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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3axsSFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3axsSFGtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase/1.000
3axtSAMtRNA (guanine(26)-N(2)/guanine(27)-N(2))-dimethyltransferase/0.768
2ytzSAHtRNA (guanine(26)-N(2))-dimethyltransferase/0.559
1g60SAMModification methylase MboII2.1.1.720.481
3v97SAHRibosomal RNA large subunit methyltransferase K/L2.1.1.1730.475
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.473
5epeSAHUncharacterized protein/0.470
3vywSAMUncharacterized protein/0.468
3rmeRMEAcidic mammalian chitinase3.2.1.140.467
1jr4CL4Catechol O-methyltransferase2.1.1.60.465
5bw4SAMUncharacterized protein/0.464
3c9tTPSThiamine-monophosphate kinase/0.462
3v8vSAMRibosomal RNA large subunit methyltransferase K/L2.1.1.1730.459
2a4xBLMMitomycin-binding protein/0.458
3g72A6TRenin3.4.23.150.456
1nbiSAMGlycine N-methyltransferase2.1.1.200.455
4kwcSAHMethyltransferase domain family/0.455
5bp7SAHSAM-dependent methyltransferase/0.455
3bi6396Wee1-like protein kinase2.7.10.20.454
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.452
2c1aI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
4uy6SAHHistidine N-alpha-methyltransferase/0.451
3ow3SMYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.450
3p9kSAHCaffeic acid O-methyltransferase/0.450
4mubOAQSulfotransferase oxamniquine resistance protein/0.450
5fhqDNCCatechol O-methyltransferase2.1.1.60.450
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.449
3k1wBFXRenin3.4.23.150.449
2y1xSAHHistone-arginine methyltransferase CARM1/0.448
3nwb659Catechol O-methyltransferase2.1.1.60.448
1kiaSAMGlycine N-methyltransferase2.1.1.200.447
1ve3SAMUncharacterized protein/0.447
2zvjKOMCatechol O-methyltransferase2.1.1.60.447
3g70A5TRenin3.4.23.150.447
2bktRPFRenin3.4.23.150.446
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.446
3ujlA8SAbscisic acid receptor PYL2/0.446
2uw5GVNcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3lhdSAHtRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI2.1.1.2190.444
3sglSAMtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.444
3uj7SAMPhosphoethanolamine N-methyltransferase/0.444
3a7dFBNCatechol O-methyltransferase2.1.1.60.443
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.443
3grrSAHProbable ribosomal RNA small subunit methyltransferase A/0.442
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.442
5dxjSFGHistone-arginine methyltransferase CARM1/0.442
4blwSAHRibosomal RNA large subunit methyltransferase J/0.441