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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
4iwn GEK Carboxy-S-adenosyl-L-methionine synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 1.171
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 1.054
2p35 SAHTrans-aconitate 2-methyltransferase / 0.742
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.738
2eg5 SAH7-methylxanthosine synthase 1 / 0.737
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.729
4lwp SAHArginine N-methyltransferase, putative / 0.727
4hh4 SAHCcbJ / 0.721
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.720
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.718
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.717
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.716
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.716
5jdz SAHMethyl transferase / 0.716
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.715
4dmg SAMUncharacterized protein / 0.713
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.711
1ori SAHProtein arginine N-methyltransferase 1 / 0.710
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.709
3ldf SAHUncharacterized protein / 0.709
2xvm SAHTellurite methyltransferase 2.1.1.265 0.707
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.707
3cbg SAHO-methyltransferase / 0.707
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.706
5je4 SAHMethyl transferase / 0.705
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.704
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.704
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.703
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.703
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.700
3gu3 SAHMethyltransferase / 0.700
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.700
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.699
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.698
3dh0 SAMUncharacterized protein / 0.696
2qe6 SAMUncharacterized protein / 0.694
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.693
2hnk SAHSAM-dependent O-methyltransferase / 0.692
4uy6 SAHHistidine N-alpha-methyltransferase / 0.692
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.691
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.690
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.687
3duw SAHO-methyltransferase, putative / 0.687
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.686
4nec SAHPutative SAM-dependent methyltransferase / 0.686
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.686
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.685
3p9c SAHCaffeic acid O-methyltransferase / 0.685
7mht SAHModification methylase HhaI 2.1.1.37 0.685
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.684
3tm4 SAMUncharacterized protein / 0.683
2gs9 SAHUncharacterized protein / 0.682
2fkn NADUrocanate hydratase 4.2.1.49 0.681
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.681
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.680
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.680
5bw4 SAMUncharacterized protein / 0.680
2p1o NLAProtein TRANSPORT INHIBITOR RESPONSE 1 / 0.679
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.679
1y9d FADPyruvate oxidase 1.2.3.3 0.678
1ve3 SAMUncharacterized protein / 0.677
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.677
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.677
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.677
3mht SAHModification methylase HhaI 2.1.1.37 0.676
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.676
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.675
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.675
1skm SAHModification methylase HhaI 2.1.1.37 0.674
3c3y SAHO-methyltransferase / 0.673
3lst SAHCalO1 / 0.671
3t7s SAMUncharacterized protein / 0.671
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.671
1f3l SAHProtein arginine N-methyltransferase 3 / 0.670
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.670
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.670
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.670
10mh SAHModification methylase HhaI 2.1.1.37 0.669
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.669
4pgh SAMCaffeic acid O-methyltransferase / 0.669
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.669
5eku SAHArginine N-methyltransferase, putative / 0.668
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.667
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.666
2ahc VNLChorismate pyruvate-lyase / 0.665
3mz9 BHNNickel-binding periplasmic protein / 0.664
3ou6 SAMSAM-dependent methyltransferase / 0.664
5je2 SAHMethyl transferase / 0.664
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.663
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.663
4yac NAIC alpha-dehydrogenase / 0.663
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.662
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.662
3kkz SAMUncharacterized protein / 0.662
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.661
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.661
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.660
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.660
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.659
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.658
4c04 SFGProtein arginine N-methyltransferase 6 / 0.658
5bxy SAHPutative RNA methylase family UPF0020 / 0.658
2hmv ADPKtr system potassium uptake protein A / 0.657
4e2x SAHMethyltransferase / 0.657
4oa5 SAHO-methyltransferase family protein / 0.657
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.656
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.656
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.655
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.654
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.654
2c7q SAHModification methylase HhaI 2.1.1.37 0.653
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.653
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.653
4ce0 SAHProbable O-methyltransferase / 0.653
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.652
2ewm NAD(S)-1-Phenylethanol dehydrogenase 1.1.1.311 0.652
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.651
1nw5 SAMModification methylase RsrI 2.1.1.72 0.651
1u4s BIHL-lactate dehydrogenase 1.1.1.27 0.651
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.651
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.650
1pox FADPyruvate oxidase 1.2.3.3 0.650
2vwq NAPGlucose 1-dehydrogenase / 0.650
2xyr SFGReplicase polyprotein 1ab 2.1.1 0.650