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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
4eer FMN Phototropin-2 2.7.11.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4eer FMNPhototropin-2 2.7.11.1 1.331
4eep FMNPhototropin-2 2.7.11.1 1.210
4ees FMNPhototropin-2 2.7.11.1 1.199
2pr5 FMNBlue-light photoreceptor / 1.159
4eeu FMNPhototropin-2 2.7.11.1 1.159
2z6d FMNPhototropin-2 2.7.11.1 1.121
5djt FMNNPH1-2 / 1.113
4eet FMNPhototropin-2 2.7.11.1 1.106
5efw FMNNPH1-1 / 1.048
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 1.046
2v0u FMNNPH1-1 / 1.024
1n9l FMNPutative blue light receptor / 1.016
3hji FADVivid PAS protein VVD / 1.004
4hj6 FMNLOV protein / 1.004
2v1a FMNNPH1-1 / 0.999
2z6c FMNPhototropin-1 2.7.11.1 0.994
4hhd FMNPhototropin-1 2.7.11.1 0.980
4kuk RBFPutative blue-light photoreceptor / 0.974
5dju FMNNPH1-2 / 0.965
4wf0 FMNNPH1-1 / 0.958
2pd7 FADVivid PAS protein VVD / 0.957
2pd8 FADVivid PAS protein VVD / 0.951
3hjk FADVivid PAS protein VVD / 0.951
2pdt FADVivid PAS protein VVD / 0.936
1g28 FMNPHY3 / 0.933
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.931
1n9n FMNPutative blue light receptor / 0.925
4kuo RBFPutative blue-light photoreceptor / 0.924
3ue6 FMNAureochrome1 / 0.916
3d72 FADVivid PAS protein VVD / 0.886
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.876
5j3w FMNSensory box protein / 0.866
4hia FMNLOV protein / 0.852
3sw1 FMNSensory box protein / 0.837
3is2 FADVivid PAS protein VVD / 0.821
5j4e FMNSensory box protein / 0.817
3p7n FMNLight-activated DNA-binding protein EL222 / 0.812
4hj3 FMNLOV protein / 0.793
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.789
4hnb FMNLOV protein / 0.787
4hj4 FMNLOV protein / 0.761
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.747
1jeh FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.746
3pl8 FADPyranose 2-oxidase / 0.738
2bkj FMNNADPH-flavin oxidoreductase / 0.730
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.716
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.715
3aeb FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.711
2yqu FADDihydrolipoyl dehydrogenase / 0.710
1b4v FADCholesterol oxidase 1.1.3.6 0.709
1cqx FADFlavohemoprotein / 0.709
2i51 FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding / 0.709
2isl FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.708
3gsi FADDimethylglycine oxidase 1.5.3.10 0.708
3gfx FMNUncharacterized protein / 0.707
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.706
2vnj FADNADPH:ferredoxin reductase / 0.706
1a8p FADFerredoxin--NADP reductase / 0.702
1ylu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.702
3in6 FMNUncharacterized protein / 0.702
3k4c FADPyranose 2-oxidase / 0.702
1efp FADElectron transfer flavoprotein subunit alpha / 0.700
1kqb FMNOxygen-insensitive NAD(P)H nitroreductase / 0.699
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.699
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.698
3gg1 FMNUncharacterized protein / 0.696
2bgi FADNADPH:ferredoxin reductase / 0.695
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.695
1mok FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.694
2wzv FMNNitroreductase NfnB / 0.694
1icu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.691
1ylr FMNOxygen-insensitive NAD(P)H nitroreductase / 0.691
5cho FADFlavin reductase / 0.691
2wzw FMNNitroreductase NfnB / 0.689
3crz FADFerredoxin--NADP+ reductase / 0.689
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.688
2gew FADCholesterol oxidase 1.1.3.6 0.688
2vnk FADNADPH:ferredoxin reductase / 0.688
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.688
4rek FADCholesterol oxidase 1.1.3.6 0.688
4u2t FADCholesterol oxidase 1.1.3.6 0.688
1n4u FAECholesterol oxidase 1.1.3.6 0.687
3gyi FADCholesterol oxidase 1.1.3.6 0.687
3gyj FADCholesterol oxidase 1.1.3.6 0.687
4u2s FDACholesterol oxidase 1.1.3.6 0.687
4xwr FADCholesterol oxidase 1.1.3.6 0.687
3cnj FADCholesterol oxidase 1.1.3.6 0.686
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.685
2gpj FADSiderophore-interacting protein / 0.685
3djl FADPutative acyl-CoA dehydrogenase AidB 1.3.99 0.685
1i0s FMNFerric-chelate reductase (NAD(P)H) / 0.684
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.684
3lsi FADPyranose 2-oxidase / 0.680
4opl FDAConserved Archaeal protein / 0.680
2yg4 FADPutrescine oxidase / 0.679
3rha FDAPutrescine oxidase / 0.679
1gaw FADFerredoxin / 0.678
3da1 FADGlycerol-3-phosphate dehydrogenase / 0.678
3k4n FADPyranose 2-oxidase / 0.678
4zoh FADPutative oxidoreductase FAD-binding subunit / 0.678
1icv FMNOxygen-insensitive NAD(P)H nitroreductase / 0.677
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.677
2ptf FMNUncharacterized protein MTH_863 / 0.677
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.677
1cc2 FADCholesterol oxidase 1.1.3.6 0.676
3lsh FADPyranose 2-oxidase / 0.676
1h83 FADPolyamine oxidase 1.5.3.14 0.675
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.673
1kqc FMNOxygen-insensitive NAD(P)H nitroreductase / 0.673
1n1p FADCholesterol oxidase 1.1.3.6 0.673
1n4v FADCholesterol oxidase 1.1.3.6 0.673
1n4w FADCholesterol oxidase 1.1.3.6 0.673
4qi7 FADCellobiose dehydrogenase / 0.673
1b8s FADCholesterol oxidase 1.1.3.6 0.672
1ijh FADCholesterol oxidase 1.1.3.6 0.672
3hj9 FMNUncharacterized protein / 0.672
4xxg FADCholesterol oxidase 1.1.3.6 0.672
1gal FADGlucose oxidase 1.1.3.4 0.671
1kif FADD-amino-acid oxidase 1.4.3.3 0.671
1oo5 FMNOxygen-insensitive NAD(P)H nitroreductase / 0.671
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.671
5i39 FADL-amino acid deaminase / 0.671
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.670
4i6g FADCryptochrome-2 / 0.670
1cbo FADCholesterol oxidase 1.1.3.6 0.669
1ewy FADFerredoxin--NADP reductase 1.18.1.2 0.669
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.669
4ytn FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.669
2yg7 FADPutrescine oxidase / 0.668
1tdn FADL-amino-acid oxidase 1.4.3.2 0.667
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.667
1ty9 FMNPhenazine biosynthesis protein PhzG 1.4 0.666
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.666
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.666
5buk FADFADH2-dependent halogenase / 0.666
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.666
3urh FADDihydrolipoyl dehydrogenase / 0.665
4hms FMNPhenazine biosynthesis protein PhzG 1.4 0.665
4ntd FADThioredoxin reductase / 0.665
1joa FADNADH peroxidase 1.11.1.1 0.664
4h2n FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.664
5j60 FADThioredoxin reductase / 0.664
1knp FADL-aspartate oxidase 1.4.3.16 0.663
1mxt FAECholesterol oxidase 1.1.3.6 0.663
3cox FADCholesterol oxidase 1.1.3.6 0.663
3nix FADFlavoprotein/dehydrogenase / 0.662
4k5r FADOxygenase / 0.662
2hay FMNPutative NAD(P)H-flavin oxidoreductase / 0.661
3gg0 FMNUncharacterized protein / 0.661
4gut FADLysine-specific histone demethylase 1B 1 0.661
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.660
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.660
2jae FADL-amino acid oxidase / 0.660
1ege FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.7 0.659
4jn9 FADDepH / 0.659
3fpk FADFerredoxin-NADP reductase / 0.658
1trb FADThioredoxin reductase 1.8.1.9 0.657
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.657
2xlp FADPutative flavin-containing monooxygenase / 0.657
2xve FADPutative flavin-containing monooxygenase / 0.657
3p4t FAOPutative acyl-CoA dehydrogenase / 0.657
1owo FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.656
1owp FADDeoxyribodipyrimidine photo-lyase 4.1.99.3 0.656
3qvr FADGlucose oxidase 1.1.3.4 0.656
1efv FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.655
1ffu FADCarbon monoxide dehydrogenase medium chain / 0.655
4fwe FADLysine-specific histone demethylase 1B 1 0.655
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.654
2vig FADShort-chain specific acyl-CoA dehydrogenase, mitochondrial 1.3.8.1 0.654
3kpf FADPolyamine oxidase 1.5.3.14 0.654
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.653
3mzi FMNActivator of photopigment and puc expression / 0.653
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.653
1tw4 CHDFatty acid-binding protein, liver / 0.652
1um0 FMNChorismate synthase / 0.652
2dji FADPyruvate oxidase / 0.652
2eq7 FADDihydrolipoyl dehydrogenase / 0.652
2yg6 FADPutrescine oxidase / 0.652
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.652
3of4 FMNNitroreductase / 0.652
4fdp FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.652
4opu FDAConserved Archaeal protein / 0.652
2xlr FADPutative flavin-containing monooxygenase / 0.651
3cty FADProbable thioredoxin reductase / 0.650
4irn FADAnaB / 0.650
4u2l SFDCholesterol oxidase 1.1.3.6 0.650