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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
3uj7 SAM Phosphoethanolamine N-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3uj7 SAMPhosphoethanolamine N-methyltransferase / 1.087
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.953
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.936
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.928
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.922
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.876
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.801
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.792
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.763
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.762
5je4 SAHMethyl transferase / 0.761
5epe SAHUncharacterized protein / 0.759
3kkz SAMUncharacterized protein / 0.756
1ri4 SAMmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.751
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.751
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.751
5f2k SAHUncharacterized protein / 0.748
3t7s SAMUncharacterized protein / 0.745
5je3 SAHMethyl transferase / 0.743
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.742
4kvz SAHPtnL protein / 0.742
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.738
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.732
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.731
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.730
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.728
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.728
3lcc SAHThiocyanate methyltransferase 1 / 0.727
2p35 SAHTrans-aconitate 2-methyltransferase / 0.725
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.724
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.724
3bwc SAMSpermidine synthase, putative / 0.721
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.720
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.719
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.719
5bp7 SAHSAM-dependent methyltransferase / 0.719
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.717
3t0i SAHPutative methyltransferase / 0.717
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.713
2pan FADGlyoxylate carboligase 4.1.1.47 0.713
3e23 SAMUncharacterized protein / 0.712
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.710
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.709
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.708
3dh0 SAMUncharacterized protein / 0.707
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.706
4hh4 SAHCcbJ / 0.706
4pgh SAMCaffeic acid O-methyltransferase / 0.706
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.702
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.701
3sxj SAMPutative methyltransferase / 0.701
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.700
2gs9 SAHUncharacterized protein / 0.697
3p9c SAHCaffeic acid O-methyltransferase / 0.696
3rw9 DSHSpermidine synthase 2.5.1.16 0.696
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.695
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.695
2qe6 SAMUncharacterized protein / 0.693
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.691
2o06 MTASpermidine synthase 2.5.1.16 0.690
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.690
4yac NAIC alpha-dehydrogenase / 0.690
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.689
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.689
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.688
1y9d FADPyruvate oxidase 1.2.3.3 0.688
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.687
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.685
3fri SAH16S rRNA methylase / 0.685
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.685
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.685
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.684
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.684
5f8f SFGPossible transcriptional regulatory protein / 0.684
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.683
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.683
4nec SAHPutative SAM-dependent methyltransferase / 0.682
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.681
4lwp SAHArginine N-methyltransferase, putative / 0.681
1wy7 SAHUncharacterized protein / 0.680
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.679
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.679
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.678
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.678
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.678
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.676
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.675
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.675
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.674
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.674
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.673
3go4 SAHUncharacterized protein / 0.673
3t7t SAHUncharacterized protein / 0.673
4g56 SAHProtein arginine N-methyltransferase 5 / 0.673
2c4c FAD[F-actin]-methionine sulfoxide oxidase MICAL1 1.14.13 0.671
2zif SAMMethyltransferase / 0.670
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.670
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.670
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.669
1f3l SAHProtein arginine N-methyltransferase 3 / 0.668
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.667
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.667
4qnv GEKtRNA U34 carboxymethyltransferase / 0.667
4qpp SAHProtein arginine N-methyltransferase 6 / 0.667
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.665
4c05 SAHProtein arginine N-methyltransferase 6 / 0.665
4nbu NAI3-oxoacyl-(Acyl-carrier-protein) reductase / 0.665
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.664
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.664
4wec NADShort chain dehydrogenase / 0.663
4kwc SAHMethyltransferase domain family / 0.661
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.661
3fpf MTAUncharacterized protein / 0.660
2eg5 SAH7-methylxanthosine synthase 1 / 0.659
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.659
3ruc NADUDP-N-acetylglucosamine 4-epimerase / 0.658
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.657
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.656
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.656
2o07 MTASpermidine synthase 2.5.1.16 0.656
2qae FADDihydrolipoyl dehydrogenase 1.8.1.4 0.656
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.656
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.656
4rvd SAMD-mycarose 3-C-methyltransferase / 0.655
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.655
4yuz S4MSpermidine synthase, putative / 0.655
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
2xe8 ACPPhosphoglycerate kinase 1 2.7.2.3 0.654
3wds NADNADH-dependent quinuclidinone reductase / 0.654
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.653
3rfx NADUronate dehydrogenase / 0.653
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.652
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
3bus SAHDemethylrebeccamycin-D-glucose O-methyltransferase / 0.651
3geg NADShort-chain dehydrogenase/reductase SDR / 0.651
5eku SAHArginine N-methyltransferase, putative / 0.651
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.650
4c03 SFGProtein arginine N-methyltransferase 6 / 0.650