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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
2pd8 FAD Vivid PAS protein VVD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pd8 FADVivid PAS protein VVD / 1.581
3hji FADVivid PAS protein VVD / 1.487
3hjk FADVivid PAS protein VVD / 1.479
2pd7 FADVivid PAS protein VVD / 1.436
3is2 FADVivid PAS protein VVD / 1.423
3d72 FADVivid PAS protein VVD / 1.384
2pdt FADVivid PAS protein VVD / 1.144
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 1.053
4eet FMNPhototropin-2 2.7.11.1 1.031
4ees FMNPhototropin-2 2.7.11.1 1.028
4eep FMNPhototropin-2 2.7.11.1 1.018
2z6d FMNPhototropin-2 2.7.11.1 0.984
5djt FMNNPH1-2 / 0.966
1n9l FMNPutative blue light receptor / 0.952
4eer FMNPhototropin-2 2.7.11.1 0.951
1n9n FMNPutative blue light receptor / 0.920
2v1a FMNNPH1-1 / 0.919
2v0u FMNNPH1-1 / 0.918
5efw FMNNPH1-1 / 0.910
4hj3 FMNLOV protein / 0.909
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.906
4kuk RBFPutative blue-light photoreceptor / 0.898
4eeu FMNPhototropin-2 2.7.11.1 0.892
5dju FMNNPH1-2 / 0.884
3sw1 FMNSensory box protein / 0.871
4wf0 FMNNPH1-1 / 0.844
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.841
3ue6 FMNAureochrome1 / 0.836
4hnb FMNLOV protein / 0.833
2pr5 FMNBlue-light photoreceptor / 0.832
3p7n FMNLight-activated DNA-binding protein EL222 / 0.814
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.799
2z6c FMNPhototropin-1 2.7.11.1 0.798
4hj4 FMNLOV protein / 0.786
5j3w FMNSensory box protein / 0.762
4kuo RBFPutative blue-light photoreceptor / 0.728
4yus FMNFamily 3 adenylate cyclase / 0.728
3ab1 FADFerredoxin--NADP reductase 1.18.1.2 0.727
4hj6 FMNLOV protein / 0.716
5buk FADFADH2-dependent halogenase / 0.713
5cho FADFlavin reductase / 0.706
5dbj FADFADH2-dependent halogenase PltA / 0.704
4hia FMNLOV protein / 0.694
2zbw FADFerredoxin--NADP reductase / 0.689
2v18 FMNDodecin / 0.686
2bf4 FADNADPH--cytochrome P450 reductase / 0.684
1kif FADD-amino-acid oxidase 1.4.3.3 0.681
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.681
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.681
2bn4 FADNADPH--cytochrome P450 reductase / 0.680
3gyj FADCholesterol oxidase 1.1.3.6 0.678
1g63 FMNEpidermin decarboxylase 4.1.1 0.676
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.675
5j4e FMNSensory box protein / 0.675
1ng3 FADGlycine oxidase 1.4.3.19 0.673
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.673
3ad9 FADSubunit beta of sarcosine oxidase / 0.673
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.673
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.672
4u2s FDACholesterol oxidase 1.1.3.6 0.671
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.671
1kyv RBF6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.669
4hhd FMNPhototropin-1 2.7.11.1 0.669
4u2t FADCholesterol oxidase 1.1.3.6 0.668
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.667
3lzx FADFerredoxin--NADP reductase 2 1.18.1.2 0.667
4opg FDAConserved Archaeal protein / 0.667
2ou5 FMNPyridoxamine 5'-phosphate oxidase-related FMN-binding protein / 0.666
3gyi FADCholesterol oxidase 1.1.3.6 0.666
4iv6 FDAIsovaleryl-CoA dehydrogenase / 0.664
1pkv RBFRiboflavin synthase 2.5.1.9 0.663
2igo FADPyranose 2-oxidase / 0.663
2q7v FADThioredoxin reductase / 0.662
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.662
3vqr FADPutative oxidoreductase / 0.661
5dkk FMNPredicted protein / 0.661
3td7 FADProbable FAD-linked sulfhydryl oxidase R596 1.8.3.2 0.659
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.659
1b8s FADCholesterol oxidase 1.1.3.6 0.658
4h4z FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.658
2pan FADGlyoxylate carboligase 4.1.1.47 0.656
4x9n FADUncharacterized protein MG039 homolog / 0.656
4ytn FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.656
2oyl IDCEndoglycoceramidase II / 0.655
2yg5 FADPutrescine oxidase / 0.655
2yg7 FADPutrescine oxidase / 0.655
3mzi FMNActivator of photopigment and puc expression / 0.653
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.652
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.652
1jr8 FADFAD-linked sulfhydryl oxidase ERV2 1.8.3.2 0.651
4bmo FMNProtein NrdI / 0.651
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.650
4z24 FADPutative GMC-type oxidoreductase R135 1 0.650