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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
3n3b FMN Protein NrdI

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3n3b FMNProtein NrdI / 1.292
3n3a FMNProtein NrdI / 1.114
3n39 FMNProtein NrdI / 1.074
4n82 FMNRibonucleotide reductase (NrdI family protein), putative / 0.909
4bmo FMNProtein NrdI / 0.897
4bmp FMNProtein NrdI / 0.858
3f6s FMNFlavodoxin / 0.800
2bf4 FMNNADPH--cytochrome P450 reductase / 0.788
4y7c FMNNADPH--cytochrome P450 reductase / 0.785
2bn4 FMNNADPH--cytochrome P450 reductase / 0.781
3ojw FMNNADPH--cytochrome P450 reductase / 0.759
1fue FMNFlavodoxin / 0.757
3ojx FMNNADPH--cytochrome P450 reductase / 0.751
2ohj FMNType A flavoprotein FprA 1 0.738
1aku FMNFlavodoxin / 0.732
4oxx FMNCindoxin / 0.732
1amo FMNNADPH--cytochrome P450 reductase / 0.730
3qe2 FMNNADPH--cytochrome P450 reductase / 0.729
2fcr FMNFlavodoxin / 0.728
2ohi FMNType A flavoprotein FprA 1 0.725
2v5v FMNFlavodoxin / 0.722
1ych FMNNitric oxide reductase 1 0.720
2g37 FADProline dehydrogenase / 0.720
3f90 FMNFlavodoxin / 0.718
1ycf FMNNitric oxide reductase 1 0.717
3qfr FMNNADPH--cytochrome P450 reductase / 0.715
2ohh FMNType A flavoprotein FprA 1 0.714
1ycg FMNNitric oxide reductase 1 0.712
3klb FMNUncharacterized protein / 0.711
4nmc FADBifunctional protein PutA / 0.710
4bf9 FMNtRNA-dihydrouridine(16) synthase / 0.709
1j8q FMNFlavodoxin / 0.706
1zwl FMNNAD(P)H dehydrogenase (quinone) 1.6.5.2 0.704
2q9u FMNA-type flavoprotein / 0.703
2w5u FMNFlavodoxin / 0.702
2gjl FMNNitronate monooxygenase 1.13.12.16 0.701
4j8p FMNFlavodoxin / 0.701
5f12 FMNNAD(P)H dehydrogenase (quinone) / 0.700
1yob FMNFlavodoxin 2 / 0.698
1xyy FMNFlavodoxin / 0.694
2gjn FMNNitronate monooxygenase 1.13.12.16 0.694
3gye FMNDihydroorotate dehydrogenase (fumarate) / 0.694
3zho FMNNAD(P)H dehydrogenase (quinone) / 0.692
1wsb FMNFlavodoxin / 0.691
4utl FNRXenobiotic reductase / 0.690
4z9r FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.690
1ofv FMNFlavodoxin / 0.688
2v5u FMNFlavodoxin / 0.688
4ycp FMNtRNA-dihydrouridine(16) synthase / 0.687
3p8i FMNPentaerythritol tetranitrate reductase / 0.685
1czn FMNFlavodoxin / 0.684
2pd7 FADVivid PAS protein VVD / 0.683
4yco FMNtRNA-dihydrouridine(16) synthase / 0.683
5a4k FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.683
1j9g FMNFlavodoxin / 0.682
3b04 OOPIsopentenyl-diphosphate delta-isomerase / 0.682
1akr FMNFlavodoxin / 0.681
2hpv FMNFMN-dependent NADH-azoreductase 1.7 0.681
3lcm FADPutative oxidoreductase / 0.680
3p8j FMNPentaerythritol tetranitrate reductase / 0.680
3haz FADBifunctional protein PutA / 0.679
4ef8 FMNDihydroorotate dehydrogenase (fumarate) / 0.678
4ef9 FMNDihydroorotate dehydrogenase (fumarate) / 0.678
1c7f FMNFlavodoxin / 0.677
4m0c FMNFMN-dependent NADH-azoreductase 1 / 0.676
2fx2 FMNFlavodoxin / 0.675
3gka FMNN-ethylmaleimide reductase / 0.674
4xq6 FMNDihydroorotate dehydrogenase (quinone) / 0.674
1h51 FMNPentaerythritol tetranitrate reductase / 0.673
2gou FMNNADH:flavin oxidoreductase Sye1 / 0.673
1akw FMNFlavodoxin / 0.672
1n9l FMNPutative blue light receptor / 0.671
2abb FMNPentaerythritol tetranitrate reductase / 0.671
4rnw FMNNADPH dehydrogenase 1 1.6.99.1 0.671
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.671
3f03 FMNPentaerythritol tetranitrate reductase / 0.670
1icq FMN12-oxophytodienoate reductase 1 1.3.1.42 0.669
3p84 FMNPentaerythritol tetranitrate reductase / 0.669
1j9z FMNNADPH--cytochrome P450 reductase / 0.668
1t5b FMNFMN-dependent NADH-azoreductase / 0.668
4jay FADUDP-N-acetylenolpyruvoylglucosamine reductase / 0.668
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.667
1azl FMNFlavodoxin / 0.666
4z38 FMNMlnA / 0.666
3kap FMNFlavodoxin / 0.665
1qbg FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.664
4m5p FMNNADPH dehydrogenase / 0.664
1d4a FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.663
4tmb FMNOld yellow enzyme / 0.663
5tgz FMNCannabinoid receptor 1 / 0.663
1ja0 FMNNADPH--cytochrome P450 reductase / 0.662
1jub FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.662
3hr4 FMNNitric oxide synthase, inducible 1.14.13.39 0.662
4fx2 FMNFlavodoxin / 0.662
1kbq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.661
1oo5 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.661
1vcf FMNIsopentenyl-diphosphate delta-isomerase / 0.661
4qof FMNRibosyldihydronicotinamide dehydrogenase [quinone] / 0.660
1ahn FMNFlavodoxin 1 / 0.659
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.659
1qlt FADVanillyl-alcohol oxidase 1.1.3.38 0.659
1z41 FMNNADPH dehydrogenase / 0.659
2gqa FMNNADH:flavin oxidoreductase Sye1 / 0.658
3i99 FADUDP-N-acetylenolpyruvoylglucosamine reductase / 0.658
4f4q FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.657
4fdp FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.657
4hj4 FMNLOV protein / 0.657
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.656
3n76 CA23-dehydroquinate dehydratase 4.2.1.10 0.656
4utk FNRXenobiotic reductase / 0.656
1h69 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.655
1ja1 FMNNADPH--cytochrome P450 reductase / 0.655
3rpe FADPutative modulator of drug activity / 0.655
4r81 FMNPredicted NADH dehydrogenase / 0.655
2isl FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.654
2r97 FMNNAD(P)H dehydrogenase (quinone) / 0.654
2z9d FMNFMN-dependent NADH-azoreductase / 0.654
5a89 FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.654
3eo8 FMNPutative nitroreductase / 0.653
3esy FMNFlavodoxin / 0.653
4n65 FMNFMN-dependent NADH-azoreductase 1 / 0.653
1s4m LUMRiboflavin biosynthesis protein / 0.652
1xyv FMNFlavodoxin / 0.652
5a8a FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.652
1dor FMNDihydroorotate dehydrogenase A (fumarate) 1.3.98.1 0.651
2djl FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.651
4e2b FMNDehydrogenase / 0.651
5j3w FMNSensory box protein / 0.651
1ep1 FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit 1.3.1.14 0.650
3c3n FMNDihydroorotate dehydrogenase (fumarate) 1.3.98.1 0.650
3hgs FMN12-oxophytodienoate reductase 3 1.3.1.42 0.650