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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
5efw FMN NPH1-1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5efw FMNNPH1-1 / 1.272
4eet FMNPhototropin-2 2.7.11.1 1.122
5djt FMNNPH1-2 / 1.101
5dju FMNNPH1-2 / 1.085
4ees FMNPhototropin-2 2.7.11.1 1.080
4eep FMNPhototropin-2 2.7.11.1 1.063
1n9l FMNPutative blue light receptor / 1.052
4eer FMNPhototropin-2 2.7.11.1 1.048
2v0u FMNNPH1-1 / 1.041
2v1a FMNNPH1-1 / 1.026
1n9n FMNPutative blue light receptor / 1.012
4wf0 FMNNPH1-1 / 1.008
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.997
2z6d FMNPhototropin-2 2.7.11.1 0.990
4eeu FMNPhototropin-2 2.7.11.1 0.973
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 0.945
3d72 FADVivid PAS protein VVD / 0.942
3hji FADVivid PAS protein VVD / 0.922
3hjk FADVivid PAS protein VVD / 0.918
2pd7 FADVivid PAS protein VVD / 0.913
4hia FMNLOV protein / 0.912
2pd8 FADVivid PAS protein VVD / 0.910
2pdt FADVivid PAS protein VVD / 0.901
2pr5 FMNBlue-light photoreceptor / 0.885
3ue6 FMNAureochrome1 / 0.865
4r38 RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.864
3is2 FADVivid PAS protein VVD / 0.853
1g28 FMNPHY3 / 0.842
2z6c FMNPhototropin-1 2.7.11.1 0.842
5j3w FMNSensory box protein / 0.820
4hj6 FMNLOV protein / 0.814
4hj3 FMNLOV protein / 0.812
4hhd FMNPhototropin-1 2.7.11.1 0.808
3p7n FMNLight-activated DNA-binding protein EL222 / 0.787
4kuk RBFPutative blue-light photoreceptor / 0.779
4kuo RBFPutative blue-light photoreceptor / 0.779
3sw1 FMNSensory box protein / 0.778
4hj4 FMNLOV protein / 0.778
5dkk FMNPredicted protein / 0.777
4r3a RBFBlue-light-activated histidine kinase 2 2.7.13.3 0.743
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.734
4d5g FADCyclohexane-1,2-dione hydrolase 3.7.1.11 0.727
2isj FMN5,6-dimethylbenzimidazole synthase 1.13.11.79 0.710
3gfz FMNUncharacterized protein / 0.705
2qa1 FADPgaE / 0.704
1tdk FADL-amino-acid oxidase 1.4.3.2 0.702
3gsi FADDimethylglycine oxidase 1.5.3.10 0.700
2isl FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.698
3ad9 FADSubunit beta of sarcosine oxidase / 0.698
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.697
3ust FADAcMNPV orf92 / 0.694
4hh0 FMNAppA protein / 0.694
3ab1 FADFerredoxin--NADP reductase 1.18.1.2 0.691
5dbj FADFADH2-dependent halogenase PltA / 0.691
1ty9 FMNPhenazine biosynthesis protein PhzG 1.4 0.690
3gfy FMNUncharacterized protein / 0.690
1x0p FADTll0078 protein / 0.687
2bkj FMNNADPH-flavin oxidoreductase / 0.685
4qi7 FADCellobiose dehydrogenase / 0.685
5kbw RBFRiboflavin transporter RibU / 0.684
3w5h FADNADH-cytochrome b5 reductase 3 1.6.2.2 0.683
1jeh FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.682
1oon FMNOxygen-insensitive NAD(P)H nitroreductase / 0.678
1tdn FADL-amino-acid oxidase 1.4.3.2 0.678
5cho FADFlavin reductase / 0.678
1cc2 FADCholesterol oxidase 1.1.3.6 0.677
3nix FADFlavoprotein/dehydrogenase / 0.677
5j4e FMNSensory box protein / 0.676
2wzw FMNNitroreductase NfnB / 0.673
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.672
2isk FNR5,6-dimethylbenzimidazole synthase 1.13.11.79 0.672
2wzv FMNNitroreductase NfnB / 0.672
3mpi FADGlutaryl-CoA dehydrogenase 1.3.99.32 0.672
1u8v FAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase / 0.671
1wsb FMNFlavodoxin / 0.671
4jy2 FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.671
4rhe FMNFlavin prenyltransferase UbiX / 0.671
1ea0 FMNGlutamate synthase [NADPH] large chain 1.4.1.13 0.669
2bgi FADNADPH:ferredoxin reductase / 0.669
4mih FADPyranose 2-oxidase 1.1.3.10 0.668
1djq FMNTrimethylamine dehydrogenase 1.5.8.2 0.667
2igo FADPyranose 2-oxidase / 0.667
3ish FADThioredoxin reductase 1.8.1.9 0.667
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.666
2dvl FADAcyl-CoA dehydrogenase / 0.665
2yqu FADDihydrolipoyl dehydrogenase / 0.665
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.665
1v0j FADUDP-galactopyranose mutase 5.4.99.9 0.664
4ntd FADThioredoxin reductase / 0.664
4i6g FADCryptochrome-2 / 0.663
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.662
2ifa FMNUncharacterized protein / 0.661
3vqr FADPutative oxidoreductase / 0.661
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.660
2zaf FADNitroalkane oxidase 1.7.3.1 0.660
3qzy FADFAD-linked sulfhydryl oxidase / 0.660
5buk FADFADH2-dependent halogenase / 0.660
1cqx FADFlavohemoprotein / 0.659
3pl8 FADPyranose 2-oxidase / 0.659
1f8w FADNADH peroxidase 1.11.1.1 0.658
1kqb FMNOxygen-insensitive NAD(P)H nitroreductase / 0.658
2a1u FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.657
2gj3 FADNitrogen fixation regulatory protein 2.7.13.3 0.657
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.656
1h81 FADPolyamine oxidase 1.5.3.14 0.655
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.655
4hnb FMNLOV protein / 0.654
1zwl FMNNAD(P)H dehydrogenase (quinone) 1.6.5.2 0.653
1icu FMNOxygen-insensitive NAD(P)H nitroreductase / 0.652
2ok8 FADFerredoxin--NADP reductase, apicoplast / 0.651
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.651
3f8d FADNADH oxidase/thioredoxin reductase / 0.651
4qi5 FADCellobiose dehydrogenase / 0.651
1ger FADGlutathione reductase 1.8.1.7 0.650
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.650
3cnj FADCholesterol oxidase 1.1.3.6 0.650
4gdp FADPolyamine oxidase FMS1 / 0.650