidoreductase FAD-binding subunit / 0.670
3mdd FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.669
1gg5 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.668
3n3a FMNProtein NrdI / 0.668
4bmo FMNProtein NrdI / 0.666
2hfo FMNActivator of photopigment and puc expression / 0.665
2zrv FNRIsopentenyl-diphosphate delta-isomerase / 0.665
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 0.665
2c12 FADNitroalkane oxidase 1.7.3.1 0.664
2vxa RBFDodecin / 0.664
3n3b FMNProtein NrdI / 0.663
4bby FADAlkyldihydroxyacetonephosphate synthase, peroxisomal 2.5.1.26 0.663
4bca FADAlkyldihydroxyacetonephosphate synthase, peroxisomal 2.5.1.26 0.663
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.662
3sf6 FDAGlutaryl-CoA dehydrogenase / 0.662
1p4m FMNRiboflavin kinase 2.7.1.26 0.661
3qfr FMNNADPH--cytochrome P450 reductase / 0.661
1kbo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.660
2dvl FADAcyl-CoA dehydrogenase / 0.660
4n65 FMNFMN-dependent NADH-azoreductase 1 / 0.660
5jsc FADPutative acyl-CoA dehydrogenase / 0.660
1dxq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.658
3hf3 FMNChromate reductase / 0.658
3gg0 FMNUncharacterized protein / 0.657
3nf4 FADAcyl-CoA dehydrogenase domain-containing protein / 0.657
4zvl FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.657
4zvn FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.657
1kbq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.656
3k4n FADPyranose 2-oxidase / 0.656
4bmp FMNProtein NrdI / 0.656
4eo3 FMNBacterioferritin comigratory protein/NADH dehydrogenase / 0.656
5a8a FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.656
1amo FMNNADPH--cytochrome P450 reductase / 0.654
1czn FMNFlavodoxin / 0.654
4qly FMNEnone reductase CLA-ER / 0.654
5j4e FMNSensory box protein / 0.654
2pia FMNPhthalate dioxygenase reductase / 0.653
4p13 FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.653
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.651
3clr FADElectron transfer flavoprotein subunit alpha / 0.651
3v76 FDAUncharacterized protein / 0.651
1ych FMNNitric oxide reductase 1 0.650
3qe2 FMNNADPH--cytochrome P450 reductase / 0.650