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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
3fpf MTA Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3fpf MTAUncharacterized protein / 0.913
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.726
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.716
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.713
2o07 MTASpermidine synthase 2.5.1.16 0.712
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.709
2o06 MTASpermidine synthase 2.5.1.16 0.708
4yv2 S4MSpermidine synthase, putative / 0.705
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.701
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.701
3lcc SAHThiocyanate methyltransferase 1 / 0.700
4c03 SFGProtein arginine N-methyltransferase 6 / 0.700
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.699
2i9k SAHModification methylase HhaI 2.1.1.37 0.697
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.696
2q28 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.695
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.695
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.692
4lwp SAHArginine N-methyltransferase, putative / 0.691
3bwc SAMSpermidine synthase, putative / 0.689
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.686
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.686
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.686
5je2 SAHMethyl transferase / 0.686
2pt6 S4MSpermidine synthase / 0.684
4nec SAHPutative SAM-dependent methyltransferase / 0.684
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.684
3cbg SAHO-methyltransferase / 0.683
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.683
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.682
4yuz S4MSpermidine synthase, putative / 0.682
1boo SAHModification methylase PvuII 2.1.1.113 0.681
3duw SAHO-methyltransferase, putative / 0.680
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.680
1mxt FAECholesterol oxidase 1.1.3.6 0.679
1n4w FADCholesterol oxidase 1.1.3.6 0.679
2ibt NEAModification methylase TaqI 2.1.1.72 0.679
4xxg FADCholesterol oxidase 1.1.3.6 0.679
1n4v FADCholesterol oxidase 1.1.3.6 0.678
2gew FADCholesterol oxidase 1.1.3.6 0.678
3go4 SAHUncharacterized protein / 0.678
3gyj FADCholesterol oxidase 1.1.3.6 0.678
3mht SAHModification methylase HhaI 2.1.1.37 0.678
4u2t FADCholesterol oxidase 1.1.3.6 0.678
4xwr FADCholesterol oxidase 1.1.3.6 0.678
1b4v FADCholesterol oxidase 1.1.3.6 0.677
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.676
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.676
2qe6 SAMUncharacterized protein / 0.675
4c04 SFGProtein arginine N-methyltransferase 6 / 0.675
1g60 SAMModification methylase MboII 2.1.1.72 0.674
3fpj SAMUncharacterized protein / 0.674
3nlc FADUncharacterized protein / 0.674
10mh SAHModification methylase HhaI 2.1.1.37 0.673
3b6d FAECholesterol oxidase 1.1.3.6 0.673
3cnj FADCholesterol oxidase 1.1.3.6 0.673
4u2s FDACholesterol oxidase 1.1.3.6 0.673
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.673
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.672
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.671
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.670
4kwc SAHMethyltransferase domain family / 0.670
5eku SAHArginine N-methyltransferase, putative / 0.670
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.669
4wec NADShort chain dehydrogenase / 0.669
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.668
2ih2 NEAModification methylase TaqI 2.1.1.72 0.668
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.668
3wv8 ATPHmd co-occurring protein HcgE / 0.668
4rtk SAHDNA adenine methylase 2.1.1.72 0.668
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.668
2gs9 SAHUncharacterized protein / 0.667
5je4 SAHMethyl transferase / 0.667
4kvz SAHPtnL protein / 0.666
1y9d FADPyruvate oxidase 1.2.3.3 0.665
2ore SAHDNA adenine methylase 2.1.1.72 0.665
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.665
3k30 ADPHistamine dehydrogenase / 0.664
3kkz SAMUncharacterized protein / 0.664
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.664
4b69 FADL-ornithine N(5)-monooxygenase / 0.664
4nzh FADL-ornithine N(5)-monooxygenase / 0.664
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.664
4yuv S4MSpermidine synthase, putative / 0.664
3lsm SFDPyranose 2-oxidase / 0.663
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.663
1cbo FADCholesterol oxidase 1.1.3.6 0.662
2fkn NADUrocanate hydratase 4.2.1.49 0.662
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.662
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.662
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.661
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.660
2hmv ADPKtr system potassium uptake protein A / 0.660
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.660
4dmg SAMUncharacterized protein / 0.660
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.659
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.658
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.658
2ign FADPyranose 2-oxidase / 0.658
2p35 SAHTrans-aconitate 2-methyltransferase / 0.658
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.657
4u2l SFDCholesterol oxidase 1.1.3.6 0.657
5dbj FADFADH2-dependent halogenase PltA / 0.657
2px2 SAHGenome polyprotein 2.7.7.48 0.656
3lov FADProtoporphyrinogen oxidase / 0.656
5epe SAHUncharacterized protein / 0.656
1ve3 SAMUncharacterized protein / 0.655
3c3y SAHO-methyltransferase / 0.655
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.654
3ish FADThioredoxin reductase 1.8.1.9 0.654
3p9u FADTetX family tetracycline inactivation enzyme / 0.654
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
3tos SAHCalS11 / 0.653
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.652
2yg6 FADPutrescine oxidase / 0.652
2yqz SAMUncharacterized protein / 0.652
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.652
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.651
3g5s FADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO / 0.651
3ics ADPCoenzyme A disulfide reductase / 0.651
5je3 SAHMethyl transferase / 0.651
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.650
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650
4k2x FADPolyketide oxygenase/hydroxylase / 0.650
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.650