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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
2h00 SAH U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.991
4lwp SAHArginine N-methyltransferase, putative / 0.799
5jdz SAHMethyl transferase / 0.792
5bp9 SAHPutative methyltransferase protein / 0.781
5je3 SAHMethyl transferase / 0.776
1f3l SAHProtein arginine N-methyltransferase 3 / 0.771
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.768
2yqz SAMUncharacterized protein / 0.764
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.762
4qpp SAHProtein arginine N-methyltransferase 6 / 0.762
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.761
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.755
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.751
1ori SAHProtein arginine N-methyltransferase 1 / 0.748
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.745
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.739
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.738
4c04 SFGProtein arginine N-methyltransferase 6 / 0.732
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.732
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.731
3lcc SAHThiocyanate methyltransferase 1 / 0.730
4hh4 SAHCcbJ / 0.728
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.727
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.727
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.724
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.719
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.719
4c03 SFGProtein arginine N-methyltransferase 6 / 0.717
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.715
3fri SAH16S rRNA methylase / 0.714
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.714
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.714
5je4 SAHMethyl transferase / 0.706
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.705
1orh SAHProtein arginine N-methyltransferase 1 / 0.703
3go4 SAHUncharacterized protein / 0.700
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.700
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.699
3e8s SAHUncharacterized protein / 0.699
1ve3 SAMUncharacterized protein / 0.697
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.696
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.696
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.695
3t7s SAMUncharacterized protein / 0.694
3dh0 SAMUncharacterized protein / 0.693
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.693
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.690
2gs9 SAHUncharacterized protein / 0.689
3p9c SAHCaffeic acid O-methyltransferase / 0.689
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.689
1x1c SAHC-20 methyltransferase / 0.688
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.688
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.687
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.684
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.684
2zfu SAHRibosomal RNA-processing protein 8 / 0.683
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.683
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.682
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.681
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.680
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.679
5je2 SAHMethyl transferase / 0.679
4kwc SAHMethyltransferase domain family / 0.677
1x1d SAHC-20 methyltransferase / 0.676
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.676
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.676
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.675
3ldg SAHUncharacterized protein / 0.674
2xvm SAHTellurite methyltransferase 2.1.1.265 0.673
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.673
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.673
2zwa SAHtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.672
4uy6 SAHHistidine N-alpha-methyltransferase / 0.672
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.671
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.671
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
3kkz SAMUncharacterized protein / 0.669
3p9k SAHCaffeic acid O-methyltransferase / 0.669
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.669
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.669
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.668
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.668
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.667
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.667
3hf8 ML0Tryptophan 5-hydroxylase 1 1.14.16.4 0.667
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.667
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.666
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.665
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.664
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.662
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.662
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.662
4dmg SAMUncharacterized protein / 0.662
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.662
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.661
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.659
2xxy KAIGlutamate receptor ionotropic, kainate 2 / 0.659
4nec SAHPutative SAM-dependent methyltransferase / 0.659
5f2k SAHUncharacterized protein / 0.659
3fpf MTAUncharacterized protein / 0.658
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.658
3t0i SAHPutative methyltransferase / 0.658
4f3g KAIGlutamate receptor 3 / 0.658
3lst SAHCalO1 / 0.657
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.656
5bxy SAHPutative RNA methylase family UPF0020 / 0.656
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.655
2p35 SAHTrans-aconitate 2-methyltransferase / 0.655
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.655
3t7t SAHUncharacterized protein / 0.654
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.653
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.653
1n77 ATPGlutamate--tRNA ligase 6.1.1.17 0.652
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
4f31 KAIGlutamate receptor 3 / 0.652
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.652
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.651
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.651
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.651
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.650