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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
1nc9IMIStreptavidin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1nc9IMIStreptavidin/1.000
1n9mBTNStreptavidin/0.583
1ndjBTNStreptavidin/0.583
1swnBTNStreptavidin/0.582
1sweBTNStreptavidin/0.568
3wypBSOStreptavidin/0.567
2rtgBTNStreptavidin/0.561
1swpBTQStreptavidin/0.558
1stpBTNStreptavidin/0.557
1swpBTNStreptavidin/0.557
1mk5BTNStreptavidin/0.554
1sriDMBStreptavidin/0.554
4ggzBTNBll1558 protein/0.554
1n43BTNStreptavidin/0.553
2rtiGLLStreptavidin/0.553
4gdaBTNStreptavidin/0.551
2izkGLLStreptavidin/0.541
4bx7B4FStreptavidin/0.541
1srgMHBStreptavidin/0.540
2izhBTNStreptavidin/0.540
3ry2BTNStreptavidin/0.540
2rtdBTNStreptavidin/0.538
2izfBTNStreptavidin/0.536
1sreHABStreptavidin/0.535
2izlIMIStreptavidin/0.535
2zscBTNTamavidin2/0.535
2rtfBTNStreptavidin/0.534
2rtnIMIStreptavidin/0.529
1lcwSHMStreptavidin/0.526
2rtoIMIStreptavidin/0.526
2izgBTNStreptavidin/0.525
2rteBTNStreptavidin/0.525
4dneDTBStreptavidin/0.524
2fhnBNIAvidin-related protein 4/5/0.521
2rtqIMIStreptavidin/0.521
2rtrIMIStreptavidin/0.521
1swdBTNStreptavidin/0.519
1swtBTNStreptavidin/0.514
1srfMTBStreptavidin/0.513
2aviBTNAvidin/0.510
3vhiVHIAvidin/0.510
1luqBTNStreptavidin/0.509
1srhMOBStreptavidin/0.509
4z28BTNHoefavidin/0.508
1df8BTNStreptavidin/0.506
1y52BTNAvidin-related protein 4/5/0.506
2rtkGLLStreptavidin/0.506
1rxhBNIStreptavidin/0.504
3wznBTNStreptavidin/0.504
1mepBTNStreptavidin/0.503
1i9hBNIStreptavidin/0.497
4yvbBTNStreptavidin/0.497
2c4iBTNAvidin/0.487
3rdqDTBStreptavidin/0.487
3vgwNVZAvidin/0.486
2uz2BTNAvd protein/0.482
1lczBH7Streptavidin/0.480
3ew2BTNHypothetical conserved protein/0.480
2uywBTNAvd protein/0.479
3vhmNPKAvidin/0.478
2y3fBTNStreptavidin/0.476
3wyqBTNStreptavidin/0.476
2rtpIMIStreptavidin/0.475
1avdBTNAvidin/0.473
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.473
4bj8BTNAvidin/0.473
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.473
1g63FMNEpidermin decarboxylase4.1.10.469
1srjNABStreptavidin/0.468
2rtmIMIStreptavidin/0.468
3t2wBTNAvidin/streptavidin/0.468
3h3qH13Collagen type IV alpha-3-binding protein/0.467
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.466
4e32DWNMethyltransferase/0.466
4dvi2IWTankyrase-12.4.2.300.464
4kxjP34Nucleoprotein/0.464
2jgsBTNAvidin/0.463
1kceCB3Thymidylate synthase/0.462
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.460
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.457
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.457
1fwkADPHomoserine kinase2.7.1.390.456
2j2pSC2Ficolin-2/0.456
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1obnASVIsopenicillin N synthase1.21.3.10.452
4bcsBTNAvidin-related protein 4/5/0.452
2iziBTNStreptavidin/0.451
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.450
2w6cBM4Acetylcholinesterase3.1.1.70.450
2izjBTNStreptavidin/0.449
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.449
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.449
2ea2F77Methionine aminopeptidase 2/0.448
1e66HUXAcetylcholinesterase3.1.1.70.447
1fvpFMANon-fluorescent flavoprotein/0.447
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.447
3ndjJHZMethyltransferase/0.447
4ey7E20Acetylcholinesterase3.1.1.70.447
1votHUPAcetylcholinesterase3.1.1.70.446
2v59LZKBiotin carboxylase6.3.4.140.446
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.446
4pnmNU1Tankyrase-22.4.2.300.446
3h3sH15Collagen type IV alpha-3-binding protein/0.445
1w6hTITPlasmepsin-23.4.23.390.444
2wo7ASVIsopenicillin N synthase1.21.3.10.443
3h7uNAPNADPH-dependent aldo-keto reductase, chloroplastic/0.443
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.443
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.443
2v5aLZLBiotin carboxylase6.3.4.140.442
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.442
4jt81NRNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.442
1yryMSGPurine nucleoside phosphorylase2.4.2.10.441
2fhlBNIAvidin-related protein 4/5/0.441
3vhhVHHAvidin/0.441
3wqmB29Diterpene synthase3.1.7.80.441
4ey6GNTAcetylcholinesterase3.1.1.70.441
4mihFADPyranose 2-oxidase1.1.3.100.441
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.440