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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
4eep FMN Phototropin-2 2.7.11.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4eep FMNPhototropin-2 2.7.11.1 1.325
4ees FMNPhototropin-2 2.7.11.1 1.215
4eer FMNPhototropin-2 2.7.11.1 1.210
4eet FMNPhototropin-2 2.7.11.1 1.198
2z6d FMNPhototropin-2 2.7.11.1 1.172
5djt FMNNPH1-2 / 1.127
2pr5 FMNBlue-light photoreceptor / 1.115
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 1.105
4eeu FMNPhototropin-2 2.7.11.1 1.081
1n9l FMNPutative blue light receptor / 1.076
2v1a FMNNPH1-1 / 1.065
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 1.065
5efw FMNNPH1-1 / 1.063
3hji FADVivid PAS protein VVD / 1.061
2z6c FMNPhototropin-1 2.7.11.1 1.052
2pd7 FADVivid PAS protein VVD / 1.049
2pdt FADVivid PAS protein VVD / 1.028
3hjk FADVivid PAS protein VVD / 1.027
2v0u FMNNPH1-1 / 1.022
2pd8 FADVivid PAS protein VVD / 1.018
1n9n FMNPutative blue light receptor / 1.016
5dju FMNNPH1-2 / 1.009
4hhd FMNPhototropin-1 2.7.11.1 1.007
3d72 FADVivid PAS protein VVD / 0.999
4wf0 FMNNPH1-1 / 0.993
4kuk RBFPutative blue-light photoreceptor / 0.985
4hia FMNLOV protein / 0.982
3ue6 FMNAureochrome1 / 0.952
3is2 FADVivid PAS protein VVD / 0.940
5j3w FMNSensory box protein / 0.932
4kuo RBFPutative blue-light photoreceptor / 0.921
1g28 FMNPHY3 / 0.915
4hj6 FMNLOV protein / 0.915
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.896
3sw1 FMNSensory box protein / 0.865
4hj4 FMNLOV protein / 0.862
4hj3 FMNLOV protein / 0.823
3p7n FMNLight-activated DNA-binding protein EL222 / 0.820
4hnb FMNLOV protein / 0.795
5j4e FMNSensory box protein / 0.793
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.760
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.752
3ad9 FADSubunit beta of sarcosine oxidase / 0.734
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.728
4zoh FADPutative oxidoreductase FAD-binding subunit / 0.727
3pl8 FADPyranose 2-oxidase / 0.724
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.720
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.720
5dkk FMNPredicted protein / 0.720
1i0s FMNFerric-chelate reductase (NAD(P)H) / 0.713
2bgj FADNADPH:ferredoxin reductase / 0.708
3k4n FADPyranose 2-oxidase / 0.705
1b4v FADCholesterol oxidase 1.1.3.6 0.704
3gsi FADDimethylglycine oxidase 1.5.3.10 0.704
1jeh FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.703
1gal FADGlucose oxidase 1.1.3.4 0.699
2bgi FADNADPH:ferredoxin reductase / 0.698
2qdx FADFerredoxin--NADP+ reductase / 0.697
4opt FDAConserved Archaeal protein / 0.697
1cbo FADCholesterol oxidase 1.1.3.6 0.694
2vnj FADNADPH:ferredoxin reductase / 0.694
5cho FADFlavin reductase / 0.694
1ty9 FMNPhenazine biosynthesis protein PhzG 1.4 0.693
1usc FMNMonooxygenase / 0.693
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.693
2q7v FADThioredoxin reductase / 0.692
4hms FMNPhenazine biosynthesis protein PhzG 1.4 0.692
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.691
3nlc FADUncharacterized protein / 0.691
4opl FDAConserved Archaeal protein / 0.691
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.690
4rek FADCholesterol oxidase 1.1.3.6 0.689
5buk FADFADH2-dependent halogenase / 0.689
3dk4 FADGlutathione reductase, mitochondrial 1.8.1.7 0.688
4yus FMNFamily 3 adenylate cyclase / 0.688
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.687
4xxg FADCholesterol oxidase 1.1.3.6 0.687
2gew FADCholesterol oxidase 1.1.3.6 0.686
4u2s FDACholesterol oxidase 1.1.3.6 0.686
4u2t FADCholesterol oxidase 1.1.3.6 0.686
1n1p FADCholesterol oxidase 1.1.3.6 0.685
1n4u FAECholesterol oxidase 1.1.3.6 0.685
1n4w FADCholesterol oxidase 1.1.3.6 0.685
3gyi FADCholesterol oxidase 1.1.3.6 0.685
3gyj FADCholesterol oxidase 1.1.3.6 0.685
4xwr FADCholesterol oxidase 1.1.3.6 0.685
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.684
3cnj FADCholesterol oxidase 1.1.3.6 0.684
3lad FADDihydrolipoyl dehydrogenase / 0.682
3lsh FADPyranose 2-oxidase / 0.682
3qvr FADGlucose oxidase 1.1.3.4 0.682
1u8v FAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase / 0.681
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.681
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.681
4y9u FADNADPH--cytochrome P450 reductase / 0.681
3aeb FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.680
3cox FADCholesterol oxidase 1.1.3.6 0.680
4hh0 FMNAppA protein / 0.680
4k5r FADOxygenase / 0.679
4z24 FADPutative GMC-type oxidoreductase R135 1 0.679
2eq7 FADDihydrolipoyl dehydrogenase / 0.678
3djl FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.678
2vnk FADNADPH:ferredoxin reductase / 0.677
1ijh FADCholesterol oxidase 1.1.3.6 0.676
3ust FADAcMNPV orf92 / 0.676
1zk7 FADMercuric reductase 1.16.1.1 0.675
2vnh FADNADPH:ferredoxin reductase / 0.675
2zaf FADNitroalkane oxidase 1.7.3.1 0.675
1mok FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.674
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.674
3gfd FMNIodotyrosine deiodinase 1 1.21.1.1 0.674
4irn FADAnaB / 0.674
4z9r FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD / 0.674
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.674
1cc2 FADCholesterol oxidase 1.1.3.6 0.673
1joa FADNADH peroxidase 1.11.1.1 0.673
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.673
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.673
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.673
1hsk FADUDP-N-acetylenolpyruvoylglucosamine reductase / 0.672
1que FADFerredoxin--NADP reductase 1.18.1.2 0.672
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.672
1zx9 FADMercuric reductase 1.16.1.1 0.672
3dgz FADThioredoxin reductase 2, mitochondrial 1.8.1.9 0.672
4qi7 FADCellobiose dehydrogenase / 0.672
1g63 FMNEpidermin decarboxylase 4.1.1 0.671
2bkj FMNNADPH-flavin oxidoreductase / 0.671
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.671
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.671
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.670
3k4c FADPyranose 2-oxidase / 0.670
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.670
2wba FADTrypanothione reductase 1.8.1.12 0.669
3of4 FMNNitroreductase / 0.669
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.668
1kbo FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.668
4jn9 FADDepH / 0.668
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.668
1b8s FADCholesterol oxidase 1.1.3.6 0.667
3qzy FADFAD-linked sulfhydryl oxidase / 0.667
4i6g FADCryptochrome-2 / 0.666
4up3 FADThioredoxin reductase / 0.666
5hsa FASAlcohol oxidase 1 1.1.3.13 0.666
2vtb FADCryptochrome DASH, chloroplastic/mitochondrial / 0.665
2vxa RBFDodecin / 0.665
1iqr FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.664
1kbq FADNAD(P)H dehydrogenase [quinone] 1 1.6.5.2 0.664
4ysh FADGlycine oxidase / 0.664
1mxt FAECholesterol oxidase 1.1.3.6 0.663
4rhe FMNFlavin prenyltransferase UbiX / 0.663
2cdu FADNADH oxidase / 0.662
4qi4 FADCellobiose dehydrogenase / 0.662
2qa1 FADPgaE / 0.661
3ge6 FMNNitroreductase / 0.661
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.661
3nix FADFlavoprotein/dehydrogenase / 0.661
4gut FADLysine-specific histone demethylase 1B 1 0.661
2yg7 FADPutrescine oxidase / 0.659
3b6d FAECholesterol oxidase 1.1.3.6 0.659
3cty FADProbable thioredoxin reductase / 0.659
2j4d FADCryptochrome DASH, chloroplastic/mitochondrial / 0.658
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.658
4b1b FADThioredoxin reductase 1.8.1.9 0.658
4opg FDAConserved Archaeal protein / 0.658
4opu FDAConserved Archaeal protein / 0.658
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.658
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.657
3i99 FADUDP-N-acetylenolpyruvoylglucosamine reductase / 0.657
4gcm FADThioredoxin reductase 1.8.1.9 0.657
4nev FADTrypanothione reductase / 0.657
1cl0 FADThioredoxin reductase 1.8.1.9 0.656
1fea FADTrypanothione reductase 1.8.1.12 0.656
4a5l FADThioredoxin reductase / 0.656
1gvh FADFlavohemoprotein / 0.655
4j33 FADKynurenine 3-monooxygenase / 0.655
2j09 FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.654
4qi5 FADCellobiose dehydrogenase / 0.654
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.653
2j07 FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.653
2ptf FMNUncharacterized protein MTH_863 / 0.653
2r9z FADGlutathione amide reductase / 0.653
2tpr FADTrypanothione reductase 1.8.1.12 0.653
3icr FADCoenzyme A disulfide reductase / 0.653
3pgx NADUncharacterized NAD-dependent oxidoreductase MAP_4146 / 0.653
5hxw FADL-amino acid deaminase / 0.653
2bab FADPutative aminooxidase / 0.652
2igo FADPyranose 2-oxidase / 0.652
3fst FAD5,10-methylenetetrahydrofolate reductase 1.5.1.20 0.652
4cnk FADL-amino acid oxidase / 0.652
1n4v FADCholesterol oxidase 1.1.3.6 0.651
2hsa FMN12-oxophytodienoate reductase 3 1.3.1.42 0.651
2yg6 FADPutrescine oxidase / 0.651
3gwd FADCyclohexanone monooxygenase / 0.651
4ykf FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.651
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.650
1lvl FADDihydrolipoyl dehydrogenase 1.8.1.4 0.650
1tez FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.650
2eix FADNADH-cytochrome b5 reductase / 0.650
4b8z GDPGDP-L-fucose synthase 1.1.1.271 0.650
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.650
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.650