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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
3nyc FAD FAD-dependent catabolic D-arginine dehydrogenase DauA

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
3nyc FADFAD-dependent catabolic D-arginine dehydrogenase DauA / 1.668
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 1.648
1ryi FADGlycine oxidase 1.4.3.19 1.010
3axb FADPutative oxidoreductase / 0.996
2rgh FADAlpha-Glycerophosphate Oxidase / 0.979
3vqr FADPutative oxidoreductase / 0.975
1c0l FADD-amino-acid oxidase 1.4.3.3 0.963
4x9n FADUncharacterized protein MG039 homolog / 0.953
2rgo FADAlpha-Glycerophosphate Oxidase / 0.950
1c0k FADD-amino-acid oxidase 1.4.3.3 0.945
1ng3 FADGlycine oxidase 1.4.3.19 0.932
3dme FADPutative conserved exported protein / 0.917
1ng4 FADGlycine oxidase 1.4.3.19 0.910
3if9 FADGlycine oxidase 1.4.3.19 0.908
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.903
3m13 FADMonomeric sarcosine oxidase 1.5.3.1 0.893
4ysh FADGlycine oxidase / 0.888
5hxw FADL-amino acid deaminase / 0.883
3znp FADD-amino-acid oxidase 1.4.3.3 0.877
3gsi FADDimethylglycine oxidase 1.5.3.10 0.863
4x9m FADUncharacterized protein MG039 homolog / 0.852
2qcu FADAerobic glycerol-3-phosphate dehydrogenase 1.1.5.3 0.830
3cuk FADD-amino-acid oxidase 1.4.3.3 0.825
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.824
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.807
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.807
3atq FDAConserved Archaeal protein / 0.806
5i39 FADL-amino acid deaminase / 0.797
1kif FADD-amino-acid oxidase 1.4.3.3 0.795
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.793
2bab FADPutative aminooxidase / 0.789
4xwz FADFructosyl amine:oxygen oxidoreductase / 0.786
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.783
5buk FADFADH2-dependent halogenase / 0.780
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.778
4tm3 FADKtzI / 0.778
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.772
4bk3 FADProbable salicylate monooxygenase / 0.768
4yjd FADD-amino-acid oxidase 1.4.3.3 0.763
3da1 FADGlycerol-3-phosphate dehydrogenase / 0.762
4guu FA9Lysine-specific histone demethylase 1B 1 0.760
4rsl FADFructosyl peptide oxidase / 0.759
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.758
1k0j FADp-hydroxybenzoate hydroxylase / 0.751
2xdo FADTetX family tetracycline inactivation enzyme / 0.750
2yg6 FADPutrescine oxidase / 0.750
4bjz FADProbable salicylate monooxygenase / 0.747
4eer FMNPhototropin-2 2.7.11.1 0.747
4wct FADFructosyl amine:oxygen oxidoreductase / 0.747
4opi FDAConserved Archaeal protein / 0.746
3pl8 FADPyranose 2-oxidase / 0.743
1z6l FADPolyamine oxidase FMS1 / 0.742
4bk2 FADProbable salicylate monooxygenase / 0.742
2y48 FADLysine-specific histone demethylase 1A 1 0.740
3ad9 FADSubunit beta of sarcosine oxidase / 0.740
4k5r FADOxygenase / 0.739
2h94 FADLysine-specific histone demethylase 1A 1 0.738
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.738
2e48 FADD-amino-acid oxidase 1.4.3.3 0.737
3sgl FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.736
1xdi FADNAD(P)H dehydrogenase (quinone) / 0.735
3atr FDAConserved Archaeal protein / 0.735
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.733
2b9w FADPutative aminooxidase / 0.732
3cty FADProbable thioredoxin reductase / 0.731
4cy8 FDA2-hydroxybiphenyl-3-monooxygenase / 0.730
1ve9 FADD-amino-acid oxidase 1.4.3.3 0.727
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.726
2q7v FADThioredoxin reductase / 0.725
4jdr FADDihydrolipoyl dehydrogenase 1.8.1.4 0.725
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.723
4j36 FADKynurenine 3-monooxygenase / 0.723
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.722
4i58 FADCyclohexylamine Oxidase / 0.722
1grh FADGlutathione reductase, mitochondrial 1.8.1.7 0.721
2du8 FADD-amino-acid oxidase 1.4.3.3 0.721
3bi2 FADPolyamine oxidase FMS1 / 0.721
2ign FADPyranose 2-oxidase / 0.720
4hj3 FMNLOV protein / 0.719
4u2l SFDCholesterol oxidase 1.1.3.6 0.718
1kf6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.717
2gqf FADUncharacterized protein HI_0933 / 0.717
3gyj FADCholesterol oxidase 1.1.3.6 0.717
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.716
4c3y FAD3-ketosteroid dehydrogenase / 0.716
1tde FADThioredoxin reductase 1.8.1.9 0.714
3t50 FMNBlue-light-activated histidine kinase 2.7.13.3 0.714
4jnq FDAThioredoxin reductase / 0.714
1lqu FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.713
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.713
4jq9 FADDihydrolipoyl dehydrogenase / 0.713
1feb FADTrypanothione reductase 1.8.1.12 0.712
3all FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.712
4jy2 FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.712
4yac NAIC alpha-dehydrogenase / 0.712
5dbj FADFADH2-dependent halogenase PltA / 0.712
2zbw FADFerredoxin--NADP reductase / 0.711
3lad FADDihydrolipoyl dehydrogenase / 0.711
3lsm SFDPyranose 2-oxidase / 0.711
2wp5 FADTrypanothione reductase / 0.710
3lsi FADPyranose 2-oxidase / 0.710
4dsh FDAUncharacterized protein / 0.709
1fea FADTrypanothione reductase 1.8.1.12 0.707
4hia FMNLOV protein / 0.707
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.706
3rp8 FADFAD-dependent urate hydroxylase / 0.706
3ukf FDAUDP-galactopyranose mutase / 0.706
4c3x FAD3-ketosteroid dehydrogenase / 0.706
5j3w FMNSensory box protein / 0.706
3d72 FADVivid PAS protein VVD / 0.705
2wba FADTrypanothione reductase 1.8.1.12 0.702
1b8s FADCholesterol oxidase 1.1.3.6 0.701
1e1k FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.700
4h2n FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.700
1xpq FADPolyamine oxidase FMS1 / 0.699
4kx6 FADFumarate reductase flavoprotein subunit 1.3.5.4 0.699
1bzl FADTrypanothione reductase 1.8.1.12 0.698
1efv FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.698
1tdk FADL-amino-acid oxidase 1.4.3.2 0.698
3cnj FADCholesterol oxidase 1.1.3.6 0.698
3ept FDAPutative FAD-monooxygenase / 0.698
3utg FDAUDP-galactopyranose mutase / 0.698
1nhs FADNADH peroxidase 1.11.1.1 0.697
2c3d FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.697
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.697
4fk1 FADPutative thioredoxin reductase / 0.697
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.696
3awi FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC 1.5 0.695
3lzx FADFerredoxin--NADP reductase 2 1.18.1.2 0.695
4nte FADDepH / 0.695
4em4 FADCoenzyme A disulfide reductase / 0.694
1trb FADThioredoxin reductase 1.8.1.9 0.693
1yy5 FADPolyamine oxidase FMS1 / 0.693
2eq9 FADDihydrolipoyl dehydrogenase / 0.693
1get FADGlutathione reductase 1.8.1.7 0.692
3dgh FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.692
4tlz FADKtzI / 0.691
1reo FADL-amino-acid oxidase 1.4.3.2 0.690
1tdo FADL-amino-acid oxidase 1.4.3.2 0.690
1yqz FADCoenzyme A disulfide reductase / 0.690
3cnt FADPolyamine oxidase FMS1 / 0.690
4opg FDAConserved Archaeal protein / 0.690
1cl0 FADThioredoxin reductase 1.8.1.9 0.689
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.689
2wow FADTrypanothione reductase / 0.689
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.689
1zk7 FADMercuric reductase 1.16.1.1 0.687
1zy8 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.687
2qa1 FADPgaE / 0.687
3bi5 FADPolyamine oxidase FMS1 / 0.687
1qg0 FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic 1.18.1.2 0.686
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.686
2hko FADLysine-specific histone demethylase 1A 1 0.686
2iw5 FADLysine-specific histone demethylase 1A 1 0.686
4mih FADPyranose 2-oxidase 1.1.3.10 0.686
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.686
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.685
4mok FADPyranose 2-oxidase / 0.684
1tdn FADL-amino-acid oxidase 1.4.3.2 0.683
3cox FADCholesterol oxidase 1.1.3.6 0.683
4at0 FADPossible succinate dehydrogenase / 0.683
1h81 FADPolyamine oxidase 1.5.3.14 0.682
2a1u FADElectron transfer flavoprotein subunit alpha, mitochondrial / 0.682
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.682
1knr FADL-aspartate oxidase 1.4.3.16 0.681
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.681
2nvk FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.681
3k4c FADPyranose 2-oxidase / 0.681
4c5o FADPutative monooxygenase / 0.681
4eqs FADCoenzyme A disulfide reductase / 0.681
4opc FDAConserved Archaeal protein / 0.681
1f8w FADNADH peroxidase 1.11.1.1 0.680
1pkv RBFRiboflavin synthase 2.5.1.9 0.680
2z6c FMNPhototropin-1 2.7.11.1 0.680
3k30 ADPHistamine dehydrogenase / 0.680
4u8k FDAUDP-galactopyranose mutase / 0.680
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.680
5ez7 FADProbable FAD-dependent oxidoreductase PA4991 / 0.680
2gew FADCholesterol oxidase 1.1.3.6 0.679
3gyi FADCholesterol oxidase 1.1.3.6 0.679
3ka7 FADPutative oxidoreductase / 0.679
3sfe FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.679
1f8s FADL-amino-acid oxidase 1.4.3.2 0.678
1nhp FADNADH peroxidase 1.11.1.1 0.678
2tpr FADTrypanothione reductase 1.8.1.12 0.678
2zz0 FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.678
3cnd FADPolyamine oxidase FMS1 / 0.678
4jn9 FADDepH / 0.678
4ntc FADThioredoxin reductase gliT / 0.678
4u2s FDACholesterol oxidase 1.1.3.6 0.677
3dk8 FADGlutathione reductase, mitochondrial 1.8.1.7 0.676
3f8d FADNADH oxidase/thioredoxin reductase / 0.676
3hji FADVivid PAS protein VVD / 0.676
3kve FADL-amino-acid oxidase / 0.676
3lov FADProtoporphyrinogen oxidase / 0.676
4eqr FADCoenzyme A disulfide reductase / 0.676
4u8l FDAUDP-galactopyranose mutase / 0.676
4yv2 S4MSpermidine synthase, putative / 0.676
3a3b RBFLumazine protein / 0.675
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.675
4u2t FADCholesterol oxidase 1.1.3.6 0.675
4xwr FADCholesterol oxidase 1.1.3.6 0.675
1b4v FADCholesterol oxidase 1.1.3.6 0.674
1e1l FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.674
1ju2 FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.674
1k4q FADGlutathione reductase, mitochondrial 1.8.1.7 0.674
3ish FADThioredoxin reductase 1.8.1.9 0.674
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.674
1tdf FADThioredoxin reductase 1.8.1.9 0.672
2bi8 FADUDP-galactopyranose mutase 5.4.99.9 0.672
2ylz FADPhenylacetone monooxygenase 1.14.13.92 0.672
3fbs FADOxidoreductase / 0.672
4eqw FADCoenzyme A disulfide reductase / 0.672
2yg4 FADPutrescine oxidase / 0.671
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.671
4em3 FADCoenzyme A disulfide reductase / 0.671
4gap FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.671
4gur FADLysine-specific histone demethylase 1B 1 0.671
4hhd FMNPhototropin-1 2.7.11.1 0.671
4nwz FADFAD-dependent pyridine nucleotide-disulfide oxidoreductase / 0.671
1fec FADTrypanothione reductase 1.8.1.12 0.670
1gra FADGlutathione reductase, mitochondrial 1.8.1.7 0.670
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.670
3dgz FADThioredoxin reductase 2, mitochondrial 1.8.1.9 0.670
4ech FADPolyamine oxidase FMS1 / 0.670
4gut FADLysine-specific histone demethylase 1B 1 0.670
1qo8 FADFumarate reductase flavoprotein subunit / 0.669
2hqm FADGlutathione reductase 1.8.1.7 0.669
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.669
4b66 FADL-ornithine N(5)-monooxygenase / 0.669
4rek FADCholesterol oxidase 1.1.3.6 0.669
1ty9 FMNPhenazine biosynthesis protein PhzG 1.4 0.668
3cn8 FADPolyamine oxidase FMS1 / 0.668
2oal FADFlavin-dependent tryptophan halogenase RebH 1.14.19.9 0.667
2uxx FAJLysine-specific histone demethylase 1A 1 0.667
1f8r FADL-amino-acid oxidase 1.4.3.2 0.666
2cfy FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.666
2w0h FADTrypanothione reductase / 0.666
3ict FADCoenzyme A disulfide reductase / 0.666
1rsg FADPolyamine oxidase FMS1 / 0.665
3a6q FMNFMN-binding protein / 0.665
5dkk FMNPredicted protein / 0.665
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.664
2z6d FMNPhototropin-2 2.7.11.1 0.664
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.664
4fwe FADLysine-specific histone demethylase 1B 1 0.664
3cgd FADCoenzyme A disulfide reductase / 0.663
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.663
3sfd FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.663
4cbq FADThioredoxin reductase / 0.663
4z44 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.663
1ger FADGlutathione reductase 1.8.1.7 0.662
1nhq FADNADH peroxidase 1.11.1.1 0.662
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.662
3gdp FAD(R)-mandelonitrile lyase 2 4.1.2.10 0.662
4fwf FADLysine-specific histone demethylase 1B 1 0.662
4u8o FDAUDP-galactopyranose mutase / 0.662
1ges FADGlutathione reductase 1.8.1.7 0.661
4hms FMNPhenazine biosynthesis protein PhzG 1.4 0.661
4j2w FADKynurenine 3-monooxygenase / 0.661
4up3 FADThioredoxin reductase / 0.661
4yus FMNFamily 3 adenylate cyclase / 0.661
1gvh FADFlavohemoprotein / 0.660
1zx9 FADMercuric reductase 1.16.1.1 0.660
2r9z FADGlutathione amide reductase / 0.660
1n4u FAECholesterol oxidase 1.1.3.6 0.659
1n4v FADCholesterol oxidase 1.1.3.6 0.659
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.659
4ntd FADThioredoxin reductase / 0.659
4wuj FMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy / 0.659
4xxg FADCholesterol oxidase 1.1.3.6 0.659
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.658
1geu FADGlutathione reductase 1.8.1.7 0.658
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.658
2b9x FADPutative aminooxidase / 0.658
3b6d FAECholesterol oxidase 1.1.3.6 0.658
3ge6 FMNNitroreductase / 0.658
3urh FADDihydrolipoyl dehydrogenase / 0.658
4dsg FADUncharacterized protein / 0.658
1kyv RBF6,7-dimethyl-8-ribityllumazine synthase 2.5.1.78 0.657
1qgy FADFerredoxin--NADP reductase 1.18.1.2 0.657
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.657
4j33 FADKynurenine 3-monooxygenase / 0.657
1n1p FADCholesterol oxidase 1.1.3.6 0.656
1n4w FADCholesterol oxidase 1.1.3.6 0.656
2zzc FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.656
3ntd FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.656
4gcm FADThioredoxin reductase 1.8.1.9 0.656
4qi5 FADCellobiose dehydrogenase / 0.656
2gv8 FADThiol-specific monooxygenase 1.14.13 0.655
3cge FADCoenzyme A disulfide reductase / 0.655
4xbf FADLysine-specific histone demethylase 1A 1 0.655
1gal FADGlucose oxidase 1.1.3.4 0.654
2dw4 FADLysine-specific histone demethylase 1A 1 0.654
4bf9 FMNtRNA-dihydrouridine(16) synthase / 0.654
4u8m FDAUDP-galactopyranose mutase / 0.654
1f3p FADFerredoxin reductase / 0.653
1gre FADGlutathione reductase, mitochondrial 1.8.1.7 0.653
2x3n FADProbable FAD-dependent monooxygenase / 0.653
3int FDAUDP-galactopyranose mutase 5.4.99.9 0.653
4ytn FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.653
2ba9 FADPutative aminooxidase / 0.652
2yg3 FADPutrescine oxidase / 0.652
1joa FADNADH peroxidase 1.11.1.1 0.651
3p9k SAHCaffeic acid O-methyltransferase / 0.651
4a5l FADThioredoxin reductase / 0.651
4h4m 494Gag-Pol polyprotein 2.7.7.49 0.651
1tyt FADTrypanothione reductase 1.8.1.12 0.650
2f5z FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.650
4kpr FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.650
4y9l FADAcyl-CoA dehydrogenase family member 11 / 0.650