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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
3t2wBTNAvidin/streptavidin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3t2wBTNAvidin/streptavidin/1.000
1srhMOBStreptavidin/0.599
2izkGLLStreptavidin/0.587
1lcwSHMStreptavidin/0.581
2rtmIMIStreptavidin/0.579
2izhBTNStreptavidin/0.574
4bx7B4FStreptavidin/0.567
2rtgBTNStreptavidin/0.566
4dneDTBStreptavidin/0.564
2rtfBTNStreptavidin/0.561
3ry2BTNStreptavidin/0.553
2izgBTNStreptavidin/0.546
2rtnIMIStreptavidin/0.542
1srfMTBStreptavidin/0.537
2rtiGLLStreptavidin/0.535
3wznBTNStreptavidin/0.534
4gdaBTNStreptavidin/0.534
1mk5BTNStreptavidin/0.532
1sreHABStreptavidin/0.531
2rtdBTNStreptavidin/0.531
2izfBTNStreptavidin/0.530
1df8BTNStreptavidin/0.525
2izjBTNStreptavidin/0.524
2rtoIMIStreptavidin/0.524
1sriDMBStreptavidin/0.519
2izlIMIStreptavidin/0.519
1luqBTNStreptavidin/0.518
1lczBH7Streptavidin/0.517
2rtpIMIStreptavidin/0.517
2rtqIMIStreptavidin/0.517
2rteBTNStreptavidin/0.516
2rtrIMIStreptavidin/0.516
2rtkGLLStreptavidin/0.515
1swtBTNStreptavidin/0.514
2fhnBNIAvidin-related protein 4/5/0.511
3ew2BTNHypothetical conserved protein/0.509
3wyqBTNStreptavidin/0.509
1i9hBNIStreptavidin/0.501
4psbGA3Cytokinin-specific binding protein/0.498
1srgMHBStreptavidin/0.497
2aviBTNAvidin/0.496
1srjNABStreptavidin/0.492
4ggzBTNBll1558 protein/0.492
4z28BTNHoefavidin/0.490
1nc9IMIStreptavidin/0.489
2y3fBTNStreptavidin/0.488
5stdUNNScytalone dehydratase4.2.1.940.487
1rxhBNIStreptavidin/0.483
3h3sH15Collagen type IV alpha-3-binding protein/0.483
4a81DXCMajor pollen allergen Bet v 1-A/0.477
2c4iBTNAvidin/0.476
1ndjBTNStreptavidin/0.473
3ivcFG4Pantothenate synthetase6.3.2.10.473
1swpBTQStreptavidin/0.472
1avdBTNAvidin/0.471
1stpBTNStreptavidin/0.471
2iziBTNStreptavidin/0.471
3h3qH13Collagen type IV alpha-3-binding protein/0.470
3h3r14HCollagen type IV alpha-3-binding protein/0.466
4a862ANMajor pollen allergen Bet v 1-A/0.466
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.465
2npfMOUElongation factor 2/0.464
3lqfNADGalactitol dehydrogenase/0.464
4a86H35Major pollen allergen Bet v 1-A/0.464
4h6pFMNChromate reductase/0.464
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.463
2zs8ADPPantothenate kinase2.7.1.330.462
2rtlIMIStreptavidin/0.461
2uywBTNAvd protein/0.460
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.458
2oegUPGUDP-glucose pyrophosphorylase/0.457
3nmpPYVAbscisic acid receptor PYL2/0.457
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
3rdqDTBStreptavidin/0.457
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.456
3h3t16HCollagen type IV alpha-3-binding protein/0.456
3t4hMD5Alpha-ketoglutarate-dependent dioxygenase AlkB1.14.11.330.456
1swnBTNStreptavidin/0.455
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.455
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.454
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
1n0uSO1Elongation factor 2/0.452
1swpBTNStreptavidin/0.452
3g7jGTXGlutathione transferase GST1-4/0.452
1n43BTNStreptavidin/0.451
3a26MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.451
1hb1OCVIsopenicillin N synthase1.21.3.10.450
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
3b4p3B4Phenazine biosynthesis protein A/B/0.450
3dcwEZLCarbonic anhydrase 24.2.1.10.449
3bk2U5PRibonuclease J/0.448
4dz5NAPAldo-keto reductase family 1 member C3/0.447
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.447
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.447
3fhxPLPPyridoxal kinase2.7.1.350.446
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4a802ANMajor pollen allergen Bet v 1-A/0.446
4g8jTHMUridine phosphorylase/0.446
2v57PRLTetR family transcriptional regulator/0.445
4a8v2ANMajor pollen allergen Bet v 1-J/0.445
4bcsBTNAvidin-related protein 4/5/0.445
2zscBTNTamavidin2/0.444
4u7wNDPMxaA/0.444
1ra3MTXDihydrofolate reductase1.5.1.30.443
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.443
3uq9TBNPutative adenosine kinase/0.443
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3ho2N323-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.442
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4kak06UDihydrofolate reductase1.5.1.30.442
1lkeDOGBilin-binding protein/0.441
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3gxfIFMGlucosylceramidase3.2.1.450.441
3ntz3TZDihydrofolate reductase1.5.1.30.441
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
8catNDPCatalase1.11.1.60.441
1x2eATXProline iminopeptidase3.4.11.50.440
2bn4FADNADPH--cytochrome P450 reductase/0.440
4bb3KKAIsopenicillin N synthase1.21.3.10.440
4ts7ADPPurine phosphoribosyltransferase (GpT-1)/0.440