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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
1kr5 SAH Protein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 1.062
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.753
5bxy SAHPutative RNA methylase family UPF0020 / 0.734
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.732
4yuv S4MSpermidine synthase, putative / 0.731
2pt6 S4MSpermidine synthase / 0.723
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.723
3cbg SAHO-methyltransferase / 0.718
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.718
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.711
4poo SAMPutative RNA methylase / 0.711
2i9k SAHModification methylase HhaI 2.1.1.37 0.710
3go4 SAHUncharacterized protein / 0.710
3ldg SAHUncharacterized protein / 0.708
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.708
1yf3 SAHDNA adenine methylase / 0.707
3bwc SAMSpermidine synthase, putative / 0.707
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.707
3ou2 SAHSAM-dependent methyltransferase / 0.706
4kwc SAHMethyltransferase domain family / 0.701
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.700
3t7s SAMUncharacterized protein / 0.700
2o07 MTASpermidine synthase 2.5.1.16 0.699
4kvz SAHPtnL protein / 0.699
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.699
2z6u SAHModification methylase HhaI 2.1.1.37 0.695
2zcj SAHModification methylase HhaI 2.1.1.37 0.695
2o06 MTASpermidine synthase 2.5.1.16 0.693
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.692
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.691
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.690
2fkn NADUrocanate hydratase 4.2.1.49 0.688
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.688
1kvr NADUDP-glucose 4-epimerase 5.1.3.2 0.687
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.686
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.685
1ve3 SAMUncharacterized protein / 0.684
2pan FADGlyoxylate carboligase 4.1.1.47 0.684
3rw9 DSHSpermidine synthase 2.5.1.16 0.684
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.684
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.683
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.682
3p9c SAHCaffeic acid O-methyltransferase / 0.682
4uy6 SAHHistidine N-alpha-methyltransferase / 0.682
3c3y SAHO-methyltransferase / 0.681
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.681
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.680
3lbf SAHProtein-L-isoaspartate O-methyltransferase 2.1.1.77 0.680
5f8f SFGPossible transcriptional regulatory protein / 0.680
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.677
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.677
5f2k SAHUncharacterized protein / 0.677
2f8l SAMLmo1582 protein / 0.676
2pzj NADPutative nucleotide sugar epimerase/ dehydratase / 0.675
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.675
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.674
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.674
1boo SAHModification methylase PvuII 2.1.1.113 0.673
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.673
3ou6 SAMSAM-dependent methyltransferase / 0.673
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.673
3fpf MTAUncharacterized protein / 0.671
2c7q SAHModification methylase HhaI 2.1.1.37 0.670
2q1t NADPutative nucleotide sugar epimerase/ dehydratase / 0.670
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.670
3sx2 NADUncharacterized protein / 0.670
3gu3 SAHMethyltransferase / 0.669
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.668
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.666
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.666
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.666
5eku SAHArginine N-methyltransferase, putative / 0.664
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.662
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.662
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.661
3vas ADNPutative adenosine kinase / 0.661
4yv2 S4MSpermidine synthase, putative / 0.661
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.660
4yv1 S4MSpermidine synthase, putative / 0.660
2c31 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.658
1xwf ADNAdenosylhomocysteinase 3.3.1.1 0.657
2eg5 SAH7-methylxanthosine synthase 1 / 0.657
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.657
3duw SAHO-methyltransferase, putative / 0.657
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.657
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.656
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.656
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.656
4yac NAIC alpha-dehydrogenase / 0.656
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.655
2np6 NEAModification methylase TaqI 2.1.1.72 0.655
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.655
4yuz S4MSpermidine synthase, putative / 0.654
1nw5 SAMModification methylase RsrI 2.1.1.72 0.653
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.653
3kkz SAMUncharacterized protein / 0.653
3lst SAHCalO1 / 0.653
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.653
3dh0 SAMUncharacterized protein / 0.652
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.651