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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
3duw SAH O-methyltransferase, putative

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3duw SAHO-methyltransferase, putative / 1.072
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.933
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.917
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.905
4oa5 SAHO-methyltransferase family protein / 0.860
3cbg SAHO-methyltransferase / 0.845
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.837
2hnk SAHSAM-dependent O-methyltransferase / 0.805
1yf3 SAHDNA adenine methylase / 0.791
3tr6 SAHO-methyltransferase / 0.782
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.777
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.770
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.757
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.750
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.750
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.749
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.747
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.743
3vyw SAMUncharacterized protein / 0.741
3c3y SAHO-methyltransferase / 0.735
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.728
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.727
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.725
5bxy SAHPutative RNA methylase family UPF0020 / 0.723
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.722
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.720
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.720
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.720
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.719
3ou2 SAHSAM-dependent methyltransferase / 0.719
4dmg SAMUncharacterized protein / 0.719
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.716
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.716
4nzh FADL-ornithine N(5)-monooxygenase / 0.715
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.713
3ldf SAHUncharacterized protein / 0.712
4gf5 SAHCalS11 / 0.710
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.707
5cku FADL-ornithine N(5)-monooxygenase / 0.707
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.706
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.705
3hvk 719Catechol O-methyltransferase 2.1.1.6 0.703
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.703
1zq9 SAMProbable dimethyladenosine transferase / 0.702
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.701
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.701
1sus SAHCaffeoyl-CoA O-methyltransferase 2.1.1.104 0.699
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.699
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.698
2gs9 SAHUncharacterized protein / 0.698
4a99 FADTetX family tetracycline inactivation enzyme / 0.697
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.696
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.696
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.695
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.695
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.694
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.694
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.693
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.692
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.692
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.692
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.692
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.692
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.691
2g1p SAHDNA adenine methylase 2.1.1.72 0.690
2cww SAHUncharacterized protein / 0.689
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.689
2qe6 SAMUncharacterized protein / 0.688
3e9y FABAcetolactate synthase, chloroplastic 2.2.1.6 0.688
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.688
4nec SAHPutative SAM-dependent methyltransferase / 0.688
1skm SAHModification methylase HhaI 2.1.1.37 0.687
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.687
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.687
5je4 SAHMethyl transferase / 0.687
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.686
4gde FDAUDP-galactopyranose mutase / 0.685
4qpp SAHProtein arginine N-methyltransferase 6 / 0.684
4c3y FAD3-ketosteroid dehydrogenase / 0.683
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.683
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.681
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.681
2ih2 NEAModification methylase TaqI 2.1.1.72 0.680
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.680
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.680
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.680
3fpf MTAUncharacterized protein / 0.680
3go4 SAHUncharacterized protein / 0.680
4guv FADTetX family tetracycline inactivation enzyme / 0.680
2bm9 SAMCephalosporin hydroxylase CmcI / 0.678
4c05 SAHProtein arginine N-methyltransferase 6 / 0.678
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.676
3ou7 SAMSAM-dependent methyltransferase / 0.676
4gbe SAHDNA adenine methylase 2.1.1.72 0.676
2p35 SAHTrans-aconitate 2-methyltransferase / 0.675
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
3mht SAHModification methylase HhaI 2.1.1.37 0.675
3tos SAHCalS11 / 0.675
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.674
3s1s SAHRestriction endonuclease BpuSI / 0.674
5d4u SAMUncharacterized protein MJ0489 / 0.674
2h39 ADQADP-glucose phosphorylase / 0.673
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.673
2rgh FADAlpha-Glycerophosphate Oxidase / 0.672
4e2x SAHMethyltransferase / 0.672
1wy7 SAHUncharacterized protein / 0.671
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.671
3lov FADProtoporphyrinogen oxidase / 0.671
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.671
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.671
1g60 SAMModification methylase MboII 2.1.1.72 0.670
2uyh SAHModification methylase HhaI 2.1.1.37 0.670
3eey SAMrRNA methylase / 0.670
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.669
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.668
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.668
2br5 SAHCephalosporin hydroxylase CmcI / 0.667
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.667
5ahk FADAcetolactate synthase II, large subunit / 0.667
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.666
2vqb FADPutative flavin-containing monooxygenase / 0.666
4k5r FADOxygenase / 0.666
4rvd SAMD-mycarose 3-C-methyltransferase / 0.666
1z6l FADPolyamine oxidase FMS1 / 0.665
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.665
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.665
5f2k SAHUncharacterized protein / 0.664
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.663
2gew FADCholesterol oxidase 1.1.3.6 0.663
4xwr FADCholesterol oxidase 1.1.3.6 0.663
4yac NAIC alpha-dehydrogenase / 0.663
1b4v FADCholesterol oxidase 1.1.3.6 0.662
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.661
7mht SAHModification methylase HhaI 2.1.1.37 0.661
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.660
4u2t FADCholesterol oxidase 1.1.3.6 0.660
1ijh FADCholesterol oxidase 1.1.3.6 0.659
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.659
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.659
2i9k SAHModification methylase HhaI 2.1.1.37 0.659
3cox FADCholesterol oxidase 1.1.3.6 0.659
1n1p FADCholesterol oxidase 1.1.3.6 0.658
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.658
3gyi FADCholesterol oxidase 1.1.3.6 0.658
1b8s FADCholesterol oxidase 1.1.3.6 0.657
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.657
1n4v FADCholesterol oxidase 1.1.3.6 0.657
3mj4 FADUDP-galactopyranose mutase / 0.657
3p9u FADTetX family tetracycline inactivation enzyme / 0.657
4xxg FADCholesterol oxidase 1.1.3.6 0.657
3oe4 610Catechol O-methyltransferase 2.1.1.6 0.656
4b69 FADL-ornithine N(5)-monooxygenase / 0.655
4jdr FADDihydrolipoyl dehydrogenase 1.8.1.4 0.655
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.655
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.654
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.654
3utg FDAUDP-galactopyranose mutase / 0.654
1reo FADL-amino-acid oxidase 1.4.3.2 0.653
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.653
3r6t LU1Catechol O-methyltransferase 2.1.1.6 0.653
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.653
1boo SAHModification methylase PvuII 2.1.1.113 0.652
2hmv ADPKtr system potassium uptake protein A / 0.652
3h5n ATPMccB protein / 0.652
1v59 NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.651
2e1m FADL-glutamate oxidase / 0.651
2xbm SAHGenome polyprotein / 0.651
3cn8 FADPolyamine oxidase FMS1 / 0.651
4u8j FDAUDP-galactopyranose mutase / 0.651
4yuz S4MSpermidine synthase, putative / 0.651
4k2x FADPolyketide oxygenase/hydroxylase / 0.650