sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Distribution of Cavity similarities measured by Shaper

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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
3pt9	SAH	DNA (cytosine-5)-methyltransferase 1	2.1.1.37

Complex with similar cavities

PDB ID	HET	Uniprot Name	EC Number	Cavity Similarity	Align
3pt9	SAH	DNA (cytosine-5)-methyltransferase 1	2.1.1.37	1.000
4wxx	SAH	DNA (cytosine-5)-methyltransferase 1	2.1.1.37	0.568
3pt6	SAH	DNA (cytosine-5)-methyltransferase 1	2.1.1.37	0.562
2hmy	SAM	Modification methylase HhaI	2.1.1.37	0.540
4h0n	SAH	Dnmt2	/	0.516
1skm	SAH	Modification methylase HhaI	2.1.1.37	0.483
4da4	SAH	DNA (cytosine-5)-methyltransferase 1	2.1.1.37	0.473
7mht	SAH	Modification methylase HhaI	2.1.1.37	0.471
4onj	SFG	DNA methyltransferase	/	0.467
1boo	SAH	Modification methylase PvuII	2.1.1.113	0.459
3qv2	SAH	5-cytosine DNA methyltransferase	/	0.459
3tm5	SFG	Uncharacterized protein	/	0.459
2zcj	SAH	Modification methylase HhaI	2.1.1.37	0.451
5mht	SAH	Modification methylase HhaI	2.1.1.37	0.451
4rtl	SFG	DNA adenine methylase	2.1.1.72	0.450
3egv	SAH	Ribosomal protein L11 methyltransferase	2.1.1	0.449
4anx	534	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform	2.7.1.153	0.443