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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
2cww SAH Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2cww SAHUncharacterized protein / 1.017
4dmg SAMUncharacterized protein / 0.835
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.785
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.755
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.749
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.739
3tos SAHCalS11 / 0.738
4gf5 SAHCalS11 / 0.732
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.727
2g1p SAHDNA adenine methylase 2.1.1.72 0.725
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.722
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.720
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.718
5il2 SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.718
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.714
2hnk SAHSAM-dependent O-methyltransferase / 0.712
3cbg SAHO-methyltransferase / 0.710
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.707
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.706
3c3y SAHO-methyltransferase / 0.705
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.704
9mht SAHModification methylase HhaI 2.1.1.37 0.703
10mh SAHModification methylase HhaI 2.1.1.37 0.702
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.699
4poo SAMPutative RNA methylase / 0.698
4rtl SFGDNA adenine methylase 2.1.1.72 0.697
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.694
5il1 SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.694
4dkj SAHCytosine-specific methyltransferase / 0.693
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.692
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.690
5mht SAHModification methylase HhaI 2.1.1.37 0.690
3duw SAHO-methyltransferase, putative / 0.689
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.685
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.684
4oa5 SAHO-methyltransferase family protein / 0.684
1skm SAHModification methylase HhaI 2.1.1.37 0.683
2c7q SAHModification methylase HhaI 2.1.1.37 0.682
2zzn SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.681
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.679
4rtj SFGDNA adenine methylase 2.1.1.72 0.679
5d4v SAHUncharacterized protein MJ0489 / 0.679
5d4u SAMUncharacterized protein MJ0489 / 0.675
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.672
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.671
2bm9 SAMCephalosporin hydroxylase CmcI / 0.671
2yxl SFG450aa long hypothetical fmu protein / 0.670
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.669
2plw SAMRibosomal RNA methyltransferase, putative / 0.668
2px2 SAHGenome polyprotein 2.7.7.48 0.668
4rtn SAHDNA adenine methylase 2.1.1.72 0.668
2zcj SAHModification methylase HhaI 2.1.1.37 0.667
3qv2 SAH5-cytosine DNA methyltransferase / 0.665
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.664
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.663
2i9k SAHModification methylase HhaI 2.1.1.37 0.662
1eg2 MTAModification methylase RsrI 2.1.1.72 0.661
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.661
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.660
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.660
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.659
3vyw SAMUncharacterized protein / 0.659
3eey SAMrRNA methylase / 0.658
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.656
4gol SA8DNA adenine methylase 2.1.1.72 0.656
1nw5 SAMModification methylase RsrI 2.1.1.72 0.655
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.654
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.653
1yf3 SAHDNA adenine methylase / 0.653
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.651
2z6u SAHModification methylase HhaI 2.1.1.37 0.651
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.651
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.651
4gbe SAHDNA adenine methylase 2.1.1.72 0.651
7mht SAHModification methylase HhaI 2.1.1.37 0.651