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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
3lhd SAH tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3lhd SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.785
1g7u PEP2-dehydro-3-deoxyphosphooctonate aldolase 2.5.1.55 0.744
4e5i 0N9Polymerase acidic protein / 0.744
3lga SAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI 2.1.1.219 0.702
4iv8 SAMPhosphoethanolamine N-methyltransferase,putative / 0.694
4yac NAIC alpha-dehydrogenase / 0.692
4qnu GEKtRNA U34 carboxymethyltransferase / 0.690
1d2h SAHGlycine N-methyltransferase 2.1.1.20 0.687
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.680
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.676
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.675
5bp9 SAHPutative methyltransferase protein / 0.673
3go4 SAHUncharacterized protein / 0.672
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.672
5je2 SAHMethyl transferase / 0.668
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.667
1wy7 SAHUncharacterized protein / 0.665
3mht SAHModification methylase HhaI 2.1.1.37 0.664
7mht SAHModification methylase HhaI 2.1.1.37 0.664
2o06 MTASpermidine synthase 2.5.1.16 0.662
2okc SAMProbable type I restriction enzyme BthVORF4518P M protein 2.1.1.72 0.662
2ag5 NAD3-hydroxybutyrate dehydrogenase type 2 / 0.661
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.661
3sx2 NADUncharacterized protein / 0.660
4e5f 0N7Polymerase acidic protein / 0.660
2fkn NADUrocanate hydratase 4.2.1.49 0.659
3t7s SAMUncharacterized protein / 0.659
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.656
2bgm NAJSecoisolariciresinol dehydrogenase 1.1.1.331 0.656
2o07 MTASpermidine synthase 2.5.1.16 0.656
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.654
4nec SAHPutative SAM-dependent methyltransferase / 0.653
3qow SAMHistone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.652
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.651
3tm4 SAMUncharacterized protein / 0.651
5eku SAHArginine N-methyltransferase, putative / 0.650