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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
3nmu SAM Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.881
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.705
4kwc SAHMethyltransferase domain family / 0.698
2o07 MTASpermidine synthase 2.5.1.16 0.689
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.685
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.684
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.683
3dlc SAMSAM (And some other nucleotide) binding motif:Generic methyltransferase / 0.680
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.680
4c03 SFGProtein arginine N-methyltransferase 6 / 0.680
4kvz SAHPtnL protein / 0.680
1wy7 SAHUncharacterized protein / 0.678
5fa5 MTAProtein arginine N-methyltransferase 5 / 0.678
4yv1 S4MSpermidine synthase, putative / 0.677
3rw9 DSHSpermidine synthase 2.5.1.16 0.676
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.674
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.674
3iv6 SAMUncharacterized protein / 0.673
3sgl SAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC / 0.673
3a27 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.672
2hmv ADPKtr system potassium uptake protein A / 0.669
4gqb 0XUProtein arginine N-methyltransferase 5 / 0.669
4yuv S4MSpermidine synthase, putative / 0.669
4mwz SAMPhosphoethanolamine N-methyltransferase, putative / 0.668
5dst SAHProtein arginine N-methyltransferase 8 2.1.1 0.668
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.667
4yv2 S4MSpermidine synthase, putative / 0.667
1aqi SAHModification methylase TaqI 2.1.1.72 0.666
1ve3 SAMUncharacterized protein / 0.665
5dwq SFGHistone-arginine methyltransferase CARM1 / 0.663
1i3l NADUDP-glucose 4-epimerase / 0.662
2i62 SAHNicotinamide N-methyltransferase 2.1.1.1 0.662
3ou7 SAMSAM-dependent methyltransferase / 0.662
2qe6 SAMUncharacterized protein / 0.661
3ldg SAHUncharacterized protein / 0.661
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.661
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.660
4wxx SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.660
5je4 SAHMethyl transferase / 0.660
1wg8 SAMRibosomal RNA small subunit methyltransferase H / 0.656
4yuz S4MSpermidine synthase, putative / 0.656
3a26 MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.655
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.654
5i39 FADL-amino acid deaminase / 0.654
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.653
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.653
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.652
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.652
1boo SAHModification methylase PvuII 2.1.1.113 0.651
5je3 SAHMethyl transferase / 0.651
2ih5 NEAModification methylase TaqI 2.1.1.72 0.650
2o06 MTASpermidine synthase 2.5.1.16 0.650
4xvy SAHMycinamicin III 3''-O-methyltransferase 2.1.1.237 0.650