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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
3sgl FAD tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 1.303
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 1.181
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.892
3vqr FADPutative oxidoreductase / 0.812
3axb FADPutative oxidoreductase / 0.809
1c0k FADD-amino-acid oxidase 1.4.3.3 0.804
1qo8 FADFumarate reductase flavoprotein subunit / 0.799
2rgh FADAlpha-Glycerophosphate Oxidase / 0.795
2e1m FADL-glutamate oxidase / 0.794
1c0l FADD-amino-acid oxidase 1.4.3.3 0.791
3ad9 FADSubunit beta of sarcosine oxidase / 0.779
3gsi FADDimethylglycine oxidase 1.5.3.10 0.777
4ysh FADGlycine oxidase / 0.770
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.768
4yjd FADD-amino-acid oxidase 1.4.3.3 0.763
4wct FADFructosyl amine:oxygen oxidoreductase / 0.762
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.757
1ryi FADGlycine oxidase 1.4.3.19 0.756
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.755
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.751
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.743
4gut FADLysine-specific histone demethylase 1B 1 0.743
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.736
4gur FADLysine-specific histone demethylase 1B 1 0.736
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.732
4ynt FDAGlucose oxidase, putative / 0.732
2yg3 FADPutrescine oxidase / 0.728
2yg7 FADPutrescine oxidase / 0.728
1kif FADD-amino-acid oxidase 1.4.3.3 0.726
3kve FADL-amino-acid oxidase / 0.725
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.724
2yg6 FADPutrescine oxidase / 0.723
4gus FADLysine-specific histone demethylase 1B 1 0.723
4gdp FADPolyamine oxidase FMS1 / 0.722
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.722
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.721
4cnk FADL-amino acid oxidase / 0.721
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.720
3ka7 FADPutative oxidoreductase / 0.720
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.720
1f8r FADL-amino-acid oxidase 1.4.3.2 0.719
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.719
3dme FADPutative conserved exported protein / 0.719
4at0 FADPossible succinate dehydrogenase / 0.719
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.718
4c3y FAD3-ketosteroid dehydrogenase / 0.718
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.717
4x9n FADUncharacterized protein MG039 homolog / 0.717
4rsl FADFructosyl peptide oxidase / 0.716
2rgo FADAlpha-Glycerophosphate Oxidase / 0.715
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.715
4hsu FADLysine-specific histone demethylase 1B 1 0.711
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.710
2yg5 FADPutrescine oxidase / 0.710
4fwe FADLysine-specific histone demethylase 1B 1 0.710
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.709
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.709
2jb1 FADL-amino acid oxidase / 0.708
4gde FDAUDP-galactopyranose mutase / 0.708
2yg4 FADPutrescine oxidase / 0.707
1f8s FADL-amino-acid oxidase 1.4.3.2 0.705
5j60 FADThioredoxin reductase / 0.705
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.704
3cty FADProbable thioredoxin reductase / 0.703
3cuk FADD-amino-acid oxidase 1.4.3.3 0.701
4i58 FADCyclohexylamine Oxidase / 0.701
4u8j FDAUDP-galactopyranose mutase / 0.699
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.698
3r9u FADThioredoxin reductase / 0.698
3qj4 FADRenalase / 0.697
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.696
3bi5 FADPolyamine oxidase FMS1 / 0.696
3cnd FADPolyamine oxidase FMS1 / 0.696
1tdo FADL-amino-acid oxidase 1.4.3.2 0.695
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.694
1yy5 FADPolyamine oxidase FMS1 / 0.693
2qa1 FADPgaE / 0.693
1ng4 FADGlycine oxidase 1.4.3.19 0.692
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.692
5hxw FADL-amino acid deaminase / 0.692
1reo FADL-amino-acid oxidase 1.4.3.2 0.691
1zk7 FADMercuric reductase 1.16.1.1 0.690
3cgc FADCoenzyme A disulfide reductase / 0.689
3zdn FADMonoamine oxidase N 1.4.3.4 0.689
4dsg FADUncharacterized protein / 0.689
4qi5 FADCellobiose dehydrogenase / 0.688
4u8n FDAUDP-galactopyranose mutase / 0.688
4u8o FDAUDP-galactopyranose mutase / 0.688
1tdk FADL-amino-acid oxidase 1.4.3.2 0.687
3cnt FADPolyamine oxidase FMS1 / 0.687
4guu FA9Lysine-specific histone demethylase 1B 1 0.687
2du8 FADD-amino-acid oxidase 1.4.3.3 0.686
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.686
4bk2 FADProbable salicylate monooxygenase / 0.686
3ukk FDAUDP-galactopyranose mutase / 0.685
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.684
3rha FDAPutrescine oxidase / 0.684
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.683
2y48 FADLysine-specific histone demethylase 1A 1 0.683
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.683
1z6l FADPolyamine oxidase FMS1 / 0.682
2v3a FADRubredoxin-NAD(+) reductase 1.18.1.1 0.682
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.682
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.682
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.681
3gd3 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.681
3ukk FADUDP-galactopyranose mutase / 0.681
1zx9 FADMercuric reductase 1.16.1.1 0.680
4h4q FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.680
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.680
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.679
2jae FADL-amino acid oxidase / 0.679
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.679
3k7t FAD6-hydroxy-L-nicotine oxidase / 0.679
3kkj FADRenalase / 0.679
1knp FADL-aspartate oxidase 1.4.3.16 0.678
1knr FADL-aspartate oxidase 1.4.3.16 0.677
2jb2 FADL-amino acid oxidase / 0.677
2ym1 FADPhenylacetone monooxygenase 1.14.13.92 0.677
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.677
4hb9 FADUncharacterized protein / 0.677
4wx1 FDAUDP-galactopyranose mutase / 0.677
2zbw FADFerredoxin--NADP reductase / 0.676
3bg7 FADPyranose 2-oxidase / 0.676
1cl0 FADThioredoxin reductase 1.8.1.9 0.675
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.675
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.675
1h81 FADPolyamine oxidase 1.5.3.14 0.674
3qvp FADGlucose oxidase 1.1.3.4 0.674
2apg FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.673
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.673
3f8d FADNADH oxidase/thioredoxin reductase / 0.672
3f8p NADNADH oxidase/thioredoxin reductase / 0.672
4c3x FAD3-ketosteroid dehydrogenase / 0.672
4dsh FDAUncharacterized protein / 0.672
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.672
2vvl FADMonoamine oxidase N 1.4.3.4 0.671
3cn8 FADPolyamine oxidase FMS1 / 0.671
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.670
1k0j FADp-hydroxybenzoate hydroxylase / 0.670
1tdn FADL-amino-acid oxidase 1.4.3.2 0.670
2iw5 FADLysine-specific histone demethylase 1A 1 0.670
4d04 FADPhenylacetone monooxygenase 1.14.13.92 0.670
2eq7 FADDihydrolipoyl dehydrogenase / 0.669
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.669
3k30 ADPHistamine dehydrogenase / 0.667
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.667
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.667
1get FADGlutathione reductase 1.8.1.7 0.666
1trb FADThioredoxin reductase 1.8.1.9 0.666
1w4x FADPhenylacetone monooxygenase 1.14.13.92 0.666
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.666
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.664
1tde FADThioredoxin reductase 1.8.1.9 0.663
1tdf FADThioredoxin reductase 1.8.1.9 0.663
2dw4 FADLysine-specific histone demethylase 1A 1 0.663
2hko FADLysine-specific histone demethylase 1A 1 0.663
2iid FADL-amino-acid oxidase 1.4.3.2 0.663
1cjc FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.662
1gpe FADGlucose oxidase 1.1.3.4 0.662
4d03 FADPhenylacetone monooxygenase 1.14.13.92 0.662
4u8i FDAUDP-galactopyranose mutase / 0.662
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.661
4jy2 FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.661
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.660
2xlp FADPutative flavin-containing monooxygenase / 0.660
3fbs FADOxidoreductase / 0.660
5i39 FADL-amino acid deaminase / 0.660
1dnc FADGlutathione reductase, mitochondrial 1.8.1.7 0.659
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.659
1o94 ADPTrimethylamine dehydrogenase 1.5.8.2 0.659
2bac FADPutative aminooxidase / 0.659
3qvr FADGlucose oxidase 1.1.3.4 0.659
4fwj FADLysine-specific histone demethylase 1B 1 0.659
4xbf FADLysine-specific histone demethylase 1A 1 0.659
2wp5 FADTrypanothione reductase / 0.658
3ef6 FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.658
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.658
3uth FDAUDP-galactopyranose mutase / 0.658
1e1l FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.657
2b9y FADPutative aminooxidase / 0.657
4x9m FADUncharacterized protein MG039 homolog / 0.656
1grb FADGlutathione reductase, mitochondrial 1.8.1.7 0.655
2aqj FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.655
2yls FADPhenylacetone monooxygenase 1.14.13.92 0.655
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.655
5buk FADFADH2-dependent halogenase / 0.655
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.654
1gxf FADTrypanothione reductase 1.8.1.12 0.654
1ng3 FADGlycine oxidase 1.4.3.19 0.654
1fea FADTrypanothione reductase 1.8.1.12 0.653
1rsg FADPolyamine oxidase FMS1 / 0.653
2hqm FADGlutathione reductase 1.8.1.7 0.653
3gyj FADCholesterol oxidase 1.1.3.6 0.653
3ish FADThioredoxin reductase 1.8.1.9 0.653
4fwf FADLysine-specific histone demethylase 1B 1 0.653
4opt FDAConserved Archaeal protein / 0.653
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.653
1djn ADPTrimethylamine dehydrogenase 1.5.8.2 0.652
1gal FADGlucose oxidase 1.1.3.4 0.652
1ger FADGlutathione reductase 1.8.1.7 0.652
2ar8 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.652
3utg FDAUDP-galactopyranose mutase / 0.652
4ykf FADAlkyl hydroperoxide reductase subunit F 1.8.1 0.652
5hsa FASAlcohol oxidase 1 1.1.3.13 0.652
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.651
1xpq FADPolyamine oxidase FMS1 / 0.651
2h94 FADLysine-specific histone demethylase 1A 1 0.651
3ukf FDAUDP-galactopyranose mutase / 0.651
4f4q FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.651
4fk1 FADPutative thioredoxin reductase / 0.651
4u8l FDAUDP-galactopyranose mutase / 0.651
5l3d FADLysine-specific histone demethylase 1A 1 0.651
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.650
2c3c FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.650
2cul FADGidA-related protein / 0.650
4ech FADPolyamine oxidase FMS1 / 0.650
4h4z FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.650
5hhf FDAUDP-galactopyranose mutase / 0.650