Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
2ytz SAH tRNA (guanine(26)-N(2))-dimethyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2ytz SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.997
2eju SAHtRNA (guanine(26)-N(2))-dimethyltransferase / 0.938
5bxy SAHPutative RNA methylase family UPF0020 / 0.715
4gek GEKCarboxy-S-adenosyl-L-methionine synthase / 0.711
4gf5 SAHCalS11 / 0.702
2yvl SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.698
3c3y SAHO-methyltransferase / 0.698
4pyn SAHCatechol O-methyltransferase 2.1.1.6 0.697
4obw SAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial / 0.693
4qdk SAHMagnesium-protoporphyrin O-methyltransferase 2.1.1.11 0.692
3v97 SAHRibosomal RNA large subunit methyltransferase K/L 2.1.1.173 0.688
2g1p SAHDNA adenine methylase 2.1.1.72 0.687
4iv0 SAMPhosphoethanolamine N-methyltransferase, putative / 0.686
1nv8 SAMRelease factor glutamine methyltransferase 2.1.1.297 0.685
1sqf SAMRibosomal RNA small subunit methyltransferase B 2.1.1.176 0.685
1z3c SA8mRNA cap guanine-N7 methyltransferase 2.1.1.56 0.684
1kr5 SAHProtein-L-isoaspartate(D-aspartate) O-methyltransferase 2.1.1.77 0.682
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.682
2i9k SAHModification methylase HhaI 2.1.1.37 0.681
2zzm SAMtRNA (guanine(37)-N1)-methyltransferase Trm5b 2.1.1.228 0.681
3u81 SAHCatechol O-methyltransferase 2.1.1.6 0.679
5ccb SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.679
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.678
2yqz SAMUncharacterized protein / 0.677
3cbg SAHO-methyltransferase / 0.677
1i9g SAMtRNA (adenine(58)-N(1))-methyltransferase TrmI / 0.676
4fgz SAHPhosphoethanolamine N-methyltransferase / 0.676
3ldf SAHUncharacterized protein / 0.674
4ymg SAMPutative SAM-dependent O-methyltranferase / 0.673
2br5 SAHCephalosporin hydroxylase CmcI / 0.671
3axs SFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase / 0.670
5bp9 SAHPutative methyltransferase protein / 0.670
3rw9 DSHSpermidine synthase 2.5.1.16 0.669
4nec SAHPutative SAM-dependent methyltransferase / 0.669
2a14 SAHIndolethylamine N-methyltransferase 2.1.1.49 0.668
4dmg SAMUncharacterized protein / 0.668
4kdr SAHUbiquinone biosynthesis O-methyltransferase / 0.668
4lwp SAHArginine N-methyltransferase, putative / 0.668
3grr SAHProbable ribosomal RNA small subunit methyltransferase A / 0.667
4fzv SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.667
1nbi SAMGlycine N-methyltransferase 2.1.1.20 0.666
1ve3 SAMUncharacterized protein / 0.665
5je2 SAHMethyl transferase / 0.665
3a25 SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase / 0.664
2hmv ADPKtr system potassium uptake protein A / 0.663
3mte SAM16S rRNA (adenine(1408)-N(1))-methyltransferase 2.1.1.180 0.663
3ou6 SAMSAM-dependent methyltransferase / 0.663
3vyw SAMUncharacterized protein / 0.663
3wst SAHProtein arginine N-methyltransferase 7 2.1.1 0.662
3lcc SAHThiocyanate methyltransferase 1 / 0.661
4o29 SAHProtein-L-isoaspartate O-methyltransferase / 0.661
4oa5 SAHO-methyltransferase family protein / 0.661
1g60 SAMModification methylase MboII 2.1.1.72 0.660
3ou2 SAHSAM-dependent methyltransferase / 0.660
5e72 SAMN2, N2-dimethylguanosine tRNA methyltransferase / 0.660
2hnk SAHSAM-dependent O-methyltransferase / 0.658
3tr6 SAHO-methyltransferase / 0.658
5e8j SAHmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.658
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.657
2gs9 SAHUncharacterized protein / 0.656
3q87 SAMN6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) / 0.656
4r6x SAHPhosphoethanolamine N-methyltransferase / 0.656
4rtk SAHDNA adenine methylase 2.1.1.72 0.656
3orh SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.655
4hh4 SAHCcbJ / 0.655
5k7w SAHN6-adenosine-methyltransferase 70 kDa subunit / 0.655
2hv9 SFGmRNA cap guanine-N7 methyltransferase 2.1.1.56 0.654
3tos SAHCalS11 / 0.654
2nxe SAMRibosomal protein L11 methyltransferase 2.1.1 0.653
2oy0 SAHGenome polyprotein / 0.653
3nmu SAMFibrillarin-like rRNA/tRNA 2'-O-methyltransferase / 0.653
4yuz S4MSpermidine synthase, putative / 0.653
1p1c SAHGuanidinoacetate N-methyltransferase 2.1.1.2 0.652
3uj7 SAMPhosphoethanolamine N-methyltransferase / 0.652
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.651
4u7t SAHDNA (cytosine-5)-methyltransferase 3A 2.1.1.37 0.651
3ou7 SAMSAM-dependent methyltransferase / 0.650
3pt9 SAHDNA (cytosine-5)-methyltransferase 1 2.1.1.37 0.650