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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
3p2e SAH 16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.900
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.888
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.738
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.737
4kvz SAHPtnL protein / 0.734
4nec SAHPutative SAM-dependent methyltransferase / 0.734
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.732
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.731
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.721
5je2 SAHMethyl transferase / 0.721
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.720
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.718
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.718
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.712
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.711
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.711
1f3l SAHProtein arginine N-methyltransferase 3 / 0.707
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.704
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.704
4kwc SAHMethyltransferase domain family / 0.701
2p35 SAHTrans-aconitate 2-methyltransferase / 0.698
3go4 SAHUncharacterized protein / 0.698
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.697
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.697
3kkz SAMUncharacterized protein / 0.696
4lwp SAHArginine N-methyltransferase, putative / 0.696
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.693
5epe SAHUncharacterized protein / 0.693
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.692
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.692
2qe6 SAMUncharacterized protein / 0.691
3p9k SAHCaffeic acid O-methyltransferase / 0.691
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.691
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.690
3lst SAHCalO1 / 0.689
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.687
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.686
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.685
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.685
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.683
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.682
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.681
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.681
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.681
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.681
5f8f SFGPossible transcriptional regulatory protein / 0.681
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.680
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.679
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.679
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.678
4c04 SFGProtein arginine N-methyltransferase 6 / 0.678
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.677
2xvm SAHTellurite methyltransferase 2.1.1.265 0.675
4e2x SAHMethyltransferase / 0.675
1uay ADNOxidoreductase / 0.674
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.674
4pne SAHMethyltransferase-like protein / 0.674
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.671
1skm SAHModification methylase HhaI 2.1.1.37 0.670
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.670
5bxy SAHPutative RNA methylase family UPF0020 / 0.670
3mht SAHModification methylase HhaI 2.1.1.37 0.669
3t7s SAMUncharacterized protein / 0.668
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.668
3gu3 SAHMethyltransferase / 0.667
3ou2 SAHSAM-dependent methyltransferase / 0.667
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.667
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.666
2gs9 SAHUncharacterized protein / 0.665
4qpp SAHProtein arginine N-methyltransferase 6 / 0.664
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.663
3dh0 SAMUncharacterized protein / 0.663
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.662
1ve3 SAMUncharacterized protein / 0.662
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.662
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.662
3e8s SAHUncharacterized protein / 0.661
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.661
4qnv GEKtRNA U34 carboxymethyltransferase / 0.661
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.660
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.660
4yac NAIC alpha-dehydrogenase / 0.660
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.660
2zfu SAHRibosomal RNA-processing protein 8 / 0.659
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.659
3lby SAHUncharacterized protein / 0.658
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.658
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.657
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.657
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.656
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.656
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.656
3t7t SAHUncharacterized protein / 0.655
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.654
2fkn NADUrocanate hydratase 4.2.1.49 0.654
4krh SAMPhosphoethanolamine N-methyltransferase 2 / 0.654
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.653
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.652
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.652
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.651
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.650
3e23 SAMUncharacterized protein / 0.650
4pgh SAMCaffeic acid O-methyltransferase / 0.650