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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
2msdGNPMHC class I alpha chain

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2msdGNPMHC class I alpha chain/1.000
2mseGNPMHC class I alpha chain/0.564
2rgeGNPGTPase HRas/0.494
3pitGNPRas-related protein M-Ras/0.490
1xtrGNPGTP-binding protein Rheb/0.478
3bbpGTPRas-related protein Rab-6A/0.478
3a6pGTPGTP-binding nuclear protein Ran/0.472
4dsnGCPGTPase KRas/0.472
1yhnGTPRas-related protein Rab-7a/0.470
2rgcGNPGTPase HRas/0.469
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.468
3ddcGNPGTPase HRas/0.468
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.466
1m7bGTPRho-related GTP-binding protein RhoE/0.464
3nbzGTPGTP-binding nuclear protein Ran/0.464
2gilGTPRas-related protein Rab-6A/0.460
2mscGDPMHC class I alpha chain/0.460
4nyiGNPGTPase HRas/0.460
2rgbGNPGTPase HRas/0.459
3lbnGNPGTPase HRas/0.459
3oesGNPGTPase RhebL1/0.459
3tgpGNPGTPase HRas/0.459
1x1bSAHC-20 methyltransferase/0.458
1kmqGNPTransforming protein RhoA/0.457
1x1dSAHC-20 methyltransferase/0.457
1zc4GNPRas-related protein Ral-A/0.457
3oivGNPGTPase HRas/0.456
1xtsGTPGTP-binding protein Rheb/0.455
3ekuCY9Actin-5C/0.455
2y60M8FIsopenicillin N synthase1.21.3.10.454
3kkoGNPRas-related protein M-Ras/0.454
3mjhGTPRas-related protein Rab-5A/0.454
3rs7GNPGTPase HRas/0.454
4k81GTPGTPase HRas/0.454
4lucGDPGTPase KRas/0.454
1zc3GNPRas-related protein Ral-A/0.453
4nyjGNPGTPase HRas/0.453
3oiwGNPGTPase HRas/0.451
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.450
3oiuGNPGTPase HRas/0.450
3i3sGNPGTPase HRas/0.449
3ox4NADAlcohol dehydrogenase 21.1.1.10.449
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.448
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.448
2fe4GDPRas-related protein Rab-6B/0.447
4g0nGNPGTPase HRas/0.447
4nv14TGFormyl transferase/0.447
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.444
3v4fGNPGTPase HRas/0.444
3w3zGTPGTP-binding nuclear protein Ran/0.444
4ambDUDPutative glycosyl transferase/0.444
1galFADGlucose oxidase1.1.3.40.443
3kz1GSPTransforming protein RhoA/0.443
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.443
1qiqACCIsopenicillin N synthase1.21.3.10.442
1krrACOGalactoside O-acetyltransferase2.3.1.180.441
1zp4FAD5,10-methylenetetrahydrofolate reductase1.5.1.200.441
3lawGNPRas-related protein Rab-7a/0.441
3tnfGNPRas-related protein Rab-8A/0.441
3a58GNPGTP-binding protein RHO1/0.440