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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
3egv SAH Ribosomal protein L11 methyltransferase 2.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 1.011
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.935
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.922
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.894
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.759
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.757
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.757
5je2 SAHMethyl transferase / 0.753
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.751
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.749
4lwp SAHArginine N-methyltransferase, putative / 0.748
3go4 SAHUncharacterized protein / 0.747
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.744
2yqz SAMUncharacterized protein / 0.738
5je3 SAHMethyl transferase / 0.735
5bxy SAHPutative RNA methylase family UPF0020 / 0.733
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.732
5jdz SAHMethyl transferase / 0.730
1f3l SAHProtein arginine N-methyltransferase 3 / 0.727
4qpp SAHProtein arginine N-methyltransferase 6 / 0.725
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.721
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.721
4nec SAHPutative SAM-dependent methyltransferase / 0.719
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.718
5je4 SAHMethyl transferase / 0.718
5bp9 SAHPutative methyltransferase protein / 0.717
4c04 SFGProtein arginine N-methyltransferase 6 / 0.715
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.715
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.714
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.714
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.713
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.713
2qe6 SAMUncharacterized protein / 0.712
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.710
3ou2 SAHSAM-dependent methyltransferase / 0.710
2p35 SAHTrans-aconitate 2-methyltransferase / 0.708
4e2x SAHMethyltransferase / 0.706
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.706
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.705
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.704
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.703
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.703
2gs9 SAHUncharacterized protein / 0.700
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.699
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.699
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.698
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.697
3lcc SAHThiocyanate methyltransferase 1 / 0.697
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.695
5icf SAH(S)-norcoclaurine 6-O-methyltransferase / 0.695
1yf3 SAHDNA adenine methylase / 0.694
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.694
3p9k SAHCaffeic acid O-methyltransferase / 0.694
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.694
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.693
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.693
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.693
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.693
5f2k SAHUncharacterized protein / 0.693
1ori SAHProtein arginine N-methyltransferase 1 / 0.691
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.690
3fri SAH16S rRNA methylase / 0.688
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.688
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.687
4c03 SFGProtein arginine N-methyltransferase 6 / 0.684
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.684
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.683
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.682
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.681
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.681
3duw SAHO-methyltransferase, putative / 0.680
3e8s SAHUncharacterized protein / 0.679
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.679
3ou6 SAMSAM-dependent methyltransferase / 0.678
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.677
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.676
3dh0 SAMUncharacterized protein / 0.676
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.675
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.673
3c3y SAHO-methyltransferase / 0.671
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.671
1bc5 SAHChemotaxis protein methyltransferase 2.1.1.80 0.670
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.670
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.670
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.670
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.669
4rvd SAMD-mycarose 3-C-methyltransferase / 0.668
3tos SAHCalS11 / 0.667
4qnv GEKtRNA U34 carboxymethyltransferase / 0.667
2zfu SAHRibosomal RNA-processing protein 8 / 0.666
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.666
3tr6 SAHO-methyltransferase / 0.666
3bwc SAMSpermidine synthase, putative / 0.665
1orh SAHProtein arginine N-methyltransferase 1 / 0.664
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.664
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.664
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.663
2ibt NEAModification methylase TaqI 2.1.1.72 0.662
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.662
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.662
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.661
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.660
2aot SAHHistamine N-methyltransferase 2.1.1.8 0.660
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.660
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.658
3rw9 DSHSpermidine synthase 2.5.1.16 0.657
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.657
4dmg SAMUncharacterized protein / 0.657
3kpj SAHPhenylethanolamine N-methyltransferase 2.1.1.28 0.656
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.656
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.655
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.654
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.654
5dx1 SFGHistone-arginine methyltransferase CARM1 / 0.654
3cbg SAHO-methyltransferase / 0.653
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.653
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.653
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.653
4pgh SAMCaffeic acid O-methyltransferase / 0.653
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.653
3t7t SAHUncharacterized protein / 0.652
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.652
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.651
4ckb SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.651
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.651
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.650