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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
3hji FAD Vivid PAS protein VVD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3hji FADVivid PAS protein VVD / 1.679
2pd8 FADVivid PAS protein VVD / 1.487
3hjk FADVivid PAS protein VVD / 1.469
3is2 FADVivid PAS protein VVD / 1.431
2pd7 FADVivid PAS protein VVD / 1.424
3d72 FADVivid PAS protein VVD / 1.388
2pdt FADVivid PAS protein VVD / 1.173
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 1.121
4ees FMNPhototropin-2 2.7.11.1 1.089
4eep FMNPhototropin-2 2.7.11.1 1.061
4eet FMNPhototropin-2 2.7.11.1 1.044
2v1a FMNNPH1-1 / 1.025
2v0u FMNNPH1-1 / 1.024
4eer FMNPhototropin-2 2.7.11.1 1.004
2z6d FMNPhototropin-2 2.7.11.1 0.993
4hia FMNLOV protein / 0.987
5djt FMNNPH1-2 / 0.986
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.972
1n9l FMNPutative blue light receptor / 0.963
2z6c FMNPhototropin-1 2.7.11.1 0.953
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.951
5dju FMNNPH1-2 / 0.948
5efw FMNNPH1-1 / 0.922
4eeu FMNPhototropin-2 2.7.11.1 0.908
4wf0 FMNNPH1-1 / 0.907
1n9n FMNPutative blue light receptor / 0.902
3sw1 FMNSensory box protein / 0.888
4kuk RBFPutative blue-light photoreceptor / 0.886
1g28 FMNPHY3 / 0.885
4hnb FMNLOV protein / 0.857
3ue6 FMNAureochrome1 / 0.853
4hj6 FMNLOV protein / 0.853
4kuo RBFPutative blue-light photoreceptor / 0.848
4hhd FMNPhototropin-1 2.7.11.1 0.828
5j4e FMNSensory box protein / 0.822
5j3w FMNSensory box protein / 0.796
4hj3 FMNLOV protein / 0.770
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.752
3ad9 FADSubunit beta of sarcosine oxidase / 0.740
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.728
2iyi FMNAppA, antirepressor of ppsR, sensor of blue light / 0.728
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.724
3gsi FADDimethylglycine oxidase 1.5.3.10 0.718
4hh0 FMNAppA protein / 0.715
2yqu FADDihydrolipoyl dehydrogenase / 0.712
4yus FMNFamily 3 adenylate cyclase / 0.712
2b9x FADPutative aminooxidase / 0.710
2yg4 FADPutrescine oxidase / 0.709
4hj4 FMNLOV protein / 0.707
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.703
1ng4 FADGlycine oxidase 1.4.3.19 0.700
2bab FADPutative aminooxidase / 0.698
1oon FMNOxygen-insensitive NAD(P)H nitroreductase / 0.693
4opc FDAConserved Archaeal protein / 0.692
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.691
3ept FDAPutative FAD-monooxygenase / 0.691
4fwe FADLysine-specific histone demethylase 1B 1 0.691
4fwf FADLysine-specific histone demethylase 1B 1 0.691
2z1q FADAcyl-CoA dehydrogenase / 0.690
2c12 FADNitroalkane oxidase 1.7.3.1 0.688
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.687
2ywl FADThioredoxin reductase related protein / 0.687
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.686
2ohj FMNType A flavoprotein FprA 1 0.686
4gdp FADPolyamine oxidase FMS1 / 0.686
1r2j FADFkbI / 0.685
2rgh FADAlpha-Glycerophosphate Oxidase / 0.685
2ign FADPyranose 2-oxidase / 0.684
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.683
1pkv RBFRiboflavin synthase 2.5.1.9 0.682
3dme FADPutative conserved exported protein / 0.682
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.681
4hsu FADLysine-specific histone demethylase 1B 1 0.681
2bac FADPutative aminooxidase / 0.680
2byc FMNBlue-light receptor of the BLUF-family / 0.679
2igo FADPyranose 2-oxidase / 0.679
3gg0 FMNUncharacterized protein / 0.679
3gyi FADCholesterol oxidase 1.1.3.6 0.679
4gut FADLysine-specific histone demethylase 1B 1 0.677
1b4v FADCholesterol oxidase 1.1.3.6 0.676
1i0s FMNFerric-chelate reductase (NAD(P)H) / 0.676
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.676
3t37 FADPyridoxine 4-oxidase / 0.676
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.676
5buk FADFADH2-dependent halogenase / 0.675
2ok7 FADFerredoxin--NADP reductase, apicoplast / 0.674
4x9m FADUncharacterized protein MG039 homolog / 0.674
1trb FADThioredoxin reductase 1.8.1.9 0.673
2yg7 FADPutrescine oxidase / 0.673
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.673
4ef9 FMNDihydroorotate dehydrogenase (fumarate) / 0.673
4rek FADCholesterol oxidase 1.1.3.6 0.673
1ofv FMNFlavodoxin / 0.672
2yg5 FADPutrescine oxidase / 0.672
2yg6 FADPutrescine oxidase / 0.672
4wzh FMNDihydroorotate dehydrogenase (fumarate) / 0.672
1kbi FMNCytochrome b2, mitochondrial 1.1.2.3 0.671
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.671
3mkh FADNitroalkane oxidase / 0.671
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.669
1yrx FMNAppA protein / 0.669
2r9z FADGlutathione amide reductase / 0.669
3cnj FADCholesterol oxidase 1.1.3.6 0.669
5a8a FMNRiboflavin biosynthesis protein RibF 2.7.1.26 0.669
2oa1 FADFlavin-dependent tryptophan halogenase RebH 1.14.19.9 0.668
4y9l FADAcyl-CoA dehydrogenase family member 11 / 0.667
3urh FADDihydrolipoyl dehydrogenase / 0.666
4h4z FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.666
1ryi FADGlycine oxidase 1.4.3.19 0.665
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.665
4ttc FMNIodotyrosine deiodinase 1 / 0.665
3k4n FADPyranose 2-oxidase / 0.664
3fcj FADNitroalkane oxidase 1.7.3.1 0.663
3hgo FMN12-oxophytodienoate reductase 3 1.3.1.42 0.663
4gur FADLysine-specific histone demethylase 1B 1 0.663
3fmw FADOxygenase / 0.662
1b8s FADCholesterol oxidase 1.1.3.6 0.660
3p7n FMNLight-activated DNA-binding protein EL222 / 0.660
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.660
1fec FADTrypanothione reductase 1.8.1.12 0.659
1get FADGlutathione reductase 1.8.1.7 0.659
3axb FADPutative oxidoreductase / 0.659
4x9n FADUncharacterized protein MG039 homolog / 0.658
1mxt FAECholesterol oxidase 1.1.3.6 0.657
1u8v FAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase / 0.657
3b6d FAECholesterol oxidase 1.1.3.6 0.657
1gg5 FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.656
1n1p FADCholesterol oxidase 1.1.3.6 0.656
1n4w FADCholesterol oxidase 1.1.3.6 0.656
2q0k FADThioredoxin reductase 1.8.1.9 0.656
2reh FADNitroalkane oxidase 1.7.3.1 0.656
3cox FADCholesterol oxidase 1.1.3.6 0.656
3lad FADDihydrolipoyl dehydrogenase / 0.656
4xwr FADCholesterol oxidase 1.1.3.6 0.656
4xxg FADCholesterol oxidase 1.1.3.6 0.656
1ijh FADCholesterol oxidase 1.1.3.6 0.655
1nb9 RBFRiboflavin kinase 2.7.1.26 0.655
4opg FDAConserved Archaeal protein / 0.655
4z24 FADPutative GMC-type oxidoreductase R135 1 0.655
1n4v FADCholesterol oxidase 1.1.3.6 0.654
2eq6 FADDihydrolipoyl dehydrogenase / 0.654
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.654
2yg3 FADPutrescine oxidase / 0.654
3kkj FADRenalase / 0.654
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.653
2dw4 FADLysine-specific histone demethylase 1A 1 0.652
3g4a FADFlavin-dependent thymidylate synthase 2.1.1.148 0.652
4cnk FADL-amino acid oxidase / 0.652
4u2t FADCholesterol oxidase 1.1.3.6 0.652
1typ FADTrypanothione reductase 1.8.1.12 0.651
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.651
1mok FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.650
2wba FADTrypanothione reductase 1.8.1.12 0.650
4z26 FADPutative GMC-type oxidoreductase R135 1 0.650