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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
2xxyKAIGlutamate receptor ionotropic, kainate 2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2xxyKAIGlutamate receptor ionotropic, kainate 2/1.000
4bdoKAIGlutamate receptor ionotropic, kainate 2/0.624
3c34KAIGlutamate receptor ionotropic, kainate 1/0.618
3c35KAIGlutamate receptor ionotropic, kainate 1/0.613
3c36KAIGlutamate receptor ionotropic, kainate 1/0.592
4bdrKAIGlutamate receptor ionotropic, kainate 2/0.575
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.569
1lbbKAIGlutamate receptor 2/0.548
3kfmKAIGlutamate receptor 4/0.546
1fw0KAIGlutamate receptor 2/0.534
4h8i11WGlutamate receptor ionotropic, kainate 2/0.533
2xxvKAIGlutamate receptor ionotropic, kainate 2/0.508
4f3gKAIGlutamate receptor 3/0.508
4gxs0YSGlutamate receptor 2/0.505
2b82ADNClass B acid phosphatase3.1.3.20.485
4f31KAIGlutamate receptor 3/0.485
2c7qSAHModification methylase HhaI2.1.1.370.482
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.480
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.480
1ftlDNQGlutamate receptor 2/0.474
3hv3R49Mitogen-activated protein kinase 14/0.471
2p5uNADUDP-glucose 4-epimerase/0.469
1skmSAHModification methylase HhaI2.1.1.370.468
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.465
3gcq1BUMitogen-activated protein kinase 14/0.464
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.459
3p6pA6BCamphor 5-monooxygenase1.14.15.10.459
4zqmXMPInosine-5'-monophosphate dehydrogenase/0.459
3lfzADPUncharacterized protein MJ1225/0.457
1r2jFADFkbI/0.456
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.456
4twnB96Ephrin type-A receptor 32.7.10.10.456
1ne4RP1cAMP-dependent protein kinase type I-alpha regulatory subunit/0.455
3sl2ATPSensor histidine kinase WalK/0.455
3uk6ADPRuvB-like 23.6.4.120.455
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.454
3be2RAJVascular endothelial growth factor receptor 22.7.10.10.453
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.453
4o4fATPKinase/0.453
4s1iPLPPyridoxal kinase, putative/0.453
2wkyIBCGlutamate receptor ionotropic, kainate 1/0.452
3biz61EWee1-like protein kinase2.7.10.20.452
3rgaILDEpoxide hydrolase LasB5.5.10.452
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.452
1dr4HBIDihydrofolate reductase1.5.1.30.451
1nw4IMHPurine nucleoside phosphorylase/0.451
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.451
1ao8MTXDihydrofolate reductase1.5.1.30.450
1uymPU3Heat shock protein HSP 90-beta/0.450
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.450
4lb9EVPSerum albumin/0.450
1jzqILAIsoleucine--tRNA ligase6.1.1.50.449
2g8yNADHydroxycarboxylate dehydrogenase B/0.449
2v58LZJBiotin carboxylase6.3.4.140.448
3v0m5GWHisto-blood group ABO system transferase/0.448
4feu537Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.448
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.447
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.447
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.446
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4hfp15UProthrombin3.4.21.50.446
7mhtSAHModification methylase HhaI2.1.1.370.446
4dldTZGGlutamate receptor ionotropic, kainate 1/0.445
2a9z26AAdenosine kinase2.7.1.200.444
2z2w770Wee1-like protein kinase2.7.10.20.444
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.444
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.444
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.444
4o4eATPKinase/0.444
1hfqMOTDihydrofolate reductase1.5.1.30.443
2b1z17MEstrogen receptor/0.443
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.443
4v0s2HN3-dehydroquinate dehydratase4.2.1.100.443
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.442
3w0hW12Vitamin D3 receptor/0.442
3wquATPCell division protein FtsA/0.442
4gkh0J9Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.442
4isg1FYGlucokinase2.7.1.20.442
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.442
1ne6SP1cAMP-dependent protein kinase type I-alpha regulatory subunit/0.441
2db3ANPATP-dependent RNA helicase vasa, isoform A3.6.4.130.440
2yejXQKHeat shock protein HSP 90-alpha/0.440
3cqeP91Wee1-like protein kinase2.7.10.20.440
3nmpPYVAbscisic acid receptor PYL2/0.440
4b6r3DQ3-dehydroquinate dehydratase4.2.1.100.440