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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
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.11.000
2jav5Z5Serine/threonine-protein kinase Nek22.7.11.10.549
2xnmWGZSerine/threonine-protein kinase Nek22.7.11.10.549
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.533
2xnoED8Serine/threonine-protein kinase Nek22.7.11.10.519
4h1j0YHProtein-tyrosine kinase 2-beta2.7.10.20.519
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.512
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.507
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.505
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.501
2yac937Serine/threonine-protein kinase PLK12.7.11.210.498
4afeGGYSerine/threonine-protein kinase Nek22.7.11.10.492
2owb626Serine/threonine-protein kinase PLK12.7.11.210.484
2xk730ESerine/threonine-protein kinase Nek22.7.11.10.483
2xkeWI2Serine/threonine-protein kinase Nek22.7.11.10.483
3uzcT4EAdenosine receptor A2a/0.479
3cr0809Wee1-like protein kinase2.7.10.20.478
4fnyI3KALK tyrosine kinase receptor2.7.10.10.478
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.476
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.474
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.474
3qakUKAAdenosine receptor A2a/0.473
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.472
1ygjRMCPyridoxal kinase2.7.1.350.470
3rfmCFFAdenosine receptor A2a/0.469
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.468
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.465
5dhgDGVNociceptin receptor/0.465
3cqeP91Wee1-like protein kinase2.7.10.20.464
3biz61EWee1-like protein kinase2.7.10.20.462
4kaoKAOFocal adhesion kinase 12.7.10.20.462
3pwhZMAAdenosine receptor A2a/0.462
3fowIMHPurine nucleoside phosphorylase/0.460
3eigMTXDihydrofolate reductase1.5.1.30.459
3p2oNADBifunctional protein FolD/0.459
3dejRXCCaspase-33.4.22.560.457
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.456
3njoPYVAbscisic acid receptor PYR1/0.456
3reyXACAdenosine receptor A2a/0.456
2io6330Wee1-like protein kinase2.7.10.20.455
3vf60H6Glucokinase2.7.1.20.455
5bn4ANPV-type ATP synthase alpha chain/0.453
2j08IRFDeoxyribodipyrimidine photo-lyase4.1.99.30.452
2zs9ADPPantothenate kinase2.7.1.330.452
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.452
5ab6CAANonspecific lipid-transfer protein, putative/0.452
1ia4TQ6Dihydrofolate reductase1.5.1.30.451
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.451
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.451
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.451
4iaq2GM5-hydroxytryptamine receptor 1B/0.451
3pqbVGPPutative oxidoreductase/0.450
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.450
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.450
2ydoADNAdenosine receptor A2a/0.449
5uviZMAAdenosine receptor A2a/0.449
5k2aZMAAdenosine receptor A2a/0.449
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.448
3c35KAIGlutamate receptor ionotropic, kainate 1/0.448
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.448
4equG6ISerine/threonine-protein kinase 102.7.11.10.448
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.448
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.447
4k9yK9YFocal adhesion kinase 12.7.10.20.447
4kbn25UDihydrofolate reductase1.5.1.30.447
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.446
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.446
4jxxATPGlutamine--tRNA ligase6.1.1.180.446
4kak06UDihydrofolate reductase1.5.1.30.446
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.445
3p3zP3ZPutative cytochrome P450/0.445
2z4sADPChromosomal replication initiator protein DnaA/0.444
3a4pDFQHepatocyte growth factor receptor2.7.10.10.444
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.444
4u0k744Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1kmsLIHDihydrofolate reductase1.5.1.30.443
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.443
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.443
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.443
2z4y252Geranylgeranyl pyrophosphate synthase/0.443
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.443
2og81N8Tyrosine-protein kinase Lck2.7.10.20.442
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.441
2wmtZYTSerine/threonine-protein kinase Chk12.7.11.10.441
3w8wFADPutative FAD-dependent oxygenase EncM/0.441
4at0FADPossible succinate dehydrogenase/0.441
4ddrMMVDihydrofolate reductase1.5.1.30.441
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.441
1cc2FADCholesterol oxidase1.1.3.60.440
2e0nSAHPrecorrin-2 C20-methyltransferase/0.440
2zs8ADPPantothenate kinase2.7.1.330.440
4bfwZVWPantothenate kinase2.7.1.330.440