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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
2nxe SAM Ribosomal protein L11 methyltransferase 2.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 1.025
3egv SAHRibosomal protein L11 methyltransferase 2.1.1 0.922
3cjt SAHRibosomal protein L11 methyltransferase 2.1.1 0.899
3cjq SAHRibosomal protein L11 methyltransferase 2.1.1 0.847
4dcm SAMRibosomal RNA large subunit methyltransferase G 2.1.1.174 0.800
5jdz SAHMethyl transferase / 0.789
5bxy SAHPutative RNA methylase family UPF0020 / 0.775
4qpp SAHProtein arginine N-methyltransferase 6 / 0.774
5je3 SAHMethyl transferase / 0.774
3go4 SAHUncharacterized protein / 0.772
4azw SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.769
2h00 SAHU6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase / 0.768
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.761
2y1x SAHHistone-arginine methyltransferase CARM1 / 0.759
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.757
5je4 SAHMethyl transferase / 0.757
3lcc SAHThiocyanate methyltransferase 1 / 0.756
2p35 SAHTrans-aconitate 2-methyltransferase / 0.755
4c04 SFGProtein arginine N-methyltransferase 6 / 0.753
4lwp SAHArginine N-methyltransferase, putative / 0.752
5fa8 SAMRibosomal protein L11 methyltransferase, putative / 0.751
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.748
1f3l SAHProtein arginine N-methyltransferase 3 / 0.747
2gs9 SAHUncharacterized protein / 0.747
2yqz SAMUncharacterized protein / 0.746
4c03 SFGProtein arginine N-methyltransferase 6 / 0.745
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.741
3dmh SAMProbable ribosomal RNA small subunit methyltransferase / 0.741
4nec SAHPutative SAM-dependent methyltransferase / 0.739
5e9w SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.737
1ori SAHProtein arginine N-methyltransferase 1 / 0.736
5je2 SAHMethyl transferase / 0.734
4hh4 SAHCcbJ / 0.731
5dxa SFGHistone-arginine methyltransferase CARM1 / 0.726
4hc4 SAHProtein arginine N-methyltransferase 6 / 0.725
2zbp SAMRibosomal protein L11 methyltransferase 2.1.1 0.724
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.721
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.718
4uy6 SAHHistidine N-alpha-methyltransferase / 0.717
2qe6 SAMUncharacterized protein / 0.716
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.716
2vdv SAMtRNA (guanine-N(7)-)-methyltransferase / 0.715
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.715
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.709
2np7 NEAModification methylase TaqI 2.1.1.72 0.706
5dx8 SFGHistone-arginine methyltransferase CARM1 / 0.706
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.705
3ou2 SAHSAM-dependent methyltransferase / 0.704
2ibt NEAModification methylase TaqI 2.1.1.72 0.701
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.701
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.701
5bp9 SAHPutative methyltransferase protein / 0.701
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.699
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.699
3epp SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.697
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.697
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.697
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.697
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.696
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.695
3lst SAHCalO1 / 0.694
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.693
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.693
3e8s SAHUncharacterized protein / 0.691
5dxj SFGHistone-arginine methyltransferase CARM1 / 0.689
3reo SAH(Iso)eugenol O-methyltransferase 2.1.1.146 0.687
4fr0 SAMArsenic methyltransferase / 0.686
1orh SAHProtein arginine N-methyltransferase 1 / 0.685
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.685
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.684
4ax8 SAMO-antigen chain terminator bifunctional methyltransferase/kinase WbdD / 0.683
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.683
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.683
3p2e SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.682
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.682
5f8f SFGPossible transcriptional regulatory protein / 0.682
3fri SAH16S rRNA methylase / 0.681
3pb3 SAH16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.681
3duw SAHO-methyltransferase, putative / 0.680
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.680
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.678
1nw3 SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.678
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.678
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.678
3t7t SAHUncharacterized protein / 0.677
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.677
1qao SAMrRNA adenine N-6-methyltransferase 2.1.1.184 0.676
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.676
7mht SAHModification methylase HhaI 2.1.1.37 0.676
1nv9 SAHRelease factor glutamine methyltransferase 2.1.1.297 0.675
1ri3 SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.675
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.675
1g1a NADdTDP-glucose 4,6-dehydratase / 0.673
1qan SAHrRNA adenine N-6-methyltransferase 2.1.1.184 0.671
2v74 SAHHistone-arginine methyltransferase CARM1 / 0.671
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.671
4ckc SAHmRNA-capping enzyme catalytic subunit 2.1.1.56 0.671
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.669
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.669
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.667
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.666
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.666
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.666
2ih5 NEAModification methylase TaqI 2.1.1.72 0.665
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.665
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.665
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.665
1rjd SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.664
1rje SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.663
1skm SAHModification methylase HhaI 2.1.1.37 0.663
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.663
3iv6 SAMUncharacterized protein / 0.663
3t7s SAMUncharacterized protein / 0.663
3tr6 SAHO-methyltransferase / 0.663
4iwn GEKCarboxy-S-adenosyl-L-methionine synthase / 0.663
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.663
3fpf MTAUncharacterized protein / 0.662
1ve3 SAMUncharacterized protein / 0.661
2y1w SFGHistone-arginine methyltransferase CARM1 / 0.661
3bwc SAMSpermidine synthase, putative / 0.661
3iei SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.661
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.661
3qgz ADNHistidine triad nucleotide-binding protein 1 3 0.660
3rw9 DSHSpermidine synthase 2.5.1.16 0.660
1x1a SAMC-20 methyltransferase / 0.657
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.657
2ji9 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.657
2uyh SAHModification methylase HhaI 2.1.1.37 0.657
3c3y SAHO-methyltransferase / 0.657
2o06 MTASpermidine synthase 2.5.1.16 0.656
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.656
3g8a SAHRibosomal RNA small subunit methyltransferase G / 0.656
1qaq SFGrRNA adenine N-6-methyltransferase 2.1.1.184 0.654
1rjg SAHLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
2i9k SAHModification methylase HhaI 2.1.1.37 0.654
3o7w SAMLeucine carboxyl methyltransferase 1 2.1.1.233 0.654
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.654
1zmc NADDihydrolipoyl dehydrogenase, mitochondrial 1.8.1.4 0.653
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.653
1sg9 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.652
2zw9 SAMtRNA wybutosine-synthesizing protein 4 2.1.1.290 0.652
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.651
1qzz SAMAclacinomycin 10-hydroxylase RdmB 4.1.1 0.651
3nwb 659Catechol O-methyltransferase 2.1.1.6 0.651
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.650
4c05 SAHProtein arginine N-methyltransferase 6 / 0.650
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.650