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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
4at0 FAD Possible succinate dehydrogenase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
4at0 FADPossible succinate dehydrogenase / 1.501
4c3x FAD3-ketosteroid dehydrogenase / 0.985
4c3y FAD3-ketosteroid dehydrogenase / 0.910
1h81 FADPolyamine oxidase 1.5.3.14 0.823
1knp FADL-aspartate oxidase 1.4.3.16 0.816
1knr FADL-aspartate oxidase 1.4.3.16 0.801
4gur FADLysine-specific histone demethylase 1B 1 0.786
4gut FADLysine-specific histone demethylase 1B 1 0.766
3pl8 FADPyranose 2-oxidase / 0.765
2bab FADPutative aminooxidase / 0.762
1cf3 FADGlucose oxidase 1.1.3.4 0.760
4ysh FADGlycine oxidase / 0.759
1h83 FADPolyamine oxidase 1.5.3.14 0.752
4xbf FADLysine-specific histone demethylase 1A 1 0.752
1c0k FADD-amino-acid oxidase 1.4.3.3 0.749
1c0l FADD-amino-acid oxidase 1.4.3.3 0.746
1qo8 FADFumarate reductase flavoprotein subunit / 0.746
3ka7 FADPutative oxidoreductase / 0.746
4qi4 FADCellobiose dehydrogenase / 0.745
4fwe FADLysine-specific histone demethylase 1B 1 0.744
4qi5 FADCellobiose dehydrogenase / 0.742
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.735
1ryi FADGlycine oxidase 1.4.3.19 0.734
4rsl FADFructosyl peptide oxidase / 0.733
3lsh FADPyranose 2-oxidase / 0.732
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.730
2eq6 FADDihydrolipoyl dehydrogenase / 0.728
2eq7 NADDihydrolipoyl dehydrogenase / 0.728
4hsu FADLysine-specific histone demethylase 1B 1 0.727
2b9y FADPutative aminooxidase / 0.726
3bi5 FADPolyamine oxidase FMS1 / 0.725
3cnd FADPolyamine oxidase FMS1 / 0.724
4d7e FADPutative lysine-N-oxygenase / 0.724
1rsg FADPolyamine oxidase FMS1 / 0.723
3bi2 FADPolyamine oxidase FMS1 / 0.723
4fwj FADLysine-specific histone demethylase 1B 1 0.723
2iw5 FADLysine-specific histone demethylase 1A 1 0.721
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.719
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.719
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.719
3v76 FDAUncharacterized protein / 0.718
2ign FADPyranose 2-oxidase / 0.717
2q7v FADThioredoxin reductase / 0.717
3cty FADProbable thioredoxin reductase / 0.717
4fwf FADLysine-specific histone demethylase 1B 1 0.717
3lsi FADPyranose 2-oxidase / 0.716
3qvr FADGlucose oxidase 1.1.3.4 0.716
2bac FADPutative aminooxidase / 0.715
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.715
2hko FADLysine-specific histone demethylase 1A 1 0.715
4guu FA9Lysine-specific histone demethylase 1B 1 0.715
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.714
3g5s FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.714
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.714
1xdi FADNAD(P)H dehydrogenase (quinone) / 0.713
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.713
3vqr FADPutative oxidoreductase / 0.711
2eq8 FADDihydrolipoyl dehydrogenase / 0.710
3lsm SFDPyranose 2-oxidase / 0.710
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.709
4gus FADLysine-specific histone demethylase 1B 1 0.708
4z24 FADPutative GMC-type oxidoreductase R135 1 0.708
1gal FADGlucose oxidase 1.1.3.4 0.707
2q0l FADThioredoxin reductase 1.8.1.9 0.707
2y48 FADLysine-specific histone demethylase 1A 1 0.705
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.705
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.705
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.704
4cnk FADL-amino acid oxidase / 0.704
4nwz FADFAD-dependent pyridine nucleotide-disulfide oxidoreductase / 0.703
4opi FDAConserved Archaeal protein / 0.703
4wct FADFructosyl amine:oxygen oxidoreductase / 0.703
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.702
2yg6 FADPutrescine oxidase / 0.702
3cnj FADCholesterol oxidase 1.1.3.6 0.702
3gyi FADCholesterol oxidase 1.1.3.6 0.702
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.701
2b9w FADPutative aminooxidase / 0.701
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.701
2uxx FAJLysine-specific histone demethylase 1A 1 0.701
1b8s FADCholesterol oxidase 1.1.3.6 0.700
1bwc FADGlutathione reductase, mitochondrial 1.8.1.7 0.700
1f8r FADL-amino-acid oxidase 1.4.3.2 0.700
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.700
2eq9 FADDihydrolipoyl dehydrogenase / 0.699
2yg3 FADPutrescine oxidase / 0.698
3nlc FADUncharacterized protein / 0.698
3rp8 FADFAD-dependent urate hydroxylase / 0.697
4rek FADCholesterol oxidase 1.1.3.6 0.697
4xwr FADCholesterol oxidase 1.1.3.6 0.697
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.696
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.696
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.696
3axb FADPutative oxidoreductase / 0.696
3k4c FADPyranose 2-oxidase / 0.696
3kpf FADPolyamine oxidase 1.5.3.14 0.696
3rha FDAPutrescine oxidase / 0.696
2b9x FADPutative aminooxidase / 0.695
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.695
4o5q FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.695
5dbj FADFADH2-dependent halogenase PltA / 0.695
1lqu FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.694
3gsi FADDimethylglycine oxidase 1.5.3.10 0.694
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.693
3cox FADCholesterol oxidase 1.1.3.6 0.693
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.693
1e1n FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.692
3dk9 FADGlutathione reductase, mitochondrial 1.8.1.7 0.692
1cl0 FADThioredoxin reductase 1.8.1.9 0.691
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.691
1ng4 FADGlycine oxidase 1.4.3.19 0.691
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.691
2yg4 FADPutrescine oxidase / 0.691
2yg5 FADPutrescine oxidase / 0.691
3cn8 FADPolyamine oxidase FMS1 / 0.691
3gmb FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.691
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.691
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.691
3t37 FADPyridoxine 4-oxidase / 0.691
1gpe FADGlucose oxidase 1.1.3.4 0.690
4ech FADPolyamine oxidase FMS1 / 0.690
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.690
2x8h FADThioredoxin glutathione reductase / 0.689
3qj4 FADRenalase / 0.689
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.688
4jdr FADDihydrolipoyl dehydrogenase 1.8.1.4 0.688
5hxw FADL-amino acid deaminase / 0.688
4yac NAIC alpha-dehydrogenase / 0.687
4u2s FDACholesterol oxidase 1.1.3.6 0.686
3qvp FADGlucose oxidase 1.1.3.4 0.684
4lii FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.684
4ykg FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.684
3k30 ADPHistamine dehydrogenase / 0.683
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.683
4bk3 FADProbable salicylate monooxygenase / 0.683
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.682
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.682
1jeh FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.682
1mxt FAECholesterol oxidase 1.1.3.6 0.682
1n4w FADCholesterol oxidase 1.1.3.6 0.682
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.682
4xxg FADCholesterol oxidase 1.1.3.6 0.682
4ynt FDAGlucose oxidase, putative / 0.682
1f3p FADFerredoxin reductase / 0.681
4hb9 FADUncharacterized protein / 0.681
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.680
2vvl FADMonoamine oxidase N 1.4.3.4 0.680
2whd FADThioredoxin reductase / 0.680
2x8g FADThioredoxin glutathione reductase / 0.680
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.680
2e1m FADL-glutamate oxidase / 0.679
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.679
2rgh FADAlpha-Glycerophosphate Oxidase / 0.679
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.679
3k4n FADPyranose 2-oxidase / 0.679
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.679
3ef6 FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.678
4emw FADCoenzyme A disulfide reductase / 0.678
1n1p FADCholesterol oxidase 1.1.3.6 0.677
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.677
3ean FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.677
3gyj FADCholesterol oxidase 1.1.3.6 0.677
4a5l FADThioredoxin reductase / 0.677
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.677
1b4v FADCholesterol oxidase 1.1.3.6 0.676
1n4v FADCholesterol oxidase 1.1.3.6 0.676
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.676
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.676
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.676
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.676
1ng3 FADGlycine oxidase 1.4.3.19 0.675
2cul FADGidA-related protein / 0.675
3q9t FAYUncharacterized protein / 0.675
2ba9 FADPutative aminooxidase / 0.674
2v6o FADThioredoxin glutathione reductase / 0.674
3bg7 FADPyranose 2-oxidase / 0.674
4gcm FADThioredoxin reductase 1.8.1.9 0.674
4uir FADOleate hydratase 4.2.1.53 0.674
1gv4 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.673
2f5z FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.673
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.673
3sqp FADGlutathione reductase, mitochondrial 1.8.1.7 0.673
4o5u FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.673
5fs9 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.673
2cdu ADPNADH oxidase / 0.672
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.672
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.672
3ad9 FADSubunit beta of sarcosine oxidase / 0.671
3dgz FADThioredoxin reductase 2, mitochondrial 1.8.1.9 0.671
4usr FADMonooxygenase / 0.671
5l3d FADLysine-specific histone demethylase 1A 1 0.671
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.670
2h94 FADLysine-specific histone demethylase 1A 1 0.670
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.670
5j60 FADThioredoxin reductase / 0.670
4dna FADProbable glutathione reductase / 0.669
1grg FADGlutathione reductase, mitochondrial 1.8.1.7 0.668
1n4u FAECholesterol oxidase 1.1.3.6 0.668
4x9n FADUncharacterized protein MG039 homolog / 0.668
4z26 FADPutative GMC-type oxidoreductase R135 1 0.668
3ad9 NADSubunit alpha of sarocosine oxidase / 0.667
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.667
3if9 FADGlycine oxidase 1.4.3.19 0.667
3kkj FADRenalase / 0.667
1ijh FADCholesterol oxidase 1.1.3.6 0.666
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.666
2tpr FADTrypanothione reductase 1.8.1.12 0.666
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.666
2gmj FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.665
2yg7 FADPutrescine oxidase / 0.665
4eqw FADCoenzyme A disulfide reductase / 0.665
2igo FADPyranose 2-oxidase / 0.664
4gdp FADPolyamine oxidase FMS1 / 0.664
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.663
2hqm FADGlutathione reductase 1.8.1.7 0.663
4u2t FADCholesterol oxidase 1.1.3.6 0.663
4yjd FADD-amino-acid oxidase 1.4.3.3 0.663
4ykf FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.663
1f8s FADL-amino-acid oxidase 1.4.3.2 0.662
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.662
3cuk FADD-amino-acid oxidase 1.4.3.3 0.662
2ywl FADThioredoxin reductase related protein / 0.661
3ish FADThioredoxin reductase 1.8.1.9 0.661
3lov FADProtoporphyrinogen oxidase / 0.661
4cnj FADL-amino acid oxidase / 0.661
4k5r FADOxygenase / 0.661
1yy5 FADPolyamine oxidase FMS1 / 0.660
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.659
2jae FADL-amino acid oxidase / 0.659
2wow FADTrypanothione reductase / 0.659
3ics FADCoenzyme A disulfide reductase / 0.659
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.659
2iid FADL-amino-acid oxidase 1.4.3.2 0.658
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.658
2cvj FADThioredoxin reductase related protein / 0.655
3uoy FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.655
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.655
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.654
2du8 FADD-amino-acid oxidase 1.4.3.3 0.654
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.654
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.654
3ukf FDAUDP-galactopyranose mutase / 0.654
4ntd FADThioredoxin reductase / 0.654
3f8d FADNADH oxidase/thioredoxin reductase / 0.653
3fbs FADOxidoreductase / 0.653
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.653
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.653
1xpq FADPolyamine oxidase FMS1 / 0.652
4gr1 FADGlutathione reductase, mitochondrial 1.8.1.7 0.652
4mih FADPyranose 2-oxidase 1.1.3.10 0.652
2gr0 FADFerredoxin reductase / 0.651
2o06 MTASpermidine synthase 2.5.1.16 0.651
4emj FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.651
5buk FADFADH2-dependent halogenase / 0.651
2eq7 FADDihydrolipoyl dehydrogenase / 0.650
2xve FADPutative flavin-containing monooxygenase / 0.650
2yqu FADDihydrolipoyl dehydrogenase / 0.650