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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
2tmd ADP Trimethylamine dehydrogenase 1.5.8.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity
Align
2tmd ADPTrimethylamine dehydrogenase 1.5.8.2 0.908
1djn ADPTrimethylamine dehydrogenase 1.5.8.2 0.899
1o94 ADPTrimethylamine dehydrogenase 1.5.8.2 0.868
1djq ADPTrimethylamine dehydrogenase 1.5.8.2 0.866
4gcm FADThioredoxin reductase 1.8.1.9 0.790
2ylx FADPhenylacetone monooxygenase 1.14.13.92 0.751
2ylr FADPhenylacetone monooxygenase 1.14.13.92 0.749
4j33 FADKynurenine 3-monooxygenase / 0.747
2c3c FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.746
1dnc FADGlutathione reductase, mitochondrial 1.8.1.7 0.743
1y56 ATPUncharacterized protein / 0.743
3lzw FADFerredoxin--NADP reductase 2 1.18.1.2 0.742
1v59 FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.738
4d03 FADPhenylacetone monooxygenase 1.14.13.92 0.738
3gwd FADCyclohexanone monooxygenase / 0.736
1zk7 FADMercuric reductase 1.16.1.1 0.734
2eq6 FADDihydrolipoyl dehydrogenase / 0.734
1zx9 FADMercuric reductase 1.16.1.1 0.733
2hqm FADGlutathione reductase 1.8.1.7 0.733
2q7v FADThioredoxin reductase / 0.732
2yls FADPhenylacetone monooxygenase 1.14.13.92 0.732
3gwf FADCyclohexanone monooxygenase / 0.732
3cge FADCoenzyme A disulfide reductase / 0.730
4icy FADPgaE / 0.730
4j34 FADKynurenine 3-monooxygenase / 0.730
2eq7 FADDihydrolipoyl dehydrogenase / 0.729
1e6e FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.727
1grb FADGlutathione reductase, mitochondrial 1.8.1.7 0.727
2zbw FADFerredoxin--NADP reductase / 0.727
1f3p FADFerredoxin reductase / 0.726
4opd FDAConserved Archaeal protein / 0.726
3djg FADGlutathione reductase, mitochondrial 1.8.1.7 0.725
4opc FDAConserved Archaeal protein / 0.725
1rp0 AHZThiamine thiazole synthase, chloroplastic / 0.723
1gre FADGlutathione reductase, mitochondrial 1.8.1.7 0.721
1ger FADGlutathione reductase 1.8.1.7 0.720
3cty FADProbable thioredoxin reductase / 0.719
3nlc FADUncharacterized protein / 0.719
1gxf FADTrypanothione reductase 1.8.1.12 0.718
3mj4 FADUDP-galactopyranose mutase / 0.718
3oc4 FADOxidoreductase, pyridine nucleotide-disulfide family / 0.718
4h4s FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.718
3r9u FADThioredoxin reductase / 0.714
2f5z FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.713
2yg3 FADPutrescine oxidase / 0.713
3atr FDAConserved Archaeal protein / 0.713
4guu FA9Lysine-specific histone demethylase 1B 1 0.713
4h4q FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.713
4h4y FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.713
1gsn FADGlutathione reductase, mitochondrial 1.8.1.7 0.712
2cul FADGidA-related protein / 0.712
2yvf FADFerredoxin reductase / 0.712
4gut FADLysine-specific histone demethylase 1B 1 0.712
3cgb FADCoenzyme A disulfide reductase / 0.711
3ish FADThioredoxin reductase 1.8.1.9 0.711
3rnm FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.711
4j2w FADKynurenine 3-monooxygenase / 0.711
2yg4 FADPutrescine oxidase / 0.710
3atq FDAConserved Archaeal protein / 0.710
3fpz AHZThiamine thiazole synthase / 0.710
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.710
1e1n FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.709
2cvj FADThioredoxin reductase related protein / 0.709
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.709
3pl8 FADPyranose 2-oxidase / 0.709
4opg FDAConserved Archaeal protein / 0.709
2i0z FADNAD(FAD)-utilizing dehydrogenases / 0.708
1m6i FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.707
2fje FADAdenylylsulfate reductase, subunit A (AprA) / 0.706
3cgd FADCoenzyme A disulfide reductase / 0.706
2bra FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.705
3ic9 FADPutative dihydrolipoamide dehydrogenase / 0.705
2ylw FADPhenylacetone monooxygenase 1.14.13.92 0.704
2qa1 FADPgaE / 0.703
4fwf FADLysine-specific histone demethylase 1B 1 0.703
2yg6 FADPutrescine oxidase / 0.702
3djj FADGlutathione reductase, mitochondrial 1.8.1.7 0.702
3l8k ADPDihydrolipoamide dehydrogenase (PdhD-3) / 0.702
1grg FADGlutathione reductase, mitochondrial 1.8.1.7 0.701
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.701
1grh FADGlutathione reductase, mitochondrial 1.8.1.7 0.700
1jnr FADAdenylylsulfate reductase, subunit A (AprA) / 0.700
3f8r NAPNADH oxidase/thioredoxin reductase / 0.700
4jnq FDAThioredoxin reductase / 0.700
2bry FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.699
2gr1 FADFerredoxin reductase / 0.699
2yg5 FADPutrescine oxidase / 0.699
2yqu FADDihydrolipoyl dehydrogenase / 0.699
3bg7 FADPyranose 2-oxidase / 0.699
3f8p NADNADH oxidase/thioredoxin reductase / 0.699
3vqr FADPutative oxidoreductase / 0.699
1rsg FADPolyamine oxidase FMS1 / 0.698
2ylt FADPhenylacetone monooxygenase 1.14.13.92 0.698
1qo8 FADFumarate reductase flavoprotein subunit / 0.697
4h4w FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.697
4jdr FADDihydrolipoyl dehydrogenase 1.8.1.4 0.697
4opi FDAConserved Archaeal protein / 0.697
1d7y FADFerredoxin reductase / 0.696
2gv8 FADThiol-specific monooxygenase 1.14.13 0.696
3ef6 FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.696
4cy8 FDA2-hydroxybiphenyl-3-monooxygenase / 0.696
4k2x FADPolyketide oxygenase/hydroxylase / 0.696
2gqw FADFerredoxin reductase / 0.695
3urh FADDihydrolipoyl dehydrogenase / 0.695
4h4r FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.695
4h4t FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.695
1d4c FADFumarate reductase flavoprotein subunit 1.3.5.4 0.694
1tdf FADThioredoxin reductase 1.8.1.9 0.694
2c7g FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.694
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.694
2v3a FADRubredoxin-NAD(+) reductase 1.18.1.1 0.694
3g5q FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.694
3lsi FADPyranose 2-oxidase / 0.694
3rha FDAPutrescine oxidase / 0.694
1geu FADGlutathione reductase 1.8.1.7 0.693
1ps9 FAD2,4-dienoyl-CoA reductase 1.3.1.34 0.693
2wba FADTrypanothione reductase 1.8.1.12 0.693
3ada NADSubunit alpha of sarocosine oxidase / 0.693
4h50 FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.693
5dbj FADFADH2-dependent halogenase PltA / 0.693
5l3d FADLysine-specific histone demethylase 1A 1 0.693
1pdh FASp-hydroxybenzoate hydroxylase / 0.692
3dk4 FADGlutathione reductase, mitochondrial 1.8.1.7 0.692
3m12 FADMonomeric sarcosine oxidase 1.5.3.1 0.692
3sz0 FADSulfide-quinone reductase / 0.692
4fwe FADLysine-specific histone demethylase 1B 1 0.692
3k30 ADPHistamine dehydrogenase / 0.691
3uoy FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.691
4h4v FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.691
1bwc FADGlutathione reductase, mitochondrial 1.8.1.7 0.690
2fjd SFDAdenylylsulfate reductase, subunit A (AprA) / 0.690
2gr0 FADFerredoxin reductase / 0.690
2gr3 FADFerredoxin reductase / 0.690
3uoz FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.690
4h4x FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.690
4nzh FADL-ornithine N(5)-monooxygenase / 0.690
1f8r FADL-amino-acid oxidase 1.4.3.2 0.689
1fec FADTrypanothione reductase 1.8.1.12 0.689
1lqu FADNADPH-ferredoxin reductase FprA 1.18.1.2 0.689
2qa2 FADPolyketide oxygenase CabE / 0.689
2wow FADTrypanothione reductase / 0.689
5hxw FADL-amino acid deaminase / 0.689
1d7l RFLp-hydroxybenzoate hydroxylase / 0.688
2iid FADL-amino-acid oxidase 1.4.3.2 0.688
3dk8 FADGlutathione reductase, mitochondrial 1.8.1.7 0.688
1tde FADThioredoxin reductase 1.8.1.9 0.687
2eq8 FADDihydrolipoyl dehydrogenase / 0.687
3cgc FADCoenzyme A disulfide reductase / 0.687
3qj4 FADRenalase / 0.687
1cl0 FADThioredoxin reductase 1.8.1.9 0.686
1e1m FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.686
1gra FADGlutathione reductase, mitochondrial 1.8.1.7 0.686
1zmd FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.686
1cjc FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.685
2fjb SFDAdenylylsulfate reductase, subunit A (AprA) / 0.685
2q0l FADThioredoxin reductase 1.8.1.9 0.685
2tpr FADTrypanothione reductase 1.8.1.12 0.685
3grs FADGlutathione reductase, mitochondrial 1.8.1.7 0.685
3int FDAUDP-galactopyranose mutase 5.4.99.9 0.685
1k4q FADGlutathione reductase, mitochondrial 1.8.1.7 0.684
2hko FADLysine-specific histone demethylase 1A 1 0.684
3ihg FADAklavinone 12-hydroxylase RdmE / 0.684
3lzx FADFerredoxin--NADP reductase 2 1.18.1.2 0.684
3uov FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.684
1trb FADThioredoxin reductase 1.8.1.9 0.683
2gmh FADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial 1.5.5.1 0.683
3dk9 FADGlutathione reductase, mitochondrial 1.8.1.7 0.683
1ges FADGlutathione reductase 1.8.1.7 0.682
3lsh FADPyranose 2-oxidase / 0.682
3m0o FADMonomeric sarcosine oxidase 1.5.3.1 0.682
1d4d FADFumarate reductase flavoprotein subunit 1.3.5.4 0.681
1e1k FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.681
3gsi FADDimethylglycine oxidase 1.5.3.10 0.681
4fk1 FADPutative thioredoxin reductase / 0.681
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.680
2xvf FADPutative flavin-containing monooxygenase / 0.680
3ad9 NADSubunit alpha of sarocosine oxidase / 0.680
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.680
4j36 FADKynurenine 3-monooxygenase / 0.680
4dsg FADUncharacterized protein / 0.679
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.679
2eq9 FADDihydrolipoyl dehydrogenase / 0.678
4bur FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.678
4ntc FADThioredoxin reductase gliT / 0.678
4udq FAD5-(hydroxymethyl)furfural oxidase / 0.678
5buk FADFADH2-dependent halogenase / 0.678
1e1l FADNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.677
1k0j FADp-hydroxybenzoate hydroxylase / 0.677
2iw5 FADLysine-specific histone demethylase 1A 1 0.677
2yg7 FADPutrescine oxidase / 0.677
3ab1 FADFerredoxin--NADP reductase 1.18.1.2 0.677
3f8d FADNADH oxidase/thioredoxin reductase / 0.677
3lb8 FADPutidaredoxin reductase 1.18.1.5 0.677
1q1r FADPutidaredoxin reductase 1.18.1.5 0.676
2q0k FADThioredoxin reductase 1.8.1.9 0.676
4fwj FADLysine-specific histone demethylase 1B 1 0.676
4fx9 FADCoenzyme A disulfide reductase 1.8.1.14 0.676
2rab FADGlutathione amide reductase / 0.675
2rgh FADAlpha-Glycerophosphate Oxidase / 0.675
3jsk AHZThiamine thiazole synthase / 0.675
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.675
3ute FADUDP-galactopyranose mutase / 0.675
2fja FADAdenylylsulfate reductase, subunit A (AprA) / 0.674
4aox FADSteroid monooxygenase / 0.674
4bv6 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.674
1bzl FADTrypanothione reductase 1.8.1.12 0.673
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.673
4h4u FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.673
1feb FADTrypanothione reductase 1.8.1.12 0.672
3kkj FADRenalase / 0.672
3kpk FADSulfide-quinone reductase / 0.672
3t2k FADSulfide-quinone reductase / 0.672
3up5 FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.672
4gr1 FADGlutathione reductase, mitochondrial 1.8.1.7 0.672
2whd FADThioredoxin reductase / 0.671
3dgz FADThioredoxin reductase 2, mitochondrial 1.8.1.9 0.671
3t37 FADPyridoxine 4-oxidase / 0.671
4h4z FADBiphenyl dioxygenase ferredoxin reductase subunit / 0.671
1k0l FADp-hydroxybenzoate hydroxylase / 0.670
3klj FADNADH-rubredoxin oxidoreductase 1.18.1.1 0.670
4gus FADLysine-specific histone demethylase 1B 1 0.670
4lii FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.670
2c3d FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.669
2x8g FADThioredoxin glutathione reductase / 0.669
3g5s FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.669
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.669
4gur FADLysine-specific histone demethylase 1B 1 0.669
4jq9 FADDihydrolipoyl dehydrogenase / 0.669
3kve FADL-amino-acid oxidase / 0.668
3pvc FADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.668
4ap1 FADSteroid monooxygenase / 0.668
4nev FADTrypanothione reductase / 0.667
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.666
2jb1 FADL-amino acid oxidase / 0.666
4hb9 FADUncharacterized protein / 0.666
4j57 FADThioredoxin reductase 2 1.8.1.9 0.666
4k5r FADOxygenase / 0.666
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.665
1lpf FADDihydrolipoyl dehydrogenase 1.8.1.4 0.664
4bjz FADProbable salicylate monooxygenase / 0.664
1get FADGlutathione reductase 1.8.1.7 0.663
1h83 FADPolyamine oxidase 1.5.3.14 0.663
2eq7 NADDihydrolipoyl dehydrogenase / 0.663
3ad9 FADSubunit beta of sarcosine oxidase / 0.663
3cnt FADPolyamine oxidase FMS1 / 0.663
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.663
4ap3 FADSteroid monooxygenase / 0.663
4b69 FADL-ornithine N(5)-monooxygenase / 0.663
1ebd FADDihydrolipoyl dehydrogenase 1.8.1.4 0.662
2xve FADPutative flavin-containing monooxygenase / 0.662
2ym1 FADPhenylacetone monooxygenase 1.14.13.92 0.662
4b64 FADL-ornithine N(5)-monooxygenase / 0.662
4bk3 FADProbable salicylate monooxygenase / 0.662
5c2t FADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial / 0.662
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.661
3t2y FADSulfide-quinone reductase / 0.661
4b63 FADL-ornithine N(5)-monooxygenase / 0.661
4i58 FADCyclohexylamine Oxidase / 0.661
2x8h FADThioredoxin glutathione reductase / 0.660
2yr5 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.660
3dme FADPutative conserved exported protein / 0.660
4hsu FADLysine-specific histone demethylase 1B 1 0.660
4la1 FADThioredoxin glutathione reductase / 0.660
5hhf FDAUDP-galactopyranose mutase / 0.660
1jeh FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.659
2igo FADPyranose 2-oxidase / 0.659
2rgj FADFlavin-containing monooxygenase / 0.659
4m52 FADDihydrolipoyl dehydrogenase 1.8.1.4 0.659
2apg FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.658
3ka7 FADPutative oxidoreductase / 0.658
4emj FADToluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component 1.18.1.3 0.658
4tm1 FDAKtzI / 0.658
5cku FADL-ornithine N(5)-monooxygenase / 0.658
5eb5 FAD(R)-mandelonitrile lyase 1 4.1.2.10 0.658
1v0j FADUDP-galactopyranose mutase 5.4.99.9 0.657
4nte FADDepH / 0.657
4z43 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.657
5br7 FADUDP-galactopyranose mutase / 0.657
1cbo FADCholesterol oxidase 1.1.3.6 0.656
3kpf FADPolyamine oxidase 1.5.3.14 0.656
5fs9 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.656
2du8 FADD-amino-acid oxidase 1.4.3.3 0.655
3p9u FADTetX family tetracycline inactivation enzyme / 0.655
3ukf FDAUDP-galactopyranose mutase / 0.655
3up4 FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.655
5fs7 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.655
1c0k FADD-amino-acid oxidase 1.4.3.3 0.654
1cc2 FADCholesterol oxidase 1.1.3.6 0.654
1gv4 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.654
1w4x FADPhenylacetone monooxygenase 1.14.13.92 0.654
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.654
2ar8 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.654
3cnj FADCholesterol oxidase 1.1.3.6 0.654
3nix FADFlavoprotein/dehydrogenase / 0.654
4ynt FDAGlucose oxidase, putative / 0.654
4z44 FADFlavin-dependent tryptophan halogenase PrnA 1.14.19.9 0.654
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.653
3cn8 FADPolyamine oxidase FMS1 / 0.653
3cox FADCholesterol oxidase 1.1.3.6 0.653
3ean FADThioredoxin reductase 1, cytoplasmic 1.8.1.9 0.653
4em4 FADCoenzyme A disulfide reductase / 0.653
2jk6 FADTrypanothione reductase / 0.652
1ng4 FADGlycine oxidase 1.4.3.19 0.651
1yqz FADCoenzyme A disulfide reductase / 0.651
4aos FADSteroid monooxygenase / 0.651
4yac NAIC alpha-dehydrogenase / 0.651
1b8s FADCholesterol oxidase 1.1.3.6 0.650
1mok FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.650
3axb FADPutative oxidoreductase / 0.650
3dh9 FADThioredoxin reductase 1, mitochondrial 1.8.1.9 0.650
4u2l SFDCholesterol oxidase 1.1.3.6 0.650
4usr FADMonooxygenase / 0.650
4z24 FADPutative GMC-type oxidoreductase R135 1 0.650
5fs6 FADApoptosis-inducing factor 1, mitochondrial 1.1.1 0.650