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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
3eey SAM rRNA methylase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3eey SAMrRNA methylase / 1.031
4poo SAMPutative RNA methylase / 0.941
3lby SAHUncharacterized protein / 0.739
4rtj SFGDNA adenine methylase 2.1.1.72 0.736
4rtk SAHDNA adenine methylase 2.1.1.72 0.736
4l7v SAHProtein-L-isoaspartate O-methyltransferase / 0.730
4gbe SAHDNA adenine methylase 2.1.1.72 0.726
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.717
1yf3 SAHDNA adenine methylase / 0.717
1skm SAHModification methylase HhaI 2.1.1.37 0.712
2g1p SAHDNA adenine methylase 2.1.1.72 0.709
7mht SAHModification methylase HhaI 2.1.1.37 0.709
3mht SAHModification methylase HhaI 2.1.1.37 0.705
1nw5 SAMModification methylase RsrI 2.1.1.72 0.704
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.700
4rtm SAMDNA adenine methylase 2.1.1.72 0.698
2i9k SAHModification methylase HhaI 2.1.1.37 0.697
3e23 SAMUncharacterized protein / 0.697
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.697
3vyw SAMUncharacterized protein / 0.695
2uyh SAHModification methylase HhaI 2.1.1.37 0.694
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.692
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.691
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.689
4dkj SAHCytosine-specific methyltransferase / 0.684
3tr6 SAHO-methyltransferase / 0.681
4dmg SAMUncharacterized protein / 0.678
2z6u SAHModification methylase HhaI 2.1.1.37 0.676
5mht SAHModification methylase HhaI 2.1.1.37 0.676
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.674
1r00 SAHAclacinomycin 10-hydroxylase RdmB 4.1.1 0.673
2yxl SFG450aa long hypothetical fmu protein / 0.673
4rtl SFGDNA adenine methylase 2.1.1.72 0.673
2c7q SAHModification methylase HhaI 2.1.1.37 0.672
5bxy SAHPutative RNA methylase family UPF0020 / 0.671
10mh SAHModification methylase HhaI 2.1.1.37 0.670
3duw SAHO-methyltransferase, putative / 0.670
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.669
1g60 SAMModification methylase MboII 2.1.1.72 0.668
3cbg SAHO-methyltransferase / 0.668
1eg2 MTAModification methylase RsrI 2.1.1.72 0.667
2zcj SAHModification methylase HhaI 2.1.1.37 0.667
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.667
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.667
8mht SAHModification methylase HhaI 2.1.1.37 0.666
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.665
4ek9 EP4Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.665
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.664
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.664
1wy7 SAHUncharacterized protein / 0.663
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.663
2bm9 SAMCephalosporin hydroxylase CmcI / 0.662
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.662
3ldg SAHUncharacterized protein / 0.662
1boo SAHModification methylase PvuII 2.1.1.113 0.661
1fjx SAHModification methylase HhaI 2.1.1.37 0.661
5k7u SAMN6-adenosine-methyltransferase 70 kDa subunit / 0.660
2bzg SAHThiopurine S-methyltransferase 2.1.1.67 0.659
2o06 MTASpermidine synthase 2.5.1.16 0.659
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.659
3qv2 SAH5-cytosine DNA methyltransferase / 0.659
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.659
5bp9 SAHPutative methyltransferase protein / 0.659
2cww SAHUncharacterized protein / 0.658
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.658
3c3y SAHO-methyltransferase / 0.658
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.656
9mht SAHModification methylase HhaI 2.1.1.37 0.655
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.654
3bgv SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
1txz APRProbable ADP-ribose 1''-phosphate phosphatase YML087W 3.1.3.84 0.652
2hnk SAHSAM-dependent O-methyltransferase / 0.652