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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
2oaeAILDipeptidyl peptidase 4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2oaeAILDipeptidyl peptidase 4/1.000
4ffw715Dipeptidyl peptidase 4/0.604
3qbjNXZDipeptidyl peptidase 4/0.568
2rgu356Dipeptidyl peptidase 4/0.557
3ccc7ACDipeptidyl peptidase 4/0.529
3vjkM51Dipeptidyl peptidase 4/0.526
3opmLUIDipeptidyl peptidase 4/0.523
3f8sPF2Dipeptidyl peptidase 4/0.512
4g1f0WGDipeptidyl peptidase 4/0.512
3g0bT22Dipeptidyl peptidase 4/0.506
3g0gRUMDipeptidyl peptidase 4/0.499
3vjlW94Dipeptidyl peptidase 4/0.497
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.489
3ccbB2YDipeptidyl peptidase 4/0.481
3g0dXIHDipeptidyl peptidase 4/0.476
2aj8SC3Dipeptidyl peptidase 4/0.475
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.474
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.472
3ribSAHN-lysine methyltransferase SMYD2/0.469
1vhzAPRADP compounds hydrolase NudE3.6.10.468
1tllFMNNitric oxide synthase, brain1.14.13.390.467
2ha6SCKAcetylcholinesterase3.1.1.70.467
4a862ANMajor pollen allergen Bet v 1-A/0.463
3h3qH13Collagen type IV alpha-3-binding protein/0.462
4ey6GNTAcetylcholinesterase3.1.1.70.461
2xugTZ4Acetylcholinesterase3.1.1.70.460
4wxg2BOSerine hydroxymethyltransferase/0.460
2whqHI6Acetylcholinesterase3.1.1.70.459
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.458
1gvv0GMEndothiapepsin3.4.23.220.457
2a3bCFFEndochitinase B13.2.1.140.456
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.456
4a81DXCMajor pollen allergen Bet v 1-A/0.456
4bfzZVZPantothenate kinase2.7.1.330.455
2cjfRP43-dehydroquinate dehydratase4.2.1.100.454
2p99YE6Methionine aminopeptidase/0.454
4zwpM44Xaa-Pro dipeptidase3.4.13.90.454
1szfFMNCytochrome b2, mitochondrial1.1.2.30.452
3f7bAG5Carbonic anhydrase 44.2.1.10.452
4gv8DUPDUTPase/0.450
2cv2GSUGlutamate--tRNA ligase6.1.1.170.449
3fsjD7KBenzoylformate decarboxylase4.1.1.70.449
1h60STRPentaerythritol tetranitrate reductase/0.447
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.447
2gqaFMNNADH:flavin oxidoreductase Sye1/0.447
3n71SFGHistone-lysine N-methyltransferase Smyd1/0.447
4fs4H24Beta-secretase 13.4.23.460.447
4a802ANMajor pollen allergen Bet v 1-A/0.446
1q1gMTIPurine nucleoside phosphorylase/0.445
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.445
1qtiGNTAcetylcholinesterase3.1.1.70.444
4a83DXCMajor pollen allergen Bet v 1-A/0.444
4d89BXDBeta-secretase 13.4.23.460.443
4ey7E20Acetylcholinesterase3.1.1.70.443
5c8d5ADProbable transcriptional regulator/0.443
1e81M91Endothiapepsin3.4.23.220.442
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.442
2b3vACODiamine acetyltransferase 1/0.442
4awsFMNNADH:flavin oxidoreductase Sye1/0.442
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.442
2qimZEAClass 10 plant pathogenesis-related protein/0.441
3t7p7SPEndothiapepsin3.4.23.220.441
1po7TZDBenzoylformate decarboxylase4.1.1.70.440
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.440
3c1oNAPEugenol synthase/0.440
3go4SAHUncharacterized protein/0.440
3t88S0N1,4-dihydroxy-2-naphthoyl-CoA synthase/0.440