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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
4yv2S4MSpermidine synthase, putative

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4yv2S4MSpermidine synthase, putative/1.000
4yuzS4MSpermidine synthase, putative/0.517
4yv0S4MSpermidine synthase, putative/0.470
3sdkP3NProteasome subunit beta type-53.4.25.10.451
3sdkP3NProteasome subunit beta type-63.4.25.10.451
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
3oibFDAPutative acyl-CoA dehydrogenase/0.450
2zgzGNPPlasmid segregation protein ParM/0.449
4q71FADBifunctional protein PutA/0.448
2a8xFADDihydrolipoyl dehydrogenase1.8.1.40.447
4l7f1V5Mitogen-activated protein kinase 82.7.11.240.446
2fznFADBifunctional protein PutA1.5.5.20.445
4g1wG1WMitogen-activated protein kinase 82.7.11.240.445
4ienCOAPutative acyl-CoA hydrolase/0.445
4q73FADBifunctional protein PutA/0.445
2pt6S4MSpermidine synthase/0.444
3rw9DSHSpermidine synthase2.5.1.160.444
2vo6M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
4an4DUDPutative glycosyl transferase/0.443
1w2xRCPAcetyl-CoA carboxylase/0.442
2uw0GVKcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
1q4t4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.441
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.441
4ekeD1IGlycogen phosphorylase, muscle form2.4.1.10.441
4nmdFDABifunctional protein PutA/0.441
1f4fTP3Thymidylate synthase/0.440
1tj0FADBifunctional protein PutA1.5.5.20.440