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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
3pvc 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
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 1.335
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 1.181
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.928
3vqr FADPutative oxidoreductase / 0.877
3axb FADPutative oxidoreductase / 0.843
1c0k FADD-amino-acid oxidase 1.4.3.3 0.838
3gsi FADDimethylglycine oxidase 1.5.3.10 0.831
2e1m FADL-glutamate oxidase / 0.820
1knr FADL-aspartate oxidase 1.4.3.16 0.808
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.807
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.804
4wct FADFructosyl amine:oxygen oxidoreductase / 0.799
2yg5 FADPutrescine oxidase / 0.789
3ad9 FADSubunit beta of sarcosine oxidase / 0.778
3cty FADProbable thioredoxin reductase / 0.777
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.775
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.774
1qo8 FADFumarate reductase flavoprotein subunit / 0.772
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.772
4c3y FAD3-ketosteroid dehydrogenase / 0.768
5c3j FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.768
4yjd FADD-amino-acid oxidase 1.4.3.3 0.767
3dme FADPutative conserved exported protein / 0.766
5i39 FADL-amino acid deaminase / 0.764
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.763
1ryi FADGlycine oxidase 1.4.3.19 0.762
1c0l FADD-amino-acid oxidase 1.4.3.3 0.761
1knp FADL-aspartate oxidase 1.4.3.16 0.761
2rgo FADAlpha-Glycerophosphate Oxidase / 0.760
2iw5 FADLysine-specific histone demethylase 1A 1 0.756
2rgh FADAlpha-Glycerophosphate Oxidase / 0.756
2yg3 FADPutrescine oxidase / 0.750
3cuk FADD-amino-acid oxidase 1.4.3.3 0.750
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.748
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.747
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.745
2yg6 FADPutrescine oxidase / 0.742
4guu FA9Lysine-specific histone demethylase 1B 1 0.742
3cn8 FADPolyamine oxidase FMS1 / 0.740
1kif FADD-amino-acid oxidase 1.4.3.3 0.739
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.739
4ynt FDAGlucose oxidase, putative / 0.739
1rsg FADPolyamine oxidase FMS1 / 0.737
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.736
3k7t FAD6-hydroxy-L-nicotine oxidase / 0.736
1w4x FADPhenylacetone monooxygenase 1.14.13.92 0.735
2yg7 FADPutrescine oxidase / 0.732
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.731
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.731
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.731
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.727
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.727
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.725
4yxd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.723
2ylz FADPhenylacetone monooxygenase 1.14.13.92 0.721
3cgc FADCoenzyme A disulfide reductase / 0.721
3qj4 FADRenalase / 0.721
4gdp FADPolyamine oxidase FMS1 / 0.721
3cgd FADCoenzyme A disulfide reductase / 0.720
4gut FADLysine-specific histone demethylase 1B 1 0.720
5hxw FADL-amino acid deaminase / 0.720
2yg4 FADPutrescine oxidase / 0.719
1zk7 FADMercuric reductase 1.16.1.1 0.718
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.718
4ytn FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.718
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.716
2dw4 FADLysine-specific histone demethylase 1A 1 0.715
4wx1 FDAUDP-galactopyranose mutase / 0.715
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.713
3gwd FADCyclohexanone monooxygenase / 0.713
3ka7 FADPutative oxidoreductase / 0.713
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.711
1reo FADL-amino-acid oxidase 1.4.3.2 0.711
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.709
4fwf FADLysine-specific histone demethylase 1B 1 0.709
4hsu FADLysine-specific histone demethylase 1B 1 0.709
5j60 FADThioredoxin reductase / 0.708
4rsl FADFructosyl peptide oxidase / 0.707
1zx9 FADMercuric reductase 1.16.1.1 0.706
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.706
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.705
3bi5 FADPolyamine oxidase FMS1 / 0.704
3ukl FADUDP-galactopyranose mutase / 0.703
3zdn FADMonoamine oxidase N 1.4.3.4 0.703
2jb1 FADL-amino acid oxidase / 0.702
2y48 FADLysine-specific histone demethylase 1A 1 0.702
1ng3 FADGlycine oxidase 1.4.3.19 0.701
2apg FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.701
2c3c FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.699
2du8 FADD-amino-acid oxidase 1.4.3.3 0.699
2v3a FADRubredoxin-NAD(+) reductase 1.18.1.1 0.699
1yy5 FADPolyamine oxidase FMS1 / 0.698
3lov FADProtoporphyrinogen oxidase / 0.698
2jb2 FADL-amino acid oxidase / 0.696
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.694
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.693
4gus FADLysine-specific histone demethylase 1B 1 0.693
3gd3 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.692
4ysh FADGlycine oxidase / 0.692
1h7w FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.690
3cgb FADCoenzyme A disulfide reductase / 0.690
3utf FDAUDP-galactopyranose mutase / 0.690
1m6i FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.689
3utg FDAUDP-galactopyranose mutase / 0.689
3rha FDAPutrescine oxidase / 0.688
1gal FADGlucose oxidase 1.1.3.4 0.687
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.687
3bi2 FADPolyamine oxidase FMS1 / 0.686
3cnt FADPolyamine oxidase FMS1 / 0.686
4i58 FADCyclohexylamine Oxidase / 0.686
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.685
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.685
4xbf FADLysine-specific histone demethylase 1A 1 0.685
3cge FADCoenzyme A disulfide reductase / 0.684
4u8j FDAUDP-galactopyranose mutase / 0.684
2jae FADL-amino acid oxidase / 0.683
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.682
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.682
1k0j FADp-hydroxybenzoate hydroxylase / 0.680
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.679
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.678
2vvl FADMonoamine oxidase N 1.4.3.4 0.677
3kpk FADSulfide-quinone reductase / 0.677
4hb9 FADUncharacterized protein / 0.677
3f8p NADNADH oxidase/thioredoxin reductase / 0.676
4u8i FDAUDP-galactopyranose mutase / 0.676
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.674
2b9y FADPutative aminooxidase / 0.674
4x9n FADUncharacterized protein MG039 homolog / 0.674
5eb5 FAD(R)-mandelonitrile lyase 1 4.1.2.10 0.674
1gte FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.673
4gde FDAUDP-galactopyranose mutase / 0.673
4gur FADLysine-specific histone demethylase 1B 1 0.673
1grb FADGlutathione reductase, mitochondrial 1.8.1.7 0.672
1o94 ADPTrimethylamine dehydrogenase 1.5.8.2 0.672
3cnd FADPolyamine oxidase FMS1 / 0.672
4b63 FADL-ornithine N(5)-monooxygenase / 0.672
2b9w FADPutative aminooxidase / 0.671
2iid FADL-amino-acid oxidase 1.4.3.2 0.671
4f4q FADDecaprenylphosphoryl-beta-D-ribose oxidase / 0.671
2x3n FADProbable FAD-dependent monooxygenase / 0.670
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.670
4u8m FDAUDP-galactopyranose mutase / 0.670
1gth FADDihydropyrimidine dehydrogenase [NADP(+)] 1.3.1.2 0.669
4c3x FAD3-ketosteroid dehydrogenase / 0.669
1sez FADProtoporphyrinogen oxidase, mitochondrial 1.3.3.4 0.668
2tmd ADPTrimethylamine dehydrogenase 1.5.8.2 0.668
1f8s FADL-amino-acid oxidase 1.4.3.2 0.667
1djn ADPTrimethylamine dehydrogenase 1.5.8.2 0.666
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.666
1xpq FADPolyamine oxidase FMS1 / 0.666
2ar8 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.666
3dk4 FADGlutathione reductase, mitochondrial 1.8.1.7 0.666
1tdn FADL-amino-acid oxidase 1.4.3.2 0.665
3t37 FADPyridoxine 4-oxidase / 0.665
3uth FDAUDP-galactopyranose mutase / 0.665
4dsh FDAUncharacterized protein / 0.665
4z26 FADPutative GMC-type oxidoreductase R135 1 0.665
1ng4 FADGlycine oxidase 1.4.3.19 0.663
2cul FADGidA-related protein / 0.663
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.663
3dk8 FADGlutathione reductase, mitochondrial 1.8.1.7 0.663
4udr FAD5-(hydroxymethyl)furfural oxidase / 0.663
1h83 FADPolyamine oxidase 1.5.3.14 0.662
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.662
4bjz FADProbable salicylate monooxygenase / 0.662
4j33 FADKynurenine 3-monooxygenase / 0.662
1get FADGlutathione reductase 1.8.1.7 0.661
1z6l FADPolyamine oxidase FMS1 / 0.661
3kpf FADPolyamine oxidase 1.5.3.14 0.661
2hko FADLysine-specific histone demethylase 1A 1 0.660
3ukk FDAUDP-galactopyranose mutase / 0.660
4eqs FADCoenzyme A disulfide reductase / 0.660
1h81 FADPolyamine oxidase 1.5.3.14 0.659
1tdk FADL-amino-acid oxidase 1.4.3.2 0.659
2ylt FADPhenylacetone monooxygenase 1.14.13.92 0.659
3ae4 FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.659
3f8r NAPNADH oxidase/thioredoxin reductase / 0.659
4at0 FADPossible succinate dehydrogenase / 0.659
4dsg FADUncharacterized protein / 0.659
4ech FADPolyamine oxidase FMS1 / 0.659
4u8l FDAUDP-galactopyranose mutase / 0.659
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
3pl8 FADPyranose 2-oxidase / 0.658
4bk3 FADProbable salicylate monooxygenase / 0.658
4nwz FADFAD-dependent pyridine nucleotide-disulfide oxidoreductase / 0.658
1k4q FADGlutathione reductase, mitochondrial 1.8.1.7 0.657
2bac FADPutative aminooxidase / 0.657
3kkj FADRenalase / 0.657
4cy8 FDA2-hydroxybiphenyl-3-monooxygenase / 0.657
4ocg FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.657
1geu FADGlutathione reductase 1.8.1.7 0.656
4b64 FADL-ornithine N(5)-monooxygenase / 0.656
4x9m FADUncharacterized protein MG039 homolog / 0.656
4z44 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.656
2aqj FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.655
3k30 ADPHistamine dehydrogenase / 0.655
3nlc FADUncharacterized protein / 0.655
4bv6 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.654
1djq ADPTrimethylamine dehydrogenase 1.5.8.2 0.653
2whd FADThioredoxin reductase / 0.653
3if9 FADGlycine oxidase 1.4.3.19 0.653
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.653
4fwj FADLysine-specific histone demethylase 1B 1 0.653
4u8k FDAUDP-galactopyranose mutase / 0.653
5fs7 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.652
5fs8 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.652
1cl0 FADThioredoxin reductase 1.8.1.9 0.651
1gxf FADTrypanothione reductase 1.8.1.12 0.651
3qvp FADGlucose oxidase 1.1.3.4 0.651
3qvr FADGlucose oxidase 1.1.3.4 0.651
4opi FDAConserved Archaeal protein / 0.651
1cf3 FADGlucose oxidase 1.1.3.4 0.650
1tde FADThioredoxin reductase 1.8.1.9 0.650
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
2h94 FADLysine-specific histone demethylase 1A 1 0.650
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.650
3fbs FADOxidoreductase / 0.650
4jnq FDAThioredoxin reductase / 0.650
4u8n FDAUDP-galactopyranose mutase / 0.650
5er0 FADUncharacterized NAD(FAD)-dependent dehydrogenase / 0.650