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
2ydb	NAP	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37

Complex with similar cavities

PDB ID	HET	Uniprot Name	EC Number	Cavity Similarity	Align
2ydb	NAP	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	1.000
2ydd	2AM	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.723
2yq9	2AM	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.684
4wdf	A2P	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.595
4wda	2AM	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.536
4wdg	A2P	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.536
3zbr	NAP	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.530
4wfr	2AM	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.524
3zbs	OVE	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.508
3zbz	OVE	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.496
2yph	QQY	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.495
2gvc	FAD	Thiol-specific monooxygenase	1.14.13	0.462
4bfv	ZVV	Pantothenate kinase	2.7.1.33	0.453
2yoz	OVE	2',3'-cyclic-nucleotide 3'-phosphodiesterase	3.1.4.37	0.446
1rne	C60	Renin	3.4.23.15	0.444
3gwd	FAD	Cyclohexanone monooxygenase	/	0.444
4kqr	VPP	Peptidoglycan D,D-transpeptidase FtsI	/	0.444
2gev	COK	Pantothenate kinase	2.7.1.33	0.440
4kqq	VPP	Peptidoglycan D,D-transpeptidase FtsI	/	0.440