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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3lgaSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.219

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3lgaSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2191.000
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.508
4oa5SAHO-methyltransferase family protein/0.506
5ccbSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.497
1i9gSAMtRNA (adenine(58)-N(1))-methyltransferase TrmI/0.488
2yvlSAMtRNA (adenine(58)-N(1))-methyltransferase TrmI/0.487
2dpmSAMModification methylase DpnIIA2.1.1.720.485
3swrSFGDNA (cytosine-5)-methyltransferase 12.1.1.370.484
3tm4SAMUncharacterized protein/0.481
2pwySAHtRNA (adenine(58)-N(1))-methyltransferase TrmI2.1.1.2200.478
3friSAH16S rRNA methylase/0.472
1nw5SAMModification methylase RsrI2.1.1.720.471
4qppSAHProtein arginine N-methyltransferase 6/0.471
3tm5SFGUncharacterized protein/0.470
3tr6SAHO-methyltransferase/0.466
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.466
1booSAHModification methylase PvuII2.1.1.1130.465
3grySAMProbable ribosomal RNA small subunit methyltransferase A/0.465
3p9kSAHCaffeic acid O-methyltransferase/0.464
3tljSAHUncharacterized protein/0.464
4c05SAHProtein arginine N-methyltransferase 6/0.464
4rtlSFGDNA adenine methylase2.1.1.720.464
5ccxSAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A2.1.1.2200.464
2g1pSAHDNA adenine methylase2.1.1.720.463
2zifSAMMethyltransferase/0.463
5ekuSAHArginine N-methyltransferase, putative/0.463
3duwSAHO-methyltransferase, putative/0.462
4gbeSAHDNA adenine methylase2.1.1.720.461
4rtpSAMDNA adenine methylase2.1.1.720.460
4wxxSAHDNA (cytosine-5)-methyltransferase 12.1.1.370.460
4rtrSAMDNA adenine methylase2.1.1.720.457
4rtnSAHDNA adenine methylase2.1.1.720.456
2eg5SAH7-methylxanthosine synthase 1/0.455
4golSA8DNA adenine methylase2.1.1.720.455
2hnkSAHSAM-dependent O-methyltransferase/0.454
2nxeSAMRibosomal protein L11 methyltransferase2.1.10.454
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
2oreSAHDNA adenine methylase2.1.1.720.451
4mwzSAMPhosphoethanolamine N-methyltransferase, putative/0.451
1bc5SAHChemotaxis protein methyltransferase2.1.1.800.450
4fr0SAMArsenic methyltransferase/0.450
4rv9SAHD-mycarose 3-C-methyltransferase/0.450
4y93746Tyrosine-protein kinase/0.450
4h0nSAHDnmt2/0.448
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.448
5je4SAHMethyl transferase/0.447
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.446
4rtmSAMDNA adenine methylase2.1.1.720.446
3qv2SAH5-cytosine DNA methyltransferase/0.445
2ih2NEAModification methylase TaqI2.1.1.720.443
1pg3PRXAcetyl-coenzyme A synthetase/0.441
3ha7B32Hydroxymycolate synthase MmaA42.1.10.441
3ldgSAHUncharacterized protein/0.441
1skmSAHModification methylase HhaI2.1.1.370.440
3a4vNADNDP-sugar epimerase/0.440
3bgiSAHThiopurine S-methyltransferase2.1.1.670.440
4rtqSAHDNA adenine methylase2.1.1.720.440