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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
3vyw SAM Uncharacterized protein

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3vyw SAMUncharacterized protein / 1.133
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.745
1yf3 SAHDNA adenine methylase / 0.744
3c3y SAHO-methyltransferase / 0.742
3duw SAHO-methyltransferase, putative / 0.741
3v8v SAMRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.733
4x7y SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.731
2hnk SAHSAM-dependent O-methyltransferase / 0.730
4gf5 SAHCalS11 / 0.724
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.721
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.717
2pwy SAHtRNA (adenine(58)-N(1))-methyltransferase TrmI 2.1.1.220 0.712
1p1b SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.711
1khh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.709
3gry SAMProbable ribosomal RNA small subunit methyltransferase A / 0.709
2plw SAMRibosomal RNA methyltransferase, putative / 0.708
4n48 SAMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 1 2.1.1.57 0.708
3dmg SAHProbable ribosomal RNA small subunit methyltransferase / 0.706
2wa2 SAMGenome polyprotein / 0.705
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.703
3evc SAHGenome polyprotein 2.1.1.56 0.698
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.697
3eey SAMrRNA methylase / 0.695
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.694
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.693
3tr6 SAHO-methyltransferase / 0.690
4poo SAMPutative RNA methylase / 0.690
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.689
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.684
3evb SAHGenome polyprotein 2.1.1.56 0.684
2zul SAMProbable ribosomal RNA small subunit methyltransferase / 0.679
3ely SAHMethyltransferase / 0.679
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.679
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.678
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.677
3p97 SAMGenome polyprotein 2.1.1.56 0.675
5jjr SAHGenome polyprotein / 0.675
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.674
3eva SAHGenome polyprotein 2.1.1.56 0.674
4oa5 SAHO-methyltransferase family protein / 0.674
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.673
3ssm SAHMycinamicin VI 2''-O-methyltransferase / 0.673
3p8z SAHGenome polyprotein 2.1.1.56 0.672
1l3i SAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) / 0.671
5dto SAHGenome polyprotein / 0.671
2bm9 SAMCephalosporin hydroxylase CmcI / 0.670
3sso SAHMycinamicin VI 2''-O-methyltransferase / 0.670
2br5 SAHCephalosporin hydroxylase CmcI / 0.668
2zwv SAHProbable ribosomal RNA small subunit methyltransferase / 0.667
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.667
3sr4 TT8Histone-lysine N-methyltransferase, H3 lysine-79 specific 2.1.1.43 0.667
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.664
1r6a SAHGenome polyprotein 2.7.7.48 0.663
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.663
4blv SAMRibosomal RNA large subunit methyltransferase J / 0.662
1l9k SAHGenome polyprotein 2.7.7.48 0.661
4ctj SAMGenome polyprotein / 0.660
4ctk SAMGenome polyprotein / 0.660
2cww SAHUncharacterized protein / 0.659
3rw9 DSHSpermidine synthase 2.5.1.16 0.659
4uck SAMLarge structural protein / 0.657
5je3 SAHMethyl transferase / 0.657
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.656
5jdz SAHMethyl transferase / 0.656
5d4u SAMUncharacterized protein MJ0489 / 0.654
1mht SAHModification methylase HhaI 2.1.1.37 0.652
3b3f SAHHistone-arginine methyltransferase CARM1 / 0.652
3eld SFGMethyltransferase / 0.652
3lcc SAHThiocyanate methyltransferase 1 / 0.652
2px5 SAHGenome polyprotein 2.7.7.48 0.650