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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
3lcu SAH 16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 1.189
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.935
3fri SAH16S rRNA methylase / 0.901
4c03 SFGProtein arginine N-methyltransferase 6 / 0.836
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.836
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.808
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.797
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.796
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.796
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.788
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.785
5bp9 SAHPutative methyltransferase protein / 0.779
5je2 SAHMethyl transferase / 0.778
5jdz SAHMethyl transferase / 0.776
5je3 SAHMethyl transferase / 0.776
3kkz SAMUncharacterized protein / 0.775
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.772
3t7s SAMUncharacterized protein / 0.771
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.770
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.769
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.766
3t7t SAHUncharacterized protein / 0.766
3e8s SAHUncharacterized protein / 0.764
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.764
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.759
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.759
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.758
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.745
4c04 SFGProtein arginine N-methyltransferase 6 / 0.739
3gxo SAHMitomycin biosynthesis 6-O-methyltransferase / 0.738
3lcc SAHThiocyanate methyltransferase 1 / 0.738
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.738
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.735
4qpp SAHProtein arginine N-methyltransferase 6 / 0.735
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.726
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.724
4uy6 SAHHistidine N-alpha-methyltransferase / 0.723
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.721
3ou2 SAHSAM-dependent methyltransferase / 0.720
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.718
3sxj SAMPutative methyltransferase / 0.717
3t0i SAHPutative methyltransferase / 0.717
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.716
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.716
4rvd SAMD-mycarose 3-C-methyltransferase / 0.716
1af7 SAHChemotaxis protein methyltransferase 2.1.1.80 0.715
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.715
3lst SAHCalO1 / 0.715
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.714
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.713
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.712
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.708
2yqz SAMUncharacterized protein / 0.708
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.708
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.705
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.705
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.704
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.702
5bxy SAHPutative RNA methylase family UPF0020 / 0.702
5je4 SAHMethyl transferase / 0.702
1ve3 SAMUncharacterized protein / 0.701
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.701
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.701
1yf3 SAHDNA adenine methylase / 0.696
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.696
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.695
1f3l SAHProtein arginine N-methyltransferase 3 / 0.694
2qe6 SAMUncharacterized protein / 0.693
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.691
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.691
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.691
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.690
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.689
2zfu SAHRibosomal RNA-processing protein 8 / 0.689
3ldf SAHUncharacterized protein / 0.689
4nec SAHPutative SAM-dependent methyltransferase / 0.689
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.688
3p9k SAHCaffeic acid O-methyltransferase / 0.688
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.688
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.688
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.686
1u5a BIKL-lactate dehydrogenase 1.1.1.27 0.686
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.686
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.684
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.683
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.683
4pne SAHMethyltransferase-like protein / 0.683
4rtj SFGDNA adenine methylase 2.1.1.72 0.682
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.681
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.681
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.681
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.681
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.680
2g1p SAHDNA adenine methylase 2.1.1.72 0.680
3b5i SAHIndole-3-acetate O-methyltransferase 1 / 0.680
4hh4 SAHCcbJ / 0.679
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.679
3go4 SAHUncharacterized protein / 0.676
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.676
3tlj SAHUncharacterized protein / 0.675
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
2nli FMNLactate oxidase / 0.673
2ore SAHDNA adenine methylase 2.1.1.72 0.673
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.673
4qnv GEKtRNA U34 carboxymethyltransferase / 0.673
7mht SAHModification methylase HhaI 2.1.1.37 0.673
2ibt NEAModification methylase TaqI 2.1.1.72 0.672
3qv2 SAH5-cytosine DNA methyltransferase / 0.672
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.672
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.671
2p35 SAHTrans-aconitate 2-methyltransferase / 0.671
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.671
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.669
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.668
3duw SAHO-methyltransferase, putative / 0.668
3c36 KAIGlutamate receptor ionotropic, kainate 1 / 0.667
4lwp SAHArginine N-methyltransferase, putative / 0.667
4qnu GEKtRNA U34 carboxymethyltransferase / 0.667
1u4s BIHL-lactate dehydrogenase 1.1.1.27 0.666
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.666
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.665
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.665
1xdu SFGAclacinomycin 10-hydroxylase RdmB 4.1.1 0.665
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.665
4yac NAIC alpha-dehydrogenase / 0.663
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.662
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.662
2f8l SAMLmo1582 protein / 0.661
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.660
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.659
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.659
2gs9 SAHUncharacterized protein / 0.659
2np7 NEAModification methylase TaqI 2.1.1.72 0.659
2xvm SAHTellurite methyltransferase 2.1.1.265 0.659
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.659
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.659
5epe SAHUncharacterized protein / 0.659
2ih2 NEAModification methylase TaqI 2.1.1.72 0.657
4bdo KAIGlutamate receptor ionotropic, kainate 2 / 0.657
2xxy KAIGlutamate receptor ionotropic, kainate 2 / 0.654
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.654
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.653
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.653
3s1s SAHRestriction endonuclease BpuSI / 0.653
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.652
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.650
2xxv KAIGlutamate receptor ionotropic, kainate 2 / 0.650
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.650
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.650
4bdr KAIGlutamate receptor ionotropic, kainate 2 / 0.650
4gc9 SAMDimethyladenosine transferase 1, mitochondrial 2.1.1 0.650