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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
4yjd FAD D-amino-acid oxidase 1.4.3.3

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4yjd FADD-amino-acid oxidase 1.4.3.3 1.512
1kif FADD-amino-acid oxidase 1.4.3.3 1.359
2du8 FADD-amino-acid oxidase 1.4.3.3 1.265
1ve9 FADD-amino-acid oxidase 1.4.3.3 1.163
3znp FADD-amino-acid oxidase 1.4.3.3 1.127
3cuk FADD-amino-acid oxidase 1.4.3.3 1.098
1c0l FADD-amino-acid oxidase 1.4.3.3 1.053
1c0k FADD-amino-acid oxidase 1.4.3.3 1.010
1ryi FADGlycine oxidase 1.4.3.19 0.961
1ng3 FADGlycine oxidase 1.4.3.19 0.924
4ysh FADGlycine oxidase / 0.899
3axb FADPutative oxidoreductase / 0.884
3vqr FADPutative oxidoreductase / 0.876
1ng4 FADGlycine oxidase 1.4.3.19 0.866
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.864
2e48 FADD-amino-acid oxidase 1.4.3.3 0.862
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.843
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.839
5hxw FADL-amino acid deaminase / 0.835
2rgh FADAlpha-Glycerophosphate Oxidase / 0.827
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.818
3gsi FADDimethylglycine oxidase 1.5.3.10 0.810
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.809
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.809
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.807
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.806
2ar8 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.804
4x9m FADUncharacterized protein MG039 homolog / 0.804
3ae4 FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.796
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.792
4x9n FADUncharacterized protein MG039 homolog / 0.791
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.788
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.788
4wct FADFructosyl amine:oxygen oxidoreductase / 0.787
3if9 FADGlycine oxidase 1.4.3.19 0.784
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.783
3aeb FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.780
3ad9 FADSubunit beta of sarcosine oxidase / 0.775
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.767
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.763
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.763
4opi FDAConserved Archaeal protein / 0.762
1grb FADGlutathione reductase, mitochondrial 1.8.1.7 0.755
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.755
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.752
4opc FDAConserved Archaeal protein / 0.750
4opd FDAConserved Archaeal protein / 0.749
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.749
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.747
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.747
3dme FADPutative conserved exported protein / 0.747
4bk2 FADProbable salicylate monooxygenase / 0.747
4c3y FAD3-ketosteroid dehydrogenase / 0.746
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.745
3atq FDAConserved Archaeal protein / 0.745
2c3c FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.744
4opt FDAConserved Archaeal protein / 0.739
1grg FADGlutathione reductase, mitochondrial 1.8.1.7 0.737
3rp8 FADFAD-dependent urate hydroxylase / 0.736
4j34 FADKynurenine 3-monooxygenase / 0.734
5i39 FADL-amino acid deaminase / 0.734
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.732
4bjz FADProbable salicylate monooxygenase / 0.732
1knr FADL-aspartate oxidase 1.4.3.16 0.731
4ytn FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.729
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.728
4opl FDAConserved Archaeal protein / 0.728
2y48 FADLysine-specific histone demethylase 1A 1 0.723
4nte FADDepH / 0.723
1knp FADL-aspartate oxidase 1.4.3.16 0.720
4c3x FAD3-ketosteroid dehydrogenase / 0.720
1gre FADGlutathione reductase, mitochondrial 1.8.1.7 0.719
3k4n FADPyranose 2-oxidase / 0.718
4rsl FADFructosyl peptide oxidase / 0.718
3dk8 FADGlutathione reductase, mitochondrial 1.8.1.7 0.716
1gsn FADGlutathione reductase, mitochondrial 1.8.1.7 0.714
1zx9 FADMercuric reductase 1.16.1.1 0.714
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.714
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.713
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.713
3lsi FADPyranose 2-oxidase / 0.713
1xdi FADNAD(P)H dehydrogenase (quinone) / 0.711
3atr FDAConserved Archaeal protein / 0.711
2v3a FADRubredoxin-NAD(+) reductase 1.18.1.1 0.710
2rgo FADAlpha-Glycerophosphate Oxidase / 0.709
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.709
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.708
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.708
1get FADGlutathione reductase 1.8.1.7 0.707
1rsg FADPolyamine oxidase FMS1 / 0.707
4opg FDAConserved Archaeal protein / 0.706
1qo8 FADFumarate reductase flavoprotein subunit / 0.704
1trb FADThioredoxin reductase 1.8.1.9 0.704
4gr1 FADGlutathione reductase, mitochondrial 1.8.1.7 0.704
1tde FADThioredoxin reductase 1.8.1.9 0.702
3kpf FADPolyamine oxidase 1.5.3.14 0.702
4j33 FADKynurenine 3-monooxygenase / 0.701
1dnc FADGlutathione reductase, mitochondrial 1.8.1.7 0.699
4u8k FDAUDP-galactopyranose mutase / 0.699
1geu FADGlutathione reductase 1.8.1.7 0.698
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.698
3lsh FADPyranose 2-oxidase / 0.696
1bwc FADGlutathione reductase, mitochondrial 1.8.1.7 0.694
4k5r FADOxygenase / 0.693
4mih FADPyranose 2-oxidase 1.1.3.10 0.693
2nvk FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.692
2uxx FAJLysine-specific histone demethylase 1A 1 0.692
4qi5 FADCellobiose dehydrogenase / 0.692
2dw4 FADLysine-specific histone demethylase 1A 1 0.691
3ab1 FADFerredoxin--NADP reductase 1.18.1.2 0.691
3fbs FADOxidoreductase / 0.691
4hsu FADLysine-specific histone demethylase 1B 1 0.691
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.690
4z44 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.690
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.688
4y9d NAIC alpha-dehydrogenase / 0.688
1tdf FADThioredoxin reductase 1.8.1.9 0.687
4j57 FADThioredoxin reductase 2 1.8.1.9 0.687
4ynt FDAGlucose oxidase, putative / 0.687
4cnk FADL-amino acid oxidase / 0.686
4ntc FADThioredoxin reductase gliT / 0.686
3uoy FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.685
2c3d FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.684
1b4v FADCholesterol oxidase 1.1.3.6 0.683
3v76 FDAUncharacterized protein / 0.682
4xxg FADCholesterol oxidase 1.1.3.6 0.682
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.681
1k4q FADGlutathione reductase, mitochondrial 1.8.1.7 0.680
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.680
5er0 FADUncharacterized NAD(FAD)-dependent dehydrogenase / 0.680
2bac FADPutative aminooxidase / 0.679
3grs FADGlutathione reductase, mitochondrial 1.8.1.7 0.679
3k30 ADPHistamine dehydrogenase / 0.679
3pl8 FADPyranose 2-oxidase / 0.679
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.678
2x8h FADThioredoxin glutathione reductase / 0.678
4b1b FADThioredoxin reductase 1.8.1.9 0.678
5fs8 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.678
1mxt FAECholesterol oxidase 1.1.3.6 0.677
1n1p FADCholesterol oxidase 1.1.3.6 0.677
1tdk FADL-amino-acid oxidase 1.4.3.2 0.677
3uth FDAUDP-galactopyranose mutase / 0.677
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.676
3f8p NADNADH oxidase/thioredoxin reductase / 0.676
1z6l FADPolyamine oxidase FMS1 / 0.675
4gdp FADPolyamine oxidase FMS1 / 0.675
4ntd FADThioredoxin reductase / 0.675
1cbo FADCholesterol oxidase 1.1.3.6 0.674
1nhq FADNADH peroxidase 1.11.1.1 0.674
2gew FADCholesterol oxidase 1.1.3.6 0.674
2iw5 FADLysine-specific histone demethylase 1A 1 0.674
3ka7 FADPutative oxidoreductase / 0.674
4mok FADPyranose 2-oxidase / 0.674
4o5u FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.674
4opu FDAConserved Archaeal protein / 0.674
3cox FADCholesterol oxidase 1.1.3.6 0.673
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.673
3lzx FADFerredoxin--NADP reductase 2 1.18.1.2 0.673
4guu FA9Lysine-specific histone demethylase 1B 1 0.672
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.671
4d7e FADPutative lysine-N-oxygenase / 0.671
4j2w FADKynurenine 3-monooxygenase / 0.671
5buk FADFADH2-dependent halogenase / 0.671
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.670
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.670
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.670
2zzc FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.670
3f8d FADNADH oxidase/thioredoxin reductase / 0.670
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.670
2gr3 FADFerredoxin reductase / 0.669
2jae FADL-amino acid oxidase / 0.669
2yg4 FADPutrescine oxidase / 0.669
2jkc FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.668
3cnd FADPolyamine oxidase FMS1 / 0.668
5fs7 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.668
1fl2 FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.667
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.667
4j36 FADKynurenine 3-monooxygenase / 0.667
4la1 FADThioredoxin glutathione reductase / 0.667
1tdn FADL-amino-acid oxidase 1.4.3.2 0.665
2v6o FADThioredoxin glutathione reductase / 0.665
2wba FADTrypanothione reductase 1.8.1.12 0.665
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.665
3klj FADNADH-rubredoxin oxidoreductase 1.18.1.1 0.665
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.665
5hsa FASAlcohol oxidase 1 1.1.3.13 0.665
1h6v FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.664
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.664
5l3d FADLysine-specific histone demethylase 1A 1 0.664
1h51 FMNPentaerythritol tetranitrate reductase / 0.663
3ef6 FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.663
4at0 FADPossible succinate dehydrogenase / 0.663
4gus FADLysine-specific histone demethylase 1B 1 0.663
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.662
3lxd FADFAD-dependent pyridine nucleotide-disulfide oxidoreductase / 0.662
3we0 FADLysine 2-monooxygenase / 0.662
4xgi NADGlutamate dehydrogenase / 0.662
1f8r FADL-amino-acid oxidase 1.4.3.2 0.661
1ijh FADCholesterol oxidase 1.1.3.6 0.661
1n4w FADCholesterol oxidase 1.1.3.6 0.661
3cnj FADCholesterol oxidase 1.1.3.6 0.661
3lad FADDihydrolipoyl dehydrogenase / 0.661
3uoz FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.661
4ocg FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.661
1n4u FAECholesterol oxidase 1.1.3.6 0.660
1tdo FADL-amino-acid oxidase 1.4.3.2 0.660
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.660
4up3 FADThioredoxin reductase / 0.660
1h83 FADPolyamine oxidase 1.5.3.14 0.659
1reo FADL-amino-acid oxidase 1.4.3.2 0.659
2npx FADNADH peroxidase 1.11.1.1 0.659
3f8r NAPNADH oxidase/thioredoxin reductase / 0.659
3kyb FADUDP-galactopyranose mutase 5.4.99.9 0.659
4u2t FADCholesterol oxidase 1.1.3.6 0.659
2iid FADL-amino-acid oxidase 1.4.3.2 0.658
3gyj FADCholesterol oxidase 1.1.3.6 0.658
4kpr FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.658
1n4v FADCholesterol oxidase 1.1.3.6 0.657
3gyi FADCholesterol oxidase 1.1.3.6 0.657
4a65 FADThioredoxin reductase / 0.657
4gap FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.657
4o5q FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.657
1f8s FADL-amino-acid oxidase 1.4.3.2 0.656
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.656
3b6d FAECholesterol oxidase 1.1.3.6 0.656
4cnj FADL-amino acid oxidase / 0.656
4fwf FADLysine-specific histone demethylase 1B 1 0.656
4xbf FADLysine-specific histone demethylase 1A 1 0.656
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.655
1grh FADGlutathione reductase, mitochondrial 1.8.1.7 0.655
3sju NDPKeto reductase / 0.655
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.655
4i58 FADCyclohexylamine Oxidase / 0.655
1npx FADNADH peroxidase 1.11.1.1 0.654
3cge FADCoenzyme A disulfide reductase / 0.654
3hgo FMN12-oxophytodienoate reductase 3 1.3.1.42 0.654
2g37 FADProline dehydrogenase / 0.653
3wv8 ATPHmd co-occurring protein HcgE / 0.653
4d03 FADPhenylacetone monooxygenase 1.14.13.92 0.653
1nhs FADNADH peroxidase 1.11.1.1 0.652
1sez FADProtoporphyrinogen oxidase, mitochondrial 1.3.3.4 0.652
3cn8 FADPolyamine oxidase FMS1 / 0.652
1nhp FADNADH peroxidase 1.11.1.1 0.651
1sbz FMNProbable UbiX-like flavin prenyltransferase / 0.651
2hfo FMNActivator of photopigment and puc expression / 0.651
2yvj FADFerredoxin reductase / 0.651
3p67 FMNPentaerythritol tetranitrate reductase / 0.651
3ukl FADUDP-galactopyranose mutase / 0.651
1h63 FMNPentaerythritol tetranitrate reductase / 0.650
2igo FADPyranose 2-oxidase / 0.650
3bi2 FADPolyamine oxidase FMS1 / 0.650
3dk4 FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
3k4c FADPyranose 2-oxidase / 0.650
4ykf FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.650