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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
3dme FAD Putative conserved exported protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3dme FADPutative conserved exported protein / 1.398
4x9n FADUncharacterized protein MG039 homolog / 1.099
4x9m FADUncharacterized protein MG039 homolog / 1.043
3vqr FADPutative oxidoreductase / 0.954
3gsi FADDimethylglycine oxidase 1.5.3.10 0.936
1ryi FADGlycine oxidase 1.4.3.19 0.934
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.917
2rgh FADAlpha-Glycerophosphate Oxidase / 0.915
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.908
4ysh FADGlycine oxidase / 0.907
5i39 FADL-amino acid deaminase / 0.907
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.895
3axb FADPutative oxidoreductase / 0.883
5hxw FADL-amino acid deaminase / 0.865
3znp FADD-amino-acid oxidase 1.4.3.3 0.855
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.854
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.851
1kif FADD-amino-acid oxidase 1.4.3.3 0.849
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.836
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.823
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.817
1c0k FADD-amino-acid oxidase 1.4.3.3 0.799
1ng4 FADGlycine oxidase 1.4.3.19 0.796
4j33 FADKynurenine 3-monooxygenase / 0.795
1c0l FADD-amino-acid oxidase 1.4.3.3 0.790
3cuk FADD-amino-acid oxidase 1.4.3.3 0.789
2du8 FADD-amino-acid oxidase 1.4.3.3 0.785
2rgo FADAlpha-Glycerophosphate Oxidase / 0.785
3qvr FADGlucose oxidase 1.1.3.4 0.784
4bjz FADProbable salicylate monooxygenase / 0.779
3kve FADL-amino-acid oxidase / 0.770
1cf3 FADGlucose oxidase 1.1.3.4 0.769
2ylz FADPhenylacetone monooxygenase 1.14.13.92 0.767
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.766
4j34 FADKynurenine 3-monooxygenase / 0.765
1gpe FADGlucose oxidase 1.1.3.4 0.764
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.763
3ad9 FADSubunit beta of sarcosine oxidase / 0.759
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.759
3qvp FADGlucose oxidase 1.1.3.4 0.757
1reo FADL-amino-acid oxidase 1.4.3.2 0.754
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.752
3ukf FDAUDP-galactopyranose mutase / 0.751
1tdn FADL-amino-acid oxidase 1.4.3.2 0.750
1f8r FADL-amino-acid oxidase 1.4.3.2 0.748
4yjd FADD-amino-acid oxidase 1.4.3.3 0.747
1f8s FADL-amino-acid oxidase 1.4.3.2 0.746
4bk3 FADProbable salicylate monooxygenase / 0.746
2iid FADL-amino-acid oxidase 1.4.3.2 0.745
3da1 FADGlycerol-3-phosphate dehydrogenase / 0.743
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.742
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.739
4j36 FADKynurenine 3-monooxygenase / 0.738
4k5r FADOxygenase / 0.737
1ng3 FADGlycine oxidase 1.4.3.19 0.736
5j60 FADThioredoxin reductase / 0.736
4rsl FADFructosyl peptide oxidase / 0.735
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.732
3pl8 FADPyranose 2-oxidase / 0.729
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.729
3rp8 FADFAD-dependent urate hydroxylase / 0.728
2jae FADL-amino acid oxidase / 0.727
4z24 FADPutative GMC-type oxidoreductase R135 1 0.726
1gal FADGlucose oxidase 1.1.3.4 0.725
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.725
1tdk FADL-amino-acid oxidase 1.4.3.2 0.725
4opc FDAConserved Archaeal protein / 0.723
3if9 FADGlycine oxidase 1.4.3.19 0.720
1dnc FADGlutathione reductase, mitochondrial 1.8.1.7 0.719
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.719
4eqs FADCoenzyme A disulfide reductase / 0.719
3q9t FAYUncharacterized protein / 0.716
2gqw FADFerredoxin reductase / 0.715
1h81 FADPolyamine oxidase 1.5.3.14 0.714
3cgc FADCoenzyme A disulfide reductase / 0.714
4hsu FADLysine-specific histone demethylase 1B 1 0.714
1knr FADL-aspartate oxidase 1.4.3.16 0.713
2jb1 FADL-amino acid oxidase / 0.713
3t37 FADPyridoxine 4-oxidase / 0.713
4b69 FADL-ornithine N(5)-monooxygenase / 0.713
4z44 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.713
2b9y FADPutative aminooxidase / 0.712
2bac FADPutative aminooxidase / 0.711
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.711
3dk8 FADGlutathione reductase, mitochondrial 1.8.1.7 0.710
4qi5 FADCellobiose dehydrogenase / 0.710
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.710
2bab FADPutative aminooxidase / 0.709
2ign FADPyranose 2-oxidase / 0.709
3cty FADProbable thioredoxin reductase / 0.709
2e1m FADL-glutamate oxidase / 0.705
4fwe FADLysine-specific histone demethylase 1B 1 0.705
5er0 FADUncharacterized NAD(FAD)-dependent dehydrogenase / 0.703
5l3d FADLysine-specific histone demethylase 1A 1 0.703
1tdo FADL-amino-acid oxidase 1.4.3.2 0.702
3ae4 FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.702
3k4c FADPyranose 2-oxidase / 0.702
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.702
3aeb FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.701
3gyj FADCholesterol oxidase 1.1.3.6 0.701
1grg FADGlutathione reductase, mitochondrial 1.8.1.7 0.700
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.700
4gur FADLysine-specific histone demethylase 1B 1 0.699
2b9x FADPutative aminooxidase / 0.697
2v3a FADRubredoxin-NAD(+) reductase 1.18.1.1 0.697
4u2s FDACholesterol oxidase 1.1.3.6 0.697
1rsg FADPolyamine oxidase FMS1 / 0.696
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.696
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.696
3ka7 FADPutative oxidoreductase / 0.696
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.694
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.694
1f3p FADFerredoxin reductase / 0.693
2q7v FADThioredoxin reductase / 0.693
3cnt FADPolyamine oxidase FMS1 / 0.693
4ech FADPolyamine oxidase FMS1 / 0.693
4xbf FADLysine-specific histone demethylase 1A 1 0.693
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.692
4dsh FDAUncharacterized protein / 0.692
3bi2 FADPolyamine oxidase FMS1 / 0.691
4f07 FADStyrene monooxygenase component 2 / 0.691
4h4z FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.691
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.691
3cox FADCholesterol oxidase 1.1.3.6 0.690
3kpf FADPolyamine oxidase 1.5.3.14 0.690
5fs7 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.690
4dsg FADUncharacterized protein / 0.689
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.688
3atq FDAConserved Archaeal protein / 0.688
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.688
4tlz FADKtzI / 0.688
2h94 FADLysine-specific histone demethylase 1A 1 0.687
2jkc FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.687
3dk4 FADGlutathione reductase, mitochondrial 1.8.1.7 0.687
1qo8 FADFumarate reductase flavoprotein subunit / 0.686
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.686
2gew FADCholesterol oxidase 1.1.3.6 0.685
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.685
3lov FADProtoporphyrinogen oxidase / 0.685
4rek FADCholesterol oxidase 1.1.3.6 0.685
1h83 FADPolyamine oxidase 1.5.3.14 0.684
1ogj FADFerredoxin--NADP reductase 1.18.1.2 0.684
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.684
2iw5 FADLysine-specific histone demethylase 1A 1 0.684
2oa1 FADFlavin-dependent tryptophan halogenase RebH 1.14.19.9 0.684
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.684
3cnj FADCholesterol oxidase 1.1.3.6 0.684
3ean FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.684
3gyi FADCholesterol oxidase 1.1.3.6 0.684
4h4r FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.684
1b8s FADCholesterol oxidase 1.1.3.6 0.683
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.683
4fwf FADLysine-specific histone demethylase 1B 1 0.683
4hb9 FADUncharacterized protein / 0.683
3hji FADVivid PAS protein VVD / 0.682
3s5w FADL-ornithine N(5)-monooxygenase / 0.682
4opg FDAConserved Archaeal protein / 0.682
2ar8 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.681
2b9w FADPutative aminooxidase / 0.681
3k4n FADPyranose 2-oxidase / 0.681
4tm4 FDAKtzI / 0.681
2apg FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.680
3f8d FADNADH oxidase/thioredoxin reductase / 0.680
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.680
2gr0 FADFerredoxin reductase / 0.679
3r9u FADThioredoxin reductase / 0.679
4u8m FDAUDP-galactopyranose mutase / 0.679
4z26 FADPutative GMC-type oxidoreductase R135 1 0.679
1grb FADGlutathione reductase, mitochondrial 1.8.1.7 0.678
2y48 FADLysine-specific histone demethylase 1A 1 0.678
3ish FADThioredoxin reductase 1.8.1.9 0.678
4nev FADTrypanothione reductase / 0.678
4o5u FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.678
4u2t FADCholesterol oxidase 1.1.3.6 0.678
3cge FADCoenzyme A disulfide reductase / 0.677
4nwz FADFAD-dependent pyridine nucleotide-disulfide oxidoreductase / 0.677
4opu FDAConserved Archaeal protein / 0.677
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.676
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.676
2jb2 FADL-amino acid oxidase / 0.676
2yg6 FADPutrescine oxidase / 0.676
3cgb FADCoenzyme A disulfide reductase / 0.676
4ykf FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.676
2e48 FADD-amino-acid oxidase 1.4.3.3 0.675
2yg3 FADPutrescine oxidase / 0.675
4gde FDAUDP-galactopyranose mutase / 0.675
4j57 FADThioredoxin reductase 2 1.8.1.9 0.675
4kpr FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.675
4wx1 FDAUDP-galactopyranose mutase / 0.675
3ict FADCoenzyme A disulfide reductase / 0.674
3cgd FADCoenzyme A disulfide reductase / 0.673
4b65 FADL-ornithine N(5)-monooxygenase / 0.672
4eqx FADCoenzyme A disulfide reductase / 0.672
4ynt FDAGlucose oxidase, putative / 0.672
4ocg FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.671
3hjk FADVivid PAS protein VVD / 0.670
3icr FADCoenzyme A disulfide reductase / 0.670
3k7t FAD6-hydroxy-L-nicotine oxidase / 0.670
4gut FADLysine-specific histone demethylase 1B 1 0.670
4aox FADSteroid monooxygenase / 0.669
4xwr FADCholesterol oxidase 1.1.3.6 0.669
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.668
4bk2 FADProbable salicylate monooxygenase / 0.668
1q1r FADPutidaredoxin reductase 1.18.1.5 0.667
1zk7 FADMercuric reductase 1.16.1.1 0.667
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.667
2yvf FADFerredoxin reductase / 0.667
3gd3 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.667
3we0 FADLysine 2-monooxygenase / 0.667
1rz1 FADPhenol 2-hydroxylase component B / 0.666
2x8h FADThioredoxin glutathione reductase / 0.666
3b6d FAECholesterol oxidase 1.1.3.6 0.666
3dk9 FADGlutathione reductase, mitochondrial 1.8.1.7 0.666
3lsh FADPyranose 2-oxidase / 0.666
4cy8 FDA2-hydroxybiphenyl-3-monooxygenase / 0.666
1cbo FADCholesterol oxidase 1.1.3.6 0.665
3cnd FADPolyamine oxidase FMS1 / 0.665
4em3 FADCoenzyme A disulfide reductase / 0.665
4eqr FADCoenzyme A disulfide reductase / 0.665
4gdp FADPolyamine oxidase FMS1 / 0.665
1k0j FADp-hydroxybenzoate hydroxylase / 0.664
2yg7 FADPutrescine oxidase / 0.664
4fwj FADLysine-specific histone demethylase 1B 1 0.664
4h4p FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.664
2rab FADGlutathione amide reductase / 0.663
3pft FMNFlavin reductase / 0.663
4lii FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.663
4opl FDAConserved Archaeal protein / 0.663
2ba9 FADPutative aminooxidase / 0.662
2eq8 FADDihydrolipoyl dehydrogenase / 0.662
3kkj FADRenalase / 0.662
1zx9 FADMercuric reductase 1.16.1.1 0.661
2gr3 FADFerredoxin reductase / 0.661
3gmb FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.661
1z6l FADPolyamine oxidase FMS1 / 0.660
2tmd ADPTrimethylamine dehydrogenase 1.5.8.2 0.660
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.660
3uth FDAUDP-galactopyranose mutase / 0.660
4h4t FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.660
4opi FDAConserved Archaeal protein / 0.660
4tlx FDAKtzI / 0.660
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.660
1ges FADGlutathione reductase 1.8.1.7 0.659
1lqu FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.659
1rz0 FADPhenol 2-hydroxylase component B / 0.659
2uxx FAJLysine-specific histone demethylase 1A 1 0.659
3atr FDAConserved Archaeal protein / 0.659
3dgz FADThioredoxin reductase 2, mitochondrial 1.8.1.9 0.659
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.659
4h4v FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.659
4h4x FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.659
2c3c FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.658
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.658
4guu FA9Lysine-specific histone demethylase 1B 1 0.658
4hj3 FMNLOV protein / 0.658
4c3x FAD3-ketosteroid dehydrogenase / 0.657
4mo2 FADUDP-galactopyranose mutase / 0.657
4yac NAIC alpha-dehydrogenase / 0.657
1tj2 FADBifunctional protein PutA 1.5.5.2 0.656
2nvk FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.656
4u8p FDAUDP-galactopyranose mutase / 0.656
1d7y FADFerredoxin reductase / 0.655
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.655
3lb8 FADPutidaredoxin reductase 1.18.1.5 0.655
3sqp FADGlutathione reductase, mitochondrial 1.8.1.7 0.655
4gus FADLysine-specific histone demethylase 1B 1 0.655
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 0.655
1b4v FADCholesterol oxidase 1.1.3.6 0.654
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.654
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.654
4gcm FADThioredoxin reductase 1.8.1.9 0.654
1e1l FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.653
1h42 FADFerredoxin--NADP reductase 1.18.1.2 0.653
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.653
2qa2 FADPolyketide oxygenase CabE / 0.653
2rc5 FADFerredoxin--NADP reductase / 0.653
2wba FADTrypanothione reductase 1.8.1.12 0.653
3zdn FADMonoamine oxidase N 1.4.3.4 0.653
2j3n FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.652
4u8j FDAUDP-galactopyranose mutase / 0.652
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.651
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.651
3ab1 FADFerredoxin--NADP reductase 1.18.1.2 0.651
3utf FDAUDP-galactopyranose mutase / 0.651
4icy FADPgaE / 0.651
4u8n FDAUDP-galactopyranose mutase / 0.651
1yy5 FADPolyamine oxidase FMS1 / 0.650
2yg5 FADPutrescine oxidase / 0.650
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.650
4u8l FDAUDP-galactopyranose mutase / 0.650
4u8o FDAUDP-galactopyranose mutase / 0.650