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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
1nbi SAM Glycine N-methyltransferase 2.1.1.20

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1nbi SAMGlycine N-methyltransferase 2.1.1.20 1.067
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.974
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.965
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.774
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.750
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.727
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.714
1yf3 SAHDNA adenine methylase / 0.713
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.710
4gf5 SAHCalS11 / 0.709
1ve3 SAMUncharacterized protein / 0.708
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.708
4yac NAIC alpha-dehydrogenase / 0.708
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.707
3tos SAHCalS11 / 0.707
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.707
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.706
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.706
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.703
3c3y SAHO-methyltransferase / 0.702
3duw SAHO-methyltransferase, putative / 0.701
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.701
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.700
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.697
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.695
2hnk SAHSAM-dependent O-methyltransferase / 0.694
4ce0 SAHProbable O-methyltransferase / 0.693
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.688
4hh4 SAHCcbJ / 0.688
3kkz SAMUncharacterized protein / 0.687
1g1a NADdTDP-glucose 4,6-dehydratase / 0.686
2p35 SAHTrans-aconitate 2-methyltransferase / 0.686
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.685
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.685
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.683
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.681
5je2 SAHMethyl transferase / 0.681
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.678
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.678
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.677
2o06 MTASpermidine synthase 2.5.1.16 0.677
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.676
4g56 SAHProtein arginine N-methyltransferase 5 / 0.676
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.675
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.675
4fn4 NADShort chain dehydrogenase / 0.675
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.675
2v7g NADUrocanate hydratase 4.2.1.49 0.674
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.674
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.673
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.673
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.672
3ldf SAHUncharacterized protein / 0.672
3p9k SAHCaffeic acid O-methyltransferase / 0.672
3cbg SAHO-methyltransferase / 0.671
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.671
4nec SAHPutative SAM-dependent methyltransferase / 0.671
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.671
5f8f SFGPossible transcriptional regulatory protein / 0.671
3geg NADShort-chain dehydrogenase/reductase SDR / 0.670
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.670
2cdu ADPNADH oxidase / 0.669
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.668
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.667
4kwc SAHMethyltransferase domain family / 0.667
4pgh SAMCaffeic acid O-methyltransferase / 0.667
2yqz SAMUncharacterized protein / 0.666
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.666
3bwc SAMSpermidine synthase, putative / 0.666
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.664
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.664
2hmv ADPKtr system potassium uptake protein A / 0.664
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.664
2zif SAMMethyltransferase / 0.663
4yag NAIC alpha-dehydrogenase / 0.663
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.663
4gbe SAHDNA adenine methylase 2.1.1.72 0.662
5jsf NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.662
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.661
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.660
3p2k SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.660
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.660
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.659
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.659
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.659
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.659
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.658
1wy7 SAHUncharacterized protein / 0.658
4kvz SAHPtnL protein / 0.658
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.657
2dki FAD3-hydroxybenzoate 4-monooxygenase 1.14.13.23 0.657
2pt6 S4MSpermidine synthase / 0.656
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.656
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.656
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.656
2i9k SAHModification methylase HhaI 2.1.1.37 0.654
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.654
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.653
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.652
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.651
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.651
3h5n ATPMccB protein / 0.651
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.650
1z7e ATPBifunctional polymyxin resistance protein ArnA / 0.650
5eku SAHArginine N-methyltransferase, putative / 0.650
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.650