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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
3b05 FNR Isopentenyl-diphosphate delta-isomerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3b05 FNRIsopentenyl-diphosphate delta-isomerase / 1.407
2zry FNRIsopentenyl-diphosphate delta-isomerase / 1.346
2zrv FNRIsopentenyl-diphosphate delta-isomerase / 1.330
2zrz FNRIsopentenyl-diphosphate delta-isomerase / 1.325
3vkj FNRIsopentenyl-diphosphate delta-isomerase / 1.313
3b03 VNRIsopentenyl-diphosphate delta-isomerase / 1.302
2zru FMNIsopentenyl-diphosphate delta-isomerase / 1.247
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 1.243
3b04 OOPIsopentenyl-diphosphate delta-isomerase / 1.121
4uth FMNXenobiotic reductase / 0.816
4utm FNRXenobiotic reductase / 0.815
1kbj FMNCytochrome b2, mitochondrial 1.1.2.3 0.814
4xq6 FMNDihydroorotate dehydrogenase (quinone) / 0.810
3l5l FMNXenobiotic reductase / 0.785
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.778
1vcf FMNIsopentenyl-diphosphate delta-isomerase / 0.777
4m5p FMNNADPH dehydrogenase / 0.771
3l67 FMNXenobiotic reductase / 0.768
1vhn FMNtRNA-dihydrouridine synthase / 0.767
1qcw FNSCytochrome b2, mitochondrial 1.1.2.3 0.766
1ofd FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.764
3tjl FMNNADPH dehydrogenase / 0.764
3n19 FNRXenobiotic reductase / 0.758
4ycp FMNtRNA-dihydrouridine(16) synthase / 0.757
1ep1 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.754
2h8x FMNXenA / 0.749
4yx6 FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.747
1ep3 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.745
2gou FMNNADH:flavin oxidoreductase Sye1 / 0.745
1szg FNSCytochrome b2, mitochondrial 1.1.2.3 0.741
4rnx FMNNADPH dehydrogenase 1 1.6.99.1 0.740
4jic FMNGTN Reductase / 0.737
3p8j FMNPentaerythritol tetranitrate reductase / 0.735
1z48 FMNNADPH dehydrogenase / 0.732
4qnw FMNChanoclavine-I aldehyde reductase easA / 0.730
4tmb FMNOld yellow enzyme / 0.725
3aty FMNProstaglandin F2a synthase / 0.724
4utk FNRXenobiotic reductase / 0.721
3f03 FMNPentaerythritol tetranitrate reductase / 0.720
4awt FMNNADH:flavin oxidoreductase Sye1 / 0.719
3hf3 FMNChromate reductase / 0.717
4e2b FMNDehydrogenase / 0.713
4utl FNRXenobiotic reductase / 0.713
1z44 FMNNADPH dehydrogenase / 0.709
1kbo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.704
1yki FMNOxygen-insensitive NAD(P)H nitroreductase / 0.701
3oix FMNDihydroorotate dehydrogenase / 0.701
4bmo FMNProtein NrdI / 0.699
4b5n FMNNAD(P)H:flavin oxidoreductase Sye4 / 0.697
2zfa FMNLactate oxidase / 0.695
3dh7 FMNIsopentenyl-diphosphate delta-isomerase / 0.695
4iql FMNEnoyl-(Acyl-carrier-protein) reductase II / 0.695
1h63 FMNPentaerythritol tetranitrate reductase / 0.694
4aws FMNNADH:flavin oxidoreductase Sye1 / 0.693
2j6x FMNLactate oxidase / 0.691
4k5r FADOxygenase / 0.691
2nli FMNLactate oxidase / 0.690
3bw2 FMNPutative 2-nitropropane dioxygenase / 0.687
3kru FMNNADH:flavin oxidoreductase/NADH oxidase / 0.687
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.685
4yco FMNtRNA-dihydrouridine(16) synthase / 0.685
3p84 FMNPentaerythritol tetranitrate reductase / 0.684
5cpm FNRNADH:flavin oxidoreductase / 0.681
2gqa FMNNADH:flavin oxidoreductase Sye1 / 0.680
1oya FMNNADPH dehydrogenase 1 1.6.99.1 0.677
3atz FMNProstaglandin F2a synthase / 0.677
4rnw FMNNADPH dehydrogenase 1 1.6.99.1 0.676
1d7y FADFerredoxin reductase / 0.674
1nec FMNOxygen-insensitive NAD(P)H nitroreductase 1 0.674
1h51 FMNPentaerythritol tetranitrate reductase / 0.672
4qai FMNNADPH dehydrogenase / 0.670
1ylu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.668
4e2d FMNDehydrogenase / 0.667
2djl FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.665
2z9d FMNFMN-dependent NADH-azoreductase / 0.665
4m0c FMNFMN-dependent NADH-azoreductase 1 / 0.664
2z6i FMN2-nitropropane dioxygenase / 0.663
3esz FMNFlavodoxin / 0.663
4q4k FMNUncharacterized protein / 0.662
4yl2 FMNLactate oxidase / 0.662
1yob FMNFlavodoxin 2 / 0.661
3p8i FMNPentaerythritol tetranitrate reductase / 0.660
1kbi FMNCytochrome b2, mitochondrial 1.1.2.3 0.659
1h50 FMNPentaerythritol tetranitrate reductase / 0.658
1szf FMNCytochrome b2, mitochondrial 1.1.2.3 0.658
2qmy FADRibosyldihydronicotinamide dehydrogenase [quinone] / 0.658
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.658
1icq FMN12-oxophytodienoate reductase 1 1.3.1.42 0.657
1vyr FMNPentaerythritol tetranitrate reductase / 0.657
2j09 FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.657
4rnv FMNNADPH dehydrogenase 1 1.6.99.1 0.657
1ics FMN12-oxophytodienoate reductase 1 1.3.1.42 0.656
2j07 FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.656
4h4x FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.656
1icp FMN12-oxophytodienoate reductase 1 1.3.1.42 0.654
4df2 FMNNADPH dehydrogenase / 0.654
4ysw FADXanthine dehydrogenase/oxidase / 0.654
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.653
1dor FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.653
2e77 FMNLactate oxidase / 0.652
1usc FMNMonooxygenase / 0.650
2dvl FADAcyl-CoA dehydrogenase / 0.650
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.650