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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
3gfd FMN Iodotyrosine deiodinase 1 1.21.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3gfd FMNIodotyrosine deiodinase 1 1.21.1.1 1.439
4ttc FMNIodotyrosine deiodinase 1 / 1.300
3gh8 FMNIodotyrosine deiodinase 1 1.21.1.1 1.106
3to0 FMNIodotyrosine deiodinase 1 1.21.1.1 1.034
4ttb FMNIodotyrosine deiodinase 1 / 1.032
3hj9 FMNUncharacterized protein / 0.932
4xoo FMNCoenzyme F420:L-glutamate ligase / 0.908
3e39 FMNNitroreductase / 0.890
4qly FMNEnone reductase CLA-ER / 0.889
2isl FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.885
3eo8 FMNPutative nitroreductase / 0.880
3ge6 FMNNitroreductase / 0.869
3x22 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.841
3gag FMNPutative NADH dehydrogenase NAD(P)H nitroreductase / 0.838
2wzw FMNNitroreductase NfnB / 0.835
3koq FMNPutative nitroreductase / 0.832
3bem FMNPutative NAD(P)H nitroreductase MhqN 1 0.820
2wzv FMNNitroreductase NfnB / 0.817
4eo3 FMNBacterioferritin comigratory protein/NADH dehydrogenase / 0.817
1oo5 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.807
3eof FMNPutative oxidase / 0.786
1vfr FMNMajor NAD(P)H-flavin oxidoreductase 1.6.99 0.785
3qdl FMNOxygen-insensitive NADPH nitroreductase / 0.785
1ds7 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.779
1ooq FMNOxygen-insensitive NAD(P)H nitroreductase / 0.779
2ifa FMNUncharacterized protein / 0.779
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.775
2fre FMNNAD(P)H-flavin oxidoreductase / 0.768
1oon FMNOxygen-insensitive NAD(P)H nitroreductase / 0.766
3x21 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.763
4p13 FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.757
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.741
4iv6 FDAIsovaleryl-CoA dehydrogenase / 0.741
2hay FMNPutative NAD(P)H-flavin oxidoreductase / 0.732
1ylr FMNOxygen-insensitive NAD(P)H nitroreductase / 0.731
1buc FADAcyl-CoA dehydrogenase, short-chain specific 1.3.8.1 0.724
1icu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.724
2eba FADPutative glutaryl-CoA dehydrogenase / 0.719
3pxv FMNNitroreductase / 0.719
2bkj FMNNADPH-flavin oxidoreductase / 0.718
1jqi FADShort-chain specific acyl-CoA dehydrogenase, mitochondrial / 0.713
1yki FMNOxygen-insensitive NAD(P)H nitroreductase / 0.711
1icv FMNOxygen-insensitive NAD(P)H nitroreductase / 0.710
5af7 FADAcyl-CoA dehydrogenase / 0.705
1ylu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.701
3u33 FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.701
3djl FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.699
2ohh FMNType A flavoprotein FprA 1 0.694
4tmc FMNOld yellow enzyme / 0.694
5jsc FADPutative acyl-CoA dehydrogenase / 0.694
3p4t FAOPutative acyl-CoA dehydrogenase / 0.689
3mdd FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.686
4y9l FADAcyl-CoA dehydrogenase family member 11 / 0.686
1nec FMNOxygen-insensitive NAD(P)H nitroreductase 1 0.684
4m9a FDAAcyl-CoA dehydrogenase / 0.682
2fcr FMNFlavodoxin / 0.679
3oib FDAPutative acyl-CoA dehydrogenase / 0.679
1rx0 FADIsobutyryl-CoA dehydrogenase, mitochondrial 1.3.99 0.676
2zry FNRIsopentenyl-diphosphate delta-isomerase / 0.676
4r81 FMNPredicted NADH dehydrogenase / 0.676
4eep FMNPhototropin-2 2.7.11.1 0.674
3k4c FADPyranose 2-oxidase / 0.672
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.671
2ign FADPyranose 2-oxidase / 0.670
3of4 FMNNitroreductase / 0.670
5fs7 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.669
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.666
3pl8 FADPyranose 2-oxidase / 0.666
1kqc FMNOxygen-insensitive NAD(P)H nitroreductase / 0.665
2bn4 FMNNADPH--cytochrome P450 reductase / 0.664
1a8p FADFerredoxin--NADP reductase / 0.663
1siq FADGlutaryl-CoA dehydrogenase, mitochondrial 1.3.8.6 0.663
1kqb FMNOxygen-insensitive NAD(P)H nitroreductase / 0.662
3mhp FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic 1.18.1.2 0.661
2b3d FADModulator of drug activity B / 0.660
3a3b RBFLumazine protein / 0.660
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.659
2c12 FADNitroalkane oxidase 1.7.3.1 0.656
1eje FMNProtein MTH_152 / 0.655
1kbj FMNCytochrome b2, mitochondrial 1.1.2.3 0.655
2gr3 FADFerredoxin reductase / 0.655
2rc5 FADFerredoxin--NADP reductase / 0.655
4b5n FMNNAD(P)H:flavin oxidoreductase Sye4 / 0.655
4tx9 AMZPhosphoribosyl isomerase A / 0.654
4x28 FDAAcyl-CoA dehydrogenase FadE26 / 0.654
4x28 FDAAcyl-CoA dehydrogenase FadE27 / 0.654
1bwl FMNNADPH dehydrogenase 1 1.6.99.1 0.653
2dvl FADAcyl-CoA dehydrogenase / 0.653
4eil UMPBifunctional dihydrofolate reductase-thymidylate synthase 1.5.1.3 0.652
2dft ADPShikimate kinase 2.7.1.71 0.651
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.650