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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
5j4e FMN Sensory box protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5j4e FMNSensory box protein / 1.365
5j3w FMNSensory box protein / 1.216
2z6d FMNPhototropin-2 2.7.11.1 0.916
4hnb FMNLOV protein / 0.895
4hia FMNLOV protein / 0.887
4hj3 FMNLOV protein / 0.881
3ue6 FMNAureochrome1 / 0.862
2pdt FADVivid PAS protein VVD / 0.856
3d72 FADVivid PAS protein VVD / 0.849
3hjk FADVivid PAS protein VVD / 0.834
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.825
3hji FADVivid PAS protein VVD / 0.822
2pd7 FADVivid PAS protein VVD / 0.817
4eer FMNPhototropin-2 2.7.11.1 0.817
3sw1 FMNSensory box protein / 0.809
4hj6 FMNLOV protein / 0.794
4eep FMNPhototropin-2 2.7.11.1 0.793
2z6c FMNPhototropin-1 2.7.11.1 0.780
4eeu FMNPhototropin-2 2.7.11.1 0.765
4kuo RBFPutative blue-light photoreceptor / 0.762
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.759
4kuk RBFPutative blue-light photoreceptor / 0.758
4hhd FMNPhototropin-1 2.7.11.1 0.757
4wqm FADToluene-4-monooxygenase electron transfer component 1.18.1.3 0.747
2a1u FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.730
2v1a FMNNPH1-1 / 0.721
3clr FADElectron transfer flavoprotein subunit alpha / 0.718
2pr5 FMNBlue-light photoreceptor / 0.716
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 0.716
5dju FMNNPH1-2 / 0.714
4yus FMNFamily 3 adenylate cyclase / 0.713
5j60 FADThioredoxin reductase / 0.709
3clt FADElectron transfer flavoprotein subunit alpha / 0.708
1n9n FMNPutative blue light receptor / 0.705
2gv8 FADThiol-specific monooxygenase 1.14.13 0.702
4hj4 FMNLOV protein / 0.699
1n9l FMNPutative blue light receptor / 0.697
2dvl FADAcyl-CoA dehydrogenase / 0.697
3djl FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.697
5djt FMNNPH1-2 / 0.696
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.695
5a89 FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.693
3gg0 FMNUncharacterized protein / 0.691
5af7 FADAcyl-CoA dehydrogenase / 0.691
2iyi FMNAppA, antirepressor of ppsR, sensor of blue light / 0.690
1g28 FMNPHY3 / 0.688
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.688
4opl FDAConserved Archaeal protein / 0.688
2v0u FMNNPH1-1 / 0.686
1cc2 FADCholesterol oxidase 1.1.3.6 0.684
2yqu FADDihydrolipoyl dehydrogenase / 0.684
2a87 FADThioredoxin reductase 1.8.1.9 0.683
5a8a FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.681
2bf4 FADNADPH--cytochrome P450 reductase / 0.679
3is2 FADVivid PAS protein VVD / 0.679
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.676
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.676
5efw FMNNPH1-1 / 0.676
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.675
2pd8 FADVivid PAS protein VVD / 0.675
4o5q FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.673
1z41 FMNNADPH dehydrogenase / 0.672
2jb2 FADL-amino acid oxidase / 0.671
2qdx FADFerredoxin--NADP+ reductase / 0.671
3fcj FADNitroalkane oxidase 1.7.3.1 0.671
3m31 FADEndoplasmic oxidoreductin-1 1.8.4 0.671
2mwg FMNBlue-light photoreceptor / 0.670
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.670
4uir FADOleate hydratase 4.2.1.53 0.670
1b8s FADCholesterol oxidase 1.1.3.6 0.668
2gew FADCholesterol oxidase 1.1.3.6 0.668
4opc FDAConserved Archaeal protein / 0.668
4rek FADCholesterol oxidase 1.1.3.6 0.668
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.667
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.667
1n4u FAECholesterol oxidase 1.1.3.6 0.667
1owm FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.667
2v18 FMNDodecin / 0.666
3cnj FADCholesterol oxidase 1.1.3.6 0.666
3gfy FMNUncharacterized protein / 0.666
3gyj FADCholesterol oxidase 1.1.3.6 0.666
4opd FDAConserved Archaeal protein / 0.666
4opu FDAConserved Archaeal protein / 0.666
4u2s FDACholesterol oxidase 1.1.3.6 0.666
1own FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.665
2ifa FMNUncharacterized protein / 0.665
2q0k FADThioredoxin reductase 1.8.1.9 0.665
4ees FMNPhototropin-2 2.7.11.1 0.663
2iid FADL-amino-acid oxidase 1.4.3.2 0.662
2xve FADPutative flavin-containing monooxygenase / 0.662
3gyi FADCholesterol oxidase 1.1.3.6 0.662
3qzy FADFAD-linked sulfhydryl oxidase / 0.662
4q71 FADBifunctional protein PutA / 0.662
2bn4 FADNADPH--cytochrome P450 reductase / 0.661
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.661
1q1r FADPutidaredoxin reductase 1.18.1.5 0.660
3fg2 FADPutative rubredoxin reductase / 0.660
5hxw FADL-amino acid deaminase / 0.660
3cnt FADPolyamine oxidase FMS1 / 0.659
4opt FDAConserved Archaeal protein / 0.658
4wf0 FMNNPH1-1 / 0.658
1h81 FADPolyamine oxidase 1.5.3.14 0.656
3ute FADUDP-galactopyranose mutase / 0.656
5br7 FADUDP-galactopyranose mutase / 0.656
1cl0 FADThioredoxin reductase 1.8.1.9 0.655
1tez FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.655
1yrx FMNAppA protein / 0.655
3kru FMNNADH:flavin oxidoreductase/NADH oxidase / 0.655
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.655
1cbo FADCholesterol oxidase 1.1.3.6 0.654
2b9x FADPutative aminooxidase / 0.654
4tmb FMNOld yellow enzyme / 0.654
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.653
3cgb FADCoenzyme A disulfide reductase / 0.653
3hf3 FMNChromate reductase / 0.653
3p7n FMNLight-activated DNA-binding protein EL222 / 0.653
1owl FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.652
1b4v FADCholesterol oxidase 1.1.3.6 0.651
1owo FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.651
3axb FADPutative oxidoreductase / 0.651
4u2t FADCholesterol oxidase 1.1.3.6 0.651
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.651
1ylu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.650
4xwr FADCholesterol oxidase 1.1.3.6 0.650