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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
4obw SAM 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 1.002
2qe6 SAMUncharacterized protein / 0.752
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.743
2f8l SAMLmo1582 protein / 0.739
1ve3 SAMUncharacterized protein / 0.735
2ih2 NEAModification methylase TaqI 2.1.1.72 0.735
2ibt NEAModification methylase TaqI 2.1.1.72 0.734
5je2 SAHMethyl transferase / 0.732
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.730
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.729
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.722
5bxy SAHPutative RNA methylase family UPF0020 / 0.721
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.714
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.713
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.708
2np6 NEAModification methylase TaqI 2.1.1.72 0.707
3tm4 SAMUncharacterized protein / 0.705
5jdz SAHMethyl transferase / 0.703
1aqi SAHModification methylase TaqI 2.1.1.72 0.701
2ih5 NEAModification methylase TaqI 2.1.1.72 0.701
1yf3 SAHDNA adenine methylase / 0.699
3go4 SAHUncharacterized protein / 0.699
1nbh SAMGlycine N-methyltransferase 2.1.1.20 0.694
3e23 SAMUncharacterized protein / 0.694
7mht SAHModification methylase HhaI 2.1.1.37 0.694
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.693
4hh4 SAHCcbJ / 0.693
4poo SAMPutative RNA methylase / 0.693
4oa5 SAHO-methyltransferase family protein / 0.690
4gbe SAHDNA adenine methylase 2.1.1.72 0.689
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.687
1eg2 MTAModification methylase RsrI 2.1.1.72 0.686
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.686
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.686
4m37 SAHProtein arginine N-methyltransferase 7 2.1.1 0.686
1g38 NEAModification methylase TaqI 2.1.1.72 0.685
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.685
3fpf MTAUncharacterized protein / 0.684
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.684
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.684
2o06 MTASpermidine synthase 2.5.1.16 0.683
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.683
2br5 SAHCephalosporin hydroxylase CmcI / 0.682
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.682
3c3y SAHO-methyltransferase / 0.680
2g1p SAHDNA adenine methylase 2.1.1.72 0.679
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.679
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.679
3gwz SAHMitomycin biosynthesis 6-O-methyltransferase / 0.679
3ldf SAHUncharacterized protein / 0.679
2hnk SAHSAM-dependent O-methyltransferase / 0.678
3rw9 DSHSpermidine synthase 2.5.1.16 0.677
4yac NAIC alpha-dehydrogenase / 0.677
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.677
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.676
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.676
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.676
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.675
3ou6 SAMSAM-dependent methyltransferase / 0.674
1kia SAMGlycine N-methyltransferase 2.1.1.20 0.673
3s1s SAHRestriction endonuclease BpuSI / 0.673
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.672
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.672
4kvz SAHPtnL protein / 0.672
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.671
3t7t SAHUncharacterized protein / 0.671
3tlj SAHUncharacterized protein / 0.671
4dmg SAMUncharacterized protein / 0.670
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.669
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.669
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.669
1ahh NAD7-alpha-hydroxysteroid dehydrogenase 1.1.1.159 0.668
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.668
4a6d SAMAcetylserotonin O-methyltransferase 2.1.1.4 0.668
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.668
1nw5 SAMModification methylase RsrI 2.1.1.72 0.667
3lcu SAH16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.665
3lst SAHCalO1 / 0.665
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.664
1jr4 CL4Catechol O-methyltransferase 2.1.1.6 0.662
3ldg SAHUncharacterized protein / 0.662
3sx2 NADUncharacterized protein / 0.662
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.662
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.661
2o07 MTASpermidine synthase 2.5.1.16 0.661
3ou2 SAHSAM-dependent methyltransferase / 0.661
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.660
3eey SAMrRNA methylase / 0.659
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.658
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.658
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.658
2uyh SAHModification methylase HhaI 2.1.1.37 0.657
4htf SAMtRNA 5-carboxymethoxyuridine methyltransferase / 0.654
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.653
3rfx NADUronate dehydrogenase / 0.653
4yuv S4MSpermidine synthase, putative / 0.653
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.652
4wec NADShort chain dehydrogenase / 0.652
3geg NADShort-chain dehydrogenase/reductase SDR / 0.651
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.651
4twr NADNAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase / 0.651
3lcv SAM16S rRNA (guanine(1405)-N(7))-methyltransferase 2.1.1.179 0.650