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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
3axsSFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3axsSFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase/1.000
3axtSAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase/0.769
2ytzSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.572
1g60SAMModification methylase MboII2.1.1.720.489
3vywSAMUncharacterized protein/0.479
3v97SAHRibosomal RNA large subunit methyltransferase K/L2.1.1.1730.478
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.475
5bp7SAHSAM-dependent methyltransferase/0.473
2ejuSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.472
3b7dCNIGlutamate receptor 2/0.470
5epeSAHUncharacterized protein/0.470
3g72A6TRenin3.4.23.150.469
3c9tTPSThiamine-monophosphate kinase/0.465
5bw4SAMUncharacterized protein/0.464
5ekuSAHArginine N-methyltransferase, putative/0.463
3g70A5TRenin3.4.23.150.462
4mubOAQSulfotransferase oxamniquine resistance protein/0.461
1jr4CL4Catechol O-methyltransferase2.1.1.60.460
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.460
3v8vSAMRibosomal RNA large subunit methyltransferase K/L2.1.1.1730.460
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.458
4kwcSAHMethyltransferase domain family/0.458
4uy6SAHHistidine N-alpha-methyltransferase/0.458
1ve3SAMUncharacterized protein/0.457
3ha3SAHHydroxymycolate synthase MmaA42.1.10.457
1nbiSAMGlycine N-methyltransferase2.1.1.200.456
3oadLPORenin3.4.23.150.455
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.454
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.453
1qzzSAMAclacinomycin 10-hydroxylase RdmB4.1.10.453
3p9kSAHCaffeic acid O-methyltransferase/0.453
1jqdSAHHistamine N-methyltransferase2.1.1.80.452
4blwSAHRibosomal RNA large subunit methyltransferase J/0.452
4pyoSAHCatechol O-methyltransferase2.1.1.60.452
1p1bSAHGuanidinoacetate N-methyltransferase2.1.1.20.450
1yf3SAHDNA adenine methylase/0.449
3uj7SAMPhosphoethanolamine N-methyltransferase/0.449
1kiaSAMGlycine N-methyltransferase2.1.1.200.448
2y1xSAHHistone-arginine methyltransferase CARM1/0.448
3nwb659Catechol O-methyltransferase2.1.1.60.448
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.448
3e8sSAHUncharacterized protein/0.447
3ujlA8SAbscisic acid receptor PYL2/0.446
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.444
3sglSAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.444
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.443
3grrSAHProbable ribosomal RNA small subunit methyltransferase A/0.442
4b7754MBeta-secretase 13.4.23.460.442
5dxjSFGHistone-arginine methyltransferase CARM1/0.442
1x1bSAHC-20 methyltransferase/0.441
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.440