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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
3vkj FNR Isopentenyl-diphosphate delta-isomerase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vkj FNRIsopentenyl-diphosphate delta-isomerase / 1.345
3b05 FNRIsopentenyl-diphosphate delta-isomerase / 1.313
2zrv FNRIsopentenyl-diphosphate delta-isomerase / 1.311
2zry FNRIsopentenyl-diphosphate delta-isomerase / 1.287
2zrz FNRIsopentenyl-diphosphate delta-isomerase / 1.275
3b04 OOPIsopentenyl-diphosphate delta-isomerase / 1.247
2zru FMNIsopentenyl-diphosphate delta-isomerase / 1.245
2zrx FMNIsopentenyl-diphosphate delta-isomerase / 1.203
3b03 VNRIsopentenyl-diphosphate delta-isomerase / 1.196
1kbj FMNCytochrome b2, mitochondrial 1.1.2.3 0.827
1vhn FMNtRNA-dihydrouridine synthase / 0.805
2hsa FMN12-oxophytodienoate reductase 3 1.3.1.42 0.804
4uth FMNXenobiotic reductase / 0.800
4qnw FMNChanoclavine-I aldehyde reductase easA / 0.797
3l67 FMNXenobiotic reductase / 0.796
1ofd FMNFerredoxin-dependent glutamate synthase 2 1.4.7.1 0.789
4utm FNRXenobiotic reductase / 0.789
3l5l FMNXenobiotic reductase / 0.785
1z48 FMNNADPH dehydrogenase / 0.779
3hgo FMN12-oxophytodienoate reductase 3 1.3.1.42 0.776
4awt FMNNADH:flavin oxidoreductase Sye1 / 0.774
1q45 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.766
4df2 FMNNADPH dehydrogenase / 0.764
3kru FMNNADH:flavin oxidoreductase/NADH oxidase / 0.760
5cpm FNRNADH:flavin oxidoreductase / 0.755
4tmc FMNOld yellow enzyme / 0.750
4yco FMNtRNA-dihydrouridine(16) synthase / 0.750
3hgs FMN12-oxophytodienoate reductase 3 1.3.1.42 0.746
4ycp FMNtRNA-dihydrouridine(16) synthase / 0.744
2hs8 FMN12-oxophytodienoate reductase 3 1.3.1.42 0.740
1oyc FMNNADPH dehydrogenase 1 1.6.99.1 0.736
2h8x FMNXenA / 0.736
4jic FMNGTN Reductase / 0.736
4b5n FMNNAD(P)H:flavin oxidoreductase Sye4 / 0.735
1vcf FMNIsopentenyl-diphosphate delta-isomerase / 0.733
4aws FMNNADH:flavin oxidoreductase Sye1 / 0.727
1z44 FMNNADPH dehydrogenase / 0.723
1gwj FMNMorphinone reductase / 0.720
4tmb FMNOld yellow enzyme / 0.719
2z6i FMN2-nitropropane dioxygenase / 0.715
2j6x FMNLactate oxidase / 0.713
1z41 FMNNADPH dehydrogenase / 0.710
1h66 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.709
1h7w FMNDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.707
1h63 FMNPentaerythritol tetranitrate reductase / 0.705
1ep1 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.700
1ep3 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.698
3atz FMNProstaglandin F2a synthase / 0.696
1icp FMN12-oxophytodienoate reductase 1 1.3.1.42 0.695
4rnx FMNNADPH dehydrogenase 1 1.6.99.1 0.695
4rnw FMNNADPH dehydrogenase 1 1.6.99.1 0.690
4k7y FMNNADPH dehydrogenase 1 1.6.99.1 0.689
4rnv FMNNADPH dehydrogenase 1 1.6.99.1 0.684
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.682
1h51 FMNPentaerythritol tetranitrate reductase / 0.679
1ics FMN12-oxophytodienoate reductase 1 1.3.1.42 0.676
4y9l FADAcyl-CoA dehydrogenase family member 11 / 0.674
1h50 FMNPentaerythritol tetranitrate reductase / 0.673
3aty FMNProstaglandin F2a synthase / 0.672
4e2b FMNDehydrogenase / 0.672
1vji FMN12-oxophytodienoate reductase 1 1.3.1.42 0.669
3ojw FMNNADPH--cytochrome P450 reductase / 0.669
1j8q FMNFlavodoxin / 0.668
4bmo FMNProtein NrdI / 0.668
4bf9 FMNtRNA-dihydrouridine(16) synthase / 0.666
3tjl FMNNADPH dehydrogenase / 0.664
1uum FMNDihydroorotate dehydrogenase (quinone), mitochondrial 1.3.5.2 0.663
2djx FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.663
3p84 FMNPentaerythritol tetranitrate reductase / 0.663
3p8j FMNPentaerythritol tetranitrate reductase / 0.663
2nli FMNLactate oxidase / 0.661
3esz FMNFlavodoxin / 0.661
2bsl FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.660
3bw3 FMNPutative 2-nitropropane dioxygenase / 0.660
3klb FMNUncharacterized protein / 0.660
3p62 FMNPentaerythritol tetranitrate reductase / 0.660
2abb FMNPentaerythritol tetranitrate reductase / 0.659
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.659
3oix FMNDihydroorotate dehydrogenase / 0.659
4utl FNRXenobiotic reductase / 0.659
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.658
1dxq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.657
2zfa FMNLactate oxidase / 0.656
5dju FMNNPH1-2 / 0.656
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.655
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.655
1dor FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.654
1nb9 RBFRiboflavin kinase 2.7.1.26 0.654
2bi7 FADUDP-galactopyranose mutase 5.4.99.9 0.654
3hgr FMN12-oxophytodienoate reductase 1 1.3.1.42 0.653
4wqm FADToluene-4-monooxygenase electron transfer component 1.18.1.3 0.653
2reh FADNitroalkane oxidase 1.7.3.1 0.652
3n19 FNRXenobiotic reductase / 0.652
2wq7 FADRE11660p / 0.651
1usc FMNMonooxygenase / 0.650
3p67 FMNPentaerythritol tetranitrate reductase / 0.650
3x22 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.650
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.650