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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
2zru FMN Isopentenyl-diphosphate delta-isomerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2zru FMNIsopentenyl-diphosphate delta-isomerase / 1.391
2zry FNRIsopentenyl-diphosphate delta-isomerase / 1.295
3b03 VNRIsopentenyl-diphosphate delta-isomerase / 1.290
3b05 FNRIsopentenyl-diphosphate delta-isomerase / 1.247
3vkj FNRIsopentenyl-diphosphate delta-isomerase / 1.245
2zrv FNRIsopentenyl-diphosphate delta-isomerase / 1.228
2zrz FNRIsopentenyl-diphosphate delta-isomerase / 1.208
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 1.173
3b04 OOPIsopentenyl-diphosphate delta-isomerase / 1.137
2h8x FMNXenA / 0.871
2hsa FMN12-oxophytodienoate reductase 3 1.3.1.42 0.867
1vhn FMNtRNA-dihydrouridine synthase / 0.859
1kbj FMNCytochrome b2, mitochondrial 1.1.2.3 0.838
2hs6 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.832
3l5l FMNXenobiotic reductase / 0.830
2gou FMNNADH:flavin oxidoreductase Sye1 / 0.827
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.823
4awt FMNNADH:flavin oxidoreductase Sye1 / 0.823
3hgo FMN12-oxophytodienoate reductase 3 1.3.1.42 0.820
4utk FNRXenobiotic reductase / 0.816
3l67 FMNXenobiotic reductase / 0.810
2hs8 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.809
1q45 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.808
1ofd FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.807
4aws FMNNADH:flavin oxidoreductase Sye1 / 0.807
3hgs FMN12-oxophytodienoate reductase 3 1.3.1.42 0.806
2gqa FMNNADH:flavin oxidoreductase Sye1 / 0.805
1ofe FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.802
4uth FMNXenobiotic reductase / 0.800
4utm FNRXenobiotic reductase / 0.800
1icp FMN12-oxophytodienoate reductase 1 1.3.1.42 0.797
4tmc FMNOld yellow enzyme / 0.797
5cpm FNRNADH:flavin oxidoreductase / 0.797
4rnx FMNNADPH dehydrogenase 1 1.6.99.1 0.794
4z9r FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.793
1icq FMN12-oxophytodienoate reductase 1 1.3.1.42 0.791
1jue FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.788
1h7w FMNDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.785
1oyc FMNNADPH dehydrogenase 1 1.6.99.1 0.781
2djl FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.779
2gjl FMNNitronate monooxygenase 1.13.12.16 0.779
4k7y FMNNADPH dehydrogenase 1 1.6.99.1 0.778
4jic FMNGTN Reductase / 0.777
4tmb FMNOld yellow enzyme / 0.776
4cw5 FMNDfnA / 0.775
1llw FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.774
4b5n FMNNAD(P)H:flavin oxidoreductase Sye4 / 0.774
4yx6 FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.774
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.772
4df2 FMNNADPH dehydrogenase / 0.771
1gwj FMNMorphinone reductase / 0.769
4rnw FMNNADPH dehydrogenase 1 1.6.99.1 0.768
1ep3 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.767
3hf3 FMNChromate reductase / 0.766
3kru FMNNADH:flavin oxidoreductase/NADH oxidase / 0.766
1z48 FMNNADPH dehydrogenase / 0.765
2j6x FMNLactate oxidase / 0.765
3p84 FMNPentaerythritol tetranitrate reductase / 0.764
1z44 FMNNADPH dehydrogenase / 0.762
4e2b FMNDehydrogenase / 0.758
1z41 FMNNADPH dehydrogenase / 0.751
3hgr FMN12-oxophytodienoate reductase 1 1.3.1.42 0.751
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.749
3p8j FMNPentaerythritol tetranitrate reductase / 0.749
2q3r FMN12-oxophytodienoate reductase 1 1.3.1.42 0.746
3gka FMNN-ethylmaleimide reductase / 0.744
1ics FMN12-oxophytodienoate reductase 1 1.3.1.42 0.743
2z6i FMN2-nitropropane dioxygenase / 0.741
1h66 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.739
2djx FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.737
2gjn FMNNitronate monooxygenase 1.13.12.16 0.737
3aty FMNProstaglandin F2a synthase / 0.736
1k02 FMNNADPH dehydrogenase 1 1.6.99.1 0.735
4rnv FMNNADPH dehydrogenase 1 1.6.99.1 0.735
1h51 FMNPentaerythritol tetranitrate reductase / 0.734
3oix FMNDihydroorotate dehydrogenase / 0.734
1h63 FMNPentaerythritol tetranitrate reductase / 0.732
3p8i FMNPentaerythritol tetranitrate reductase / 0.730
4e2d FMNDehydrogenase / 0.730
1kbq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.729
3f03 FMNPentaerythritol tetranitrate reductase / 0.729
2nli FMNLactate oxidase / 0.728
4rnu FMNNADPH dehydrogenase 1 1.6.99.1 0.725
1h50 FMNPentaerythritol tetranitrate reductase / 0.724
2zfa FMNLactate oxidase / 0.721
1vji FMN12-oxophytodienoate reductase 1 1.3.1.42 0.720
3atz FMNProstaglandin F2a synthase / 0.720
3p74 FMNPentaerythritol tetranitrate reductase / 0.716
4z38 FMNMlnA / 0.715
1gg5 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.714
1dxo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.713
3bw2 FMNPutative 2-nitropropane dioxygenase / 0.711
2b3d FADModulator of drug activity B / 0.706
1h69 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.703
2abb FMNPentaerythritol tetranitrate reductase / 0.700
1d4a FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.699
1kbo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.698
1vcf FMNIsopentenyl-diphosphate delta-isomerase / 0.691
2a1t FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.691
3gye FMNDihydroorotate dehydrogenase (fumarate) / 0.691
3gr8 FMNNADPH dehydrogenase / 0.689
5eai FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.689
3rpe FADPutative modulator of drug activity / 0.688
1uum FMNDihydroorotate dehydrogenase (quinone), mitochondrial 1.3.5.2 0.687
4qnw FMNChanoclavine-I aldehyde reductase easA / 0.687
5a89 FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.686
3giy FMN(S)-mandelate dehydrogenase 1.1.99.31 0.685
4hmx FMNPyridoxamine 5'-phosphate oxidase / 0.683
4xq6 FMNDihydroorotate dehydrogenase (quinone) / 0.680
2bsl FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.679
3p82 FMNPentaerythritol tetranitrate reductase / 0.678
4utl FNRXenobiotic reductase / 0.677
2bi8 FADUDP-galactopyranose mutase 5.4.99.9 0.671
1dor FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.670
3tjl FMNNADPH dehydrogenase / 0.667
3l0n S5PUridine 5'-monophosphate synthase 4.1.1.23 0.663
1jub FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.662
3ne6 DCPDNA-directed DNA polymerase / 0.662
1szg FNSCytochrome b2, mitochondrial 1.1.2.3 0.661
3c3n FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.661
1czn FMNFlavodoxin / 0.660
1ofv FMNFlavodoxin / 0.660
3ept FDAPutative FAD-monooxygenase / 0.658
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.658
4h6k FMNNADPH dehydrogenase 1 1.6.99.1 0.654
1yrx FMNAppA protein / 0.653
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.652
1ep1 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.651
2qmy FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.651
3int FDAUDP-galactopyranose mutase 5.4.99.9 0.651
3ojx FMNNADPH--cytochrome P450 reductase / 0.650