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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
3m6v SAM Ribosomal RNA small subunit methyltransferase F

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3m6v SAMRibosomal RNA small subunit methyltransferase F / 1.058
3m6w SAMRibosomal RNA small subunit methyltransferase F / 0.906
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.801
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.775
3a4t SFGtRNA (cytosine(48)-C(5))-methyltransferase 2.1.1 0.749
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.747
2dpm SAMModification methylase DpnIIA 2.1.1.72 0.711
2yx1 SFGtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.710
4rtk SAHDNA adenine methylase 2.1.1.72 0.701
2yxl SFG450aa long hypothetical fmu protein / 0.692
1yf3 SAHDNA adenine methylase / 0.688
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.679
2g1p SAHDNA adenine methylase 2.1.1.72 0.676
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.676
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.667
4blw SAHRibosomal RNA large subunit methyltransferase J / 0.666
3cbg SAHO-methyltransferase / 0.662
4rtj SFGDNA adenine methylase 2.1.1.72 0.662
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.660
4rtm SAMDNA adenine methylase 2.1.1.72 0.659
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.657
3axt SAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.656
3ldg SAHUncharacterized protein / 0.655
3pt6 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.650