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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
2pd7 FAD Vivid PAS protein VVD

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2pd7 FADVivid PAS protein VVD / 1.645
2pd8 FADVivid PAS protein VVD / 1.436
3hji FADVivid PAS protein VVD / 1.424
3hjk FADVivid PAS protein VVD / 1.389
3is2 FADVivid PAS protein VVD / 1.366
3d72 FADVivid PAS protein VVD / 1.336
2pdt FADVivid PAS protein VVD / 1.148
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 1.071
4ees FMNPhototropin-2 2.7.11.1 1.053
4eep FMNPhototropin-2 2.7.11.1 1.049
4eet FMNPhototropin-2 2.7.11.1 1.048
2z6d FMNPhototropin-2 2.7.11.1 0.991
2pr5 FMNBlue-light photoreceptor / 0.982
2z6c FMNPhototropin-1 2.7.11.1 0.980
1n9l FMNPutative blue light receptor / 0.979
4eeu FMNPhototropin-2 2.7.11.1 0.977
2v0u FMNNPH1-1 / 0.968
5djt FMNNPH1-2 / 0.960
4eer FMNPhototropin-2 2.7.11.1 0.957
4hia FMNLOV protein / 0.953
1n9n FMNPutative blue light receptor / 0.952
2v1a FMNNPH1-1 / 0.952
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.932
5efw FMNNPH1-1 / 0.913
5j3w FMNSensory box protein / 0.892
4hnb FMNLOV protein / 0.883
4kuk RBFPutative blue-light photoreceptor / 0.881
5dju FMNNPH1-2 / 0.880
4wf0 FMNNPH1-1 / 0.872
3sw1 FMNSensory box protein / 0.866
4kuo RBFPutative blue-light photoreceptor / 0.851
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.832
5j4e FMNSensory box protein / 0.817
4hj6 FMNLOV protein / 0.813
3p7n FMNLight-activated DNA-binding protein EL222 / 0.786
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.784
4hhd FMNPhototropin-1 2.7.11.1 0.782
4hj3 FMNLOV protein / 0.781
5j60 FADThioredoxin reductase / 0.736
4hj4 FMNLOV protein / 0.723
2yqu FADDihydrolipoyl dehydrogenase / 0.716
3gag FMNPutative NADH dehydrogenase NAD(P)H nitroreductase / 0.714
2q0k FADThioredoxin reductase 1.8.1.9 0.711
1g28 FMNPHY3 / 0.707
4mok FADPyranose 2-oxidase / 0.707
1i0s FMNFerric-chelate reductase (NAD(P)H) / 0.705
2ign FADPyranose 2-oxidase / 0.702
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.700
2igo FADPyranose 2-oxidase / 0.699
3a3b RBFLumazine protein / 0.698
3gsi FADDimethylglycine oxidase 1.5.3.10 0.696
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.695
4wct FADFructosyl amine:oxygen oxidoreductase / 0.694
3lsi FADPyranose 2-oxidase / 0.692
4z24 FADPutative GMC-type oxidoreductase R135 1 0.692
4iil RBFMembrane lipoprotein TpN38(b) / 0.691
4mih FADPyranose 2-oxidase 1.1.3.10 0.691
2yg4 FADPutrescine oxidase / 0.690
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.690
4opd FDAConserved Archaeal protein / 0.689
1trb FADThioredoxin reductase 1.8.1.9 0.687
1b4v FADCholesterol oxidase 1.1.3.6 0.686
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.686
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.685
1ryi FADGlycine oxidase 1.4.3.19 0.685
3k4c FADPyranose 2-oxidase / 0.684
3n3b FMNProtein NrdI / 0.683
2hfn FMNActivator of photopigment and puc expression / 0.682
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.682
2iyi FMNAppA, antirepressor of ppsR, sensor of blue light / 0.682
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.682
3lsh FADPyranose 2-oxidase / 0.682
1tde FADThioredoxin reductase 1.8.1.9 0.681
5cho FADFlavin reductase / 0.680
1tdf FADThioredoxin reductase 1.8.1.9 0.679
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.679
1ng4 FADGlycine oxidase 1.4.3.19 0.678
1z6l FADPolyamine oxidase FMS1 / 0.678
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.678
3gg1 FMNUncharacterized protein / 0.678
4rsl FADFructosyl peptide oxidase / 0.678
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.677
3cnd FADPolyamine oxidase FMS1 / 0.675
1b8s FADCholesterol oxidase 1.1.3.6 0.674
3cox FADCholesterol oxidase 1.1.3.6 0.673
1ewy FADFerredoxin--NADP reductase 1.18.1.2 0.672
3a3g DLZLumazine protein / 0.672
3urh FADDihydrolipoyl dehydrogenase / 0.672
4opu FDAConserved Archaeal protein / 0.672
2yg7 FADPutrescine oxidase / 0.670
4opc FDAConserved Archaeal protein / 0.670
2yg5 FADPutrescine oxidase / 0.669
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.668
2whd FADThioredoxin reductase / 0.668
3rp8 FADFAD-dependent urate hydroxylase / 0.666
3cgc FADCoenzyme A disulfide reductase / 0.665
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.665
4rek FADCholesterol oxidase 1.1.3.6 0.665
3nlc FADUncharacterized protein / 0.664
4fwf FADLysine-specific histone demethylase 1B 1 0.664
2hko FADLysine-specific histone demethylase 1A 1 0.663
1mok FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.662
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.662
1g63 FMNEpidermin decarboxylase 4.1.1 0.661
2yg6 FADPutrescine oxidase / 0.661
4gut FADLysine-specific histone demethylase 1B 1 0.661
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.661
4z26 FADPutative GMC-type oxidoreductase R135 1 0.661
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.661
2ptf FMNUncharacterized protein MTH_863 / 0.660
3k4n FADPyranose 2-oxidase / 0.660
4gur FADLysine-specific histone demethylase 1B 1 0.660
1d4a FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.659
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.659
4gcm FADThioredoxin reductase 1.8.1.9 0.659
1eje FMNProtein MTH_152 / 0.658
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.658
2oa1 FADFlavin-dependent tryptophan halogenase RebH 1.14.19.9 0.658
3cls FADElectron transfer flavoprotein subunit alpha / 0.658
5br7 FADUDP-galactopyranose mutase / 0.658
1h81 FADPolyamine oxidase 1.5.3.14 0.657
2a1u FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.657
2gew FADCholesterol oxidase 1.1.3.6 0.657
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.657
3qvp FADGlucose oxidase 1.1.3.4 0.657
4ylf FADDihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog / 0.657
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.656
1n4u FAECholesterol oxidase 1.1.3.6 0.656
3gyi FADCholesterol oxidase 1.1.3.6 0.656
1get FADGlutathione reductase 1.8.1.7 0.655
2h94 FADLysine-specific histone demethylase 1A 1 0.655
4a65 FADThioredoxin reductase / 0.655
3clt FADElectron transfer flavoprotein subunit alpha / 0.654
4a5l FADThioredoxin reductase / 0.654
1cc2 FADCholesterol oxidase 1.1.3.6 0.653
1yy5 FADPolyamine oxidase FMS1 / 0.652
3lsm SFDPyranose 2-oxidase / 0.652
4ech FADPolyamine oxidase FMS1 / 0.652
2j09 FMNDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.651
3itj FADThioredoxin reductase 1 1.8.1.9 0.651
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.651
4bmo FMNProtein NrdI / 0.651
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.650
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.650
4jnq FDAThioredoxin reductase / 0.650