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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
3gyq SAM 23S rRNA (adenosine(1067)-2'-O)-methyltransferase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3gyq SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 1.003
3n4k SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.754
4cnf MTASpoU rRNA methylase / 0.740
2egv SAMRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.736
4cng SAHSpoU rRNA methylase / 0.736
4kgn SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.730
4pzk SAHPutative tRNA (cytidine(34)-2'-O)-methyltransferase / 0.730
4jal SAHtRNA (cytidine(34)-2'-O)-methyltransferase / 0.715
2ha8 SAHProbable methyltransferase TARBP1 / 0.709
4x3l MTARNA 2'-O ribose methyltransferase / 0.705
4fak SAMRibosomal RNA large subunit methyltransferase H / 0.703
5a7y SAHtRNA (adenine(9)-N1)-methyltransferase 2.1.1.218 0.703
4xbo SAHtRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ 2.1.1.200 0.699
3nk7 SAM23S rRNA (adenosine(1067)-2'-O)-methyltransferase / 0.690
2egw SAHRibosomal RNA small subunit methyltransferase E 2.1.1.193 0.688
5c77 SAHProtein arginine N-methyltransferase SFM1 / 0.676
1kh2 ATPArgininosuccinate synthase / 0.667
3oii SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.667
4x3m ADNRNA 2'-O ribose methyltransferase / 0.664
1kor ANPArgininosuccinate synthase / 0.663
1uam SAHtRNA (guanine-N(1)-)-methyltransferase 2.1.1.228 0.663
4h3z SAHtRNA (guanine-N(1)-)-methyltransferase / 0.661
3oij SAHRibosomal RNA small subunit methyltransferase NEP1 / 0.659
3nd1 SAHPrecorrin-6A synthase (Deacetylating) / 0.652