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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
3dmg SAH Probable ribosomal RNA small subunit methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 1.015
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.969
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.934
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.932
3ou2 SAHSAM-dependent methyltransferase / 0.813
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.805
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.801
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.786
3kkz SAMUncharacterized protein / 0.784
4nec SAHPutative SAM-dependent methyltransferase / 0.782
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.771
3t7s SAMUncharacterized protein / 0.769
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.765
4c03 SFGProtein arginine N-methyltransferase 6 / 0.762
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.761
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.760
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.757
4c04 SFGProtein arginine N-methyltransferase 6 / 0.756
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.756
3p9k SAHCaffeic acid O-methyltransferase / 0.754
5je2 SAHMethyl transferase / 0.746
3fri SAH16S rRNA methylase / 0.744
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.743
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.742
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.741
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.741
3lst SAHCalO1 / 0.739
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.739
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.738
2yqz SAMUncharacterized protein / 0.736
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.735
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.735
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.734
4qtu SAM18S rRNA (guanine(1575)-N(7))-methyltransferase / 0.734
2xvm SAHTellurite methyltransferase 2.1.1.265 0.732
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.732
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.732
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.732
4hh4 SAHCcbJ / 0.730
4qpp SAHProtein arginine N-methyltransferase 6 / 0.729
4kvz SAHPtnL protein / 0.728
5bxy SAHPutative RNA methylase family UPF0020 / 0.725
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.721
3e23 SAMUncharacterized protein / 0.720
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.719
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.718
5je3 SAHMethyl transferase / 0.717
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.714
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.713
5bp9 SAHPutative methyltransferase protein / 0.713
3e8s SAHUncharacterized protein / 0.711
3lcc SAHThiocyanate methyltransferase 1 / 0.711
3t0i SAHPutative methyltransferase / 0.710
1f3l SAHProtein arginine N-methyltransferase 3 / 0.709
2f8l SAMLmo1582 protein / 0.708
4lwp SAHArginine N-methyltransferase, putative / 0.708
3ldg SAHUncharacterized protein / 0.707
3vyw SAMUncharacterized protein / 0.706
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.705
1eg2 MTAModification methylase RsrI 2.1.1.72 0.704
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.704
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.703
1ori SAHProtein arginine N-methyltransferase 1 / 0.701
2g1p SAHDNA adenine methylase 2.1.1.72 0.701
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.701
1orh SAHProtein arginine N-methyltransferase 1 / 0.699
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.699
3gu3 SAHMethyltransferase / 0.699
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.699
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.697
5jdz SAHMethyl transferase / 0.696
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.695
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.695
4gbe SAHDNA adenine methylase 2.1.1.72 0.695
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.695
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.694
3duw SAHO-methyltransferase, putative / 0.692
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.692
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.691
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.690
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.688
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.687
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.687
2o06 MTASpermidine synthase 2.5.1.16 0.686
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.686
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.686
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.686
1skm SAHModification methylase HhaI 2.1.1.37 0.685
5epe SAHUncharacterized protein / 0.685
5f2k SAHUncharacterized protein / 0.683
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.682
2i9k SAHModification methylase HhaI 2.1.1.37 0.682
2zcj SAHModification methylase HhaI 2.1.1.37 0.682
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.682
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.682
1kph SAHCyclopropane mycolic acid synthase 1 2.1.1.79 0.681
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.681
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.681
2p35 SAHTrans-aconitate 2-methyltransferase / 0.680
3vc1 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.680
1boo SAHModification methylase PvuII 2.1.1.113 0.679
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.679
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.679
3sxj SAMPutative methyltransferase / 0.678
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.677
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.676
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.676
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.676
2z6u SAHModification methylase HhaI 2.1.1.37 0.675
3p9c SAHCaffeic acid O-methyltransferase / 0.675
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.675
4pgh SAMCaffeic acid O-methyltransferase / 0.675
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.675
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.674
1wy7 SAHUncharacterized protein / 0.674
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.673
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.672
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.672
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.671
3go4 SAHUncharacterized protein / 0.671
4rvd SAMD-mycarose 3-C-methyltransferase / 0.671
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.670
2zfu SAHRibosomal RNA-processing protein 8 / 0.669
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.665
3rw9 DSHSpermidine synthase 2.5.1.16 0.664
10mh SAHModification methylase HhaI 2.1.1.37 0.663
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.662
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.662
7mht SAHModification methylase HhaI 2.1.1.37 0.662
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.661
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.661
4dmg SAMUncharacterized protein / 0.661
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.661
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.660
5bp7 SAHSAM-dependent methyltransferase / 0.660
1jqd SAHHistamine N-methyltransferase 2.1.1.8 0.659
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.659
3eey SAMrRNA methylase / 0.659
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.659
3vc2 SAHGeranyl diphosphate 2-C-methyltransferase 2.1.1.255 0.659
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.657
2c7q SAHModification methylase HhaI 2.1.1.37 0.657
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.656
3c3y SAHO-methyltransferase / 0.656
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.654
1nw5 SAMModification methylase RsrI 2.1.1.72 0.653
2ore SAHDNA adenine methylase 2.1.1.72 0.653
3mht SAHModification methylase HhaI 2.1.1.37 0.653
3tm5 SFGUncharacterized protein / 0.652
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.652
4rtk SAHDNA adenine methylase 2.1.1.72 0.652
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.652
5jjr SAHGenome polyprotein / 0.652
8mht SAHModification methylase HhaI 2.1.1.37 0.651
1nah NADUDP-glucose 4-epimerase 5.1.3.2 0.650
2bm9 SAMCephalosporin hydroxylase CmcI / 0.650