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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
3gag FMN Putative NADH dehydrogenase NAD(P)H nitroreductase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3gag FMNPutative NADH dehydrogenase NAD(P)H nitroreductase / 1.205
3ge6 FMNNitroreductase / 1.050
4qly FMNEnone reductase CLA-ER / 0.971
2wzv FMNNitroreductase NfnB / 0.968
2wzw FMNNitroreductase NfnB / 0.967
3koq FMNPutative nitroreductase / 0.963
1oon FMNOxygen-insensitive NAD(P)H nitroreductase / 0.951
3x22 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.947
1oo5 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.935
3eo8 FMNPutative nitroreductase / 0.928
1icu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.915
3e39 FMNNitroreductase / 0.914
1ooq FMNOxygen-insensitive NAD(P)H nitroreductase / 0.908
1yki FMNOxygen-insensitive NAD(P)H nitroreductase / 0.900
1ds7 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.887
1ylr FMNOxygen-insensitive NAD(P)H nitroreductase / 0.875
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.867
4ttb FMNIodotyrosine deiodinase 1 / 0.864
1kqb FMNOxygen-insensitive NAD(P)H nitroreductase / 0.863
1nec FMNOxygen-insensitive NAD(P)H nitroreductase 1 0.862
1ylu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.862
4xoo FMNCoenzyme F420:L-glutamate ligase / 0.861
1kqc FMNOxygen-insensitive NAD(P)H nitroreductase / 0.854
3gfd FMNIodotyrosine deiodinase 1 1.21.1.1 0.838
2ifa FMNUncharacterized protein / 0.833
3of4 FMNNitroreductase / 0.832
2isl FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.830
4ttc FMNIodotyrosine deiodinase 1 / 0.829
3pxv FMNNitroreductase / 0.827
3bem FMNPutative NAD(P)H nitroreductase MhqN 1 0.819
1vfr FMNMajor NAD(P)H-flavin oxidoreductase 1.6.99 0.818
3x21 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.803
4eo3 FMNBacterioferritin comigratory protein/NADH dehydrogenase / 0.796
2bkj FMNNADPH-flavin oxidoreductase / 0.780
3to0 FMNIodotyrosine deiodinase 1 1.21.1.1 0.780
1icv FMNOxygen-insensitive NAD(P)H nitroreductase / 0.776
3eof FMNPutative oxidase / 0.770
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.761
3gh8 FMNIodotyrosine deiodinase 1 1.21.1.1 0.740
2fre FMNNAD(P)H-flavin oxidoreductase / 0.738
3qdl FMNOxygen-insensitive NADPH nitroreductase / 0.732
2hay FMNPutative NAD(P)H-flavin oxidoreductase / 0.725
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.718
2pd7 FADVivid PAS protein VVD / 0.714
1rx0 FADIsobutyryl-CoA dehydrogenase, mitochondrial 1.3.99 0.708
4iv6 FDAIsovaleryl-CoA dehydrogenase / 0.702
2dvl FADAcyl-CoA dehydrogenase / 0.701
4opc FDAConserved Archaeal protein / 0.699
4opd FDAConserved Archaeal protein / 0.697
2d29 FADAcyl-CoA dehydrogenase / 0.696
3pl8 FADPyranose 2-oxidase / 0.694
3hj9 FMNUncharacterized protein / 0.693
3hjk FADVivid PAS protein VVD / 0.693
3p4t FAOPutative acyl-CoA dehydrogenase / 0.689
4qi5 FADCellobiose dehydrogenase / 0.688
3mdd FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.687
3mkh FADNitroalkane oxidase / 0.686
3oib FDAPutative acyl-CoA dehydrogenase / 0.686
3djl FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.684
1b4v FADCholesterol oxidase 1.1.3.6 0.682
3atq FDAConserved Archaeal protein / 0.682
1cc2 FADCholesterol oxidase 1.1.3.6 0.681
2hfo FMNActivator of photopigment and puc expression / 0.681
3in6 FMNUncharacterized protein / 0.678
4hj4 FMNLOV protein / 0.678
3nf4 FADAcyl-CoA dehydrogenase domain-containing protein / 0.677
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.676
4hj6 FMNLOV protein / 0.676
1a8p FADFerredoxin--NADP reductase / 0.675
3atr FDAConserved Archaeal protein / 0.675
4a3u FMNNADH:flavin oxidoreductase/NADH oxidase / 0.675
4opl FDAConserved Archaeal protein / 0.675
4x28 FDAAcyl-CoA dehydrogenase FadE26 / 0.674
4x28 FDAAcyl-CoA dehydrogenase FadE27 / 0.674
4opi FDAConserved Archaeal protein / 0.673
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.672
2apg FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.668
4opt FDAConserved Archaeal protein / 0.668
3mpi FADGlutaryl-CoA dehydrogenase 1.3.99.32 0.667
1mxt FAECholesterol oxidase 1.1.3.6 0.666
1n9n FMNPutative blue light receptor / 0.666
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.666
3d72 FADVivid PAS protein VVD / 0.666
1cbo FADCholesterol oxidase 1.1.3.6 0.665
3b6d FAECholesterol oxidase 1.1.3.6 0.665
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.664
4m9a FDAAcyl-CoA dehydrogenase / 0.664
2zaf FADNitroalkane oxidase 1.7.3.1 0.663
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.663
2z1q FADAcyl-CoA dehydrogenase / 0.662
4hnb FMNLOV protein / 0.662
2hq9 FADMll6688 protein / 0.661
1pkv RBFRiboflavin synthase 2.5.1.9 0.659
1siq FADGlutaryl-CoA dehydrogenase, mitochondrial 1.3.8.6 0.658
3au2 DGTDNA polymerase beta family (X family) / 0.658
4hia FMNLOV protein / 0.658
1ib0 FADNADH-cytochrome b5 reductase 3 1.6.2.2 0.657
3rh7 FMNUncharacterized protein / 0.657
4k5r FADOxygenase / 0.657
2a1t FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.655
2yg7 FADPutrescine oxidase / 0.655
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.655
2z6d FMNPhototropin-2 2.7.11.1 0.654
2vig FADShort-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.1 0.652
1usc FMNMonooxygenase / 0.651
2c12 FADNitroalkane oxidase 1.7.3.1 0.651
4wqm FADToluene-4-monooxygenase electron transfer component 1.18.1.3 0.651
3k4c FADPyranose 2-oxidase / 0.650
4h6k FMNNADPH dehydrogenase 1 1.6.99.1 0.650
4xq6 FMNDihydroorotate dehydrogenase (quinone) / 0.650