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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
4pyo SAH Catechol O-methyltransferase 2.1.1.6

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.914
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.874
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.858
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.803
4oa5 SAHO-methyltransferase family protein / 0.803
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.780
3duw SAHO-methyltransferase, putative / 0.743
2hnk SAHSAM-dependent O-methyltransferase / 0.730
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.716
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.713
1yf3 SAHDNA adenine methylase / 0.712
3c3y SAHO-methyltransferase / 0.710
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.709
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.708
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.708
3tr6 SAHO-methyltransferase / 0.705
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.704
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.704
1skm SAHModification methylase HhaI 2.1.1.37 0.703
2ih2 NEAModification methylase TaqI 2.1.1.72 0.702
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.702
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.701
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.701
5je4 SAHMethyl transferase / 0.701
4b69 FADL-ornithine N(5)-monooxygenase / 0.700
4c04 SFGProtein arginine N-methyltransferase 6 / 0.699
5bxy SAHPutative RNA methylase family UPF0020 / 0.699
2c7q SAHModification methylase HhaI 2.1.1.37 0.698
1cbo FADCholesterol oxidase 1.1.3.6 0.697
2uyh SAHModification methylase HhaI 2.1.1.37 0.697
4nzh FADL-ornithine N(5)-monooxygenase / 0.697
10mh SAHModification methylase HhaI 2.1.1.37 0.696
3ldf SAHUncharacterized protein / 0.696
4nec SAHPutative SAM-dependent methyltransferase / 0.696
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.695
3lcc SAHThiocyanate methyltransferase 1 / 0.695
3ou2 SAHSAM-dependent methyltransferase / 0.695
4b63 FADL-ornithine N(5)-monooxygenase / 0.695
5bp9 SAHPutative methyltransferase protein / 0.695
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.695
1mxt FAECholesterol oxidase 1.1.3.6 0.694
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.694
4yuz S4MSpermidine synthase, putative / 0.694
2gew FADCholesterol oxidase 1.1.3.6 0.693
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.693
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.693
2i9k SAHModification methylase HhaI 2.1.1.37 0.692
2q7v FADThioredoxin reductase / 0.692
2xdo FADTetX family tetracycline inactivation enzyme / 0.692
4tm1 FDAKtzI / 0.692
4u2t FADCholesterol oxidase 1.1.3.6 0.692
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.691
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.691
4c05 SAHProtein arginine N-methyltransferase 6 / 0.691
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.691
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.690
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.690
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.689
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.688
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.688
4a99 FADTetX family tetracycline inactivation enzyme / 0.688
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.687
1tdo FADL-amino-acid oxidase 1.4.3.2 0.687
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.687
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.687
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.687
3rw9 DSHSpermidine synthase 2.5.1.16 0.687
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.686
1reo FADL-amino-acid oxidase 1.4.3.2 0.685
1tdn FADL-amino-acid oxidase 1.4.3.2 0.685
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.685
3lsm SFDPyranose 2-oxidase / 0.685
4e2x SAHMethyltransferase / 0.685
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.685
7mht SAHModification methylase HhaI 2.1.1.37 0.685
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.684
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
3mht SAHModification methylase HhaI 2.1.1.37 0.683
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.683
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.683
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.683
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.682
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.682
1zk7 FADMercuric reductase 1.16.1.1 0.682
3cbg SAHO-methyltransferase / 0.682
3lsh FADPyranose 2-oxidase / 0.682
3lsi FADPyranose 2-oxidase / 0.682
1zx9 FADMercuric reductase 1.16.1.1 0.681
2br5 SAHCephalosporin hydroxylase CmcI / 0.681
2p35 SAHTrans-aconitate 2-methyltransferase / 0.681
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.680
2hms NAIKtr system potassium uptake protein A / 0.679
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.679
4tm4 FDAKtzI / 0.679
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.678
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.678
3kkj FADRenalase / 0.678
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.678
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.677
1b4v FADCholesterol oxidase 1.1.3.6 0.676
2plw SAMRibosomal RNA methyltransferase, putative / 0.676
3gyj FADCholesterol oxidase 1.1.3.6 0.676
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.676
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.676
4icy FADPgaE / 0.676
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.675
4guv FADTetX family tetracycline inactivation enzyme / 0.675
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.675
2pan FADGlyoxylate carboligase 4.1.1.47 0.674
3s5w FADL-ornithine N(5)-monooxygenase / 0.674
4tlx FDAKtzI / 0.674
1boo SAHModification methylase PvuII 2.1.1.113 0.673
1y56 FAD382aa long hypothetical sarcosine oxidase / 0.673
1n4u FAECholesterol oxidase 1.1.3.6 0.672
2yg4 FADPutrescine oxidase / 0.672
2yg7 FADPutrescine oxidase / 0.672
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.672
4u2s FDACholesterol oxidase 1.1.3.6 0.672
1b8s FADCholesterol oxidase 1.1.3.6 0.671
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.671
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.671
4g6h NAIRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial 1.6.5.9 0.671
3bg7 FADPyranose 2-oxidase / 0.670
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.670
4k2x FADPolyketide oxygenase/hydroxylase / 0.670
3gsi FADDimethylglycine oxidase 1.5.3.10 0.669
3ict FADCoenzyme A disulfide reductase / 0.669
3p9u FADTetX family tetracycline inactivation enzyme / 0.669
2ih5 NEAModification methylase TaqI 2.1.1.72 0.668
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.667
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.667
1zmc FADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.667
9mht SAHModification methylase HhaI 2.1.1.37 0.667
1tdk FADL-amino-acid oxidase 1.4.3.2 0.666
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.666
3ozt OZZCatechol O-methyltransferase 2.1.1.6 0.666
3rfx NADUronate dehydrogenase / 0.666
4uy6 SAHHistidine N-alpha-methyltransferase / 0.666
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
2ign FADPyranose 2-oxidase / 0.665
2z6u SAHModification methylase HhaI 2.1.1.37 0.665
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.665
3ka7 FADPutative oxidoreductase / 0.665
3nwe 662Catechol O-methyltransferase 2.1.1.6 0.665
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.664
3e23 SAMUncharacterized protein / 0.664
3vyw SAMUncharacterized protein / 0.664
1mht SAHModification methylase HhaI 2.1.1.37 0.663
1zq9 SAMProbable dimethyladenosine transferase / 0.663
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.662
4hh4 SAHCcbJ / 0.662
4j2w FADKynurenine 3-monooxygenase / 0.662
4j36 FADKynurenine 3-monooxygenase / 0.662
2ibt NEAModification methylase TaqI 2.1.1.72 0.661
3alj FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.661
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.661
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.661
4yai NAIC alpha-dehydrogenase / 0.661
1jnz FADAdenylylsulfate reductase, subunit A (AprA) / 0.660
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.660
4k5r FADOxygenase / 0.660
4x4j FADPutative oxygenase / 0.660
1k0l FADp-hydroxybenzoate hydroxylase / 0.659
1z6l FADPolyamine oxidase FMS1 / 0.659
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.659
3nwb 659Catechol O-methyltransferase 2.1.1.6 0.659
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.659
4yag NAIC alpha-dehydrogenase / 0.659
2bi8 FADUDP-galactopyranose mutase 5.4.99.9 0.658
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.658
3qj4 FADRenalase / 0.658
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.657
2px5 SAHGenome polyprotein 2.7.7.48 0.656
2ym2 FADPhenylacetone monooxygenase 1.14.13.92 0.656
3b6d FAECholesterol oxidase 1.1.3.6 0.656
3cty FADProbable thioredoxin reductase / 0.656
4eqx FADCoenzyme A disulfide reductase / 0.656
5d1n SAHUncharacterized protein / 0.656
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.655
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.655
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.655
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.655
3alm FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase / 0.655
3oz2 FADDigeranylgeranylglycerophospholipid reductase / 0.655
4b66 FADL-ornithine N(5)-monooxygenase / 0.655
4u2l SFDCholesterol oxidase 1.1.3.6 0.655
1cc2 FADCholesterol oxidase 1.1.3.6 0.654
1pdh FASp-hydroxybenzoate hydroxylase / 0.654
1uxj NADMalate dehydrogenase / 0.654
3cox FADCholesterol oxidase 1.1.3.6 0.654
3kkz SAMUncharacterized protein / 0.654
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.654
4rvd SAMD-mycarose 3-C-methyltransferase / 0.654
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.653
2o07 MTASpermidine synthase 2.5.1.16 0.653
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.653
4emw FADCoenzyme A disulfide reductase / 0.653
4ysh FADGlycine oxidase / 0.653
5mht SAHModification methylase HhaI 2.1.1.37 0.653
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.652
1ryi FADGlycine oxidase 1.4.3.19 0.652
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.652
2hmv ADPKtr system potassium uptake protein A / 0.652
3lby SAHUncharacterized protein / 0.652
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.652
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.652
2cdu ADPNADH oxidase / 0.651
3ec7 NADInositol 2-dehydrogenase / 0.651
3k30 ADPHistamine dehydrogenase / 0.651
3nlc FADUncharacterized protein / 0.651
1y9d FADPyruvate oxidase 1.2.3.3 0.650
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.650
3cgd FADCoenzyme A disulfide reductase / 0.650
3r6t LU1Catechol O-methyltransferase 2.1.1.6 0.650