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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
4hyvPEPPyruvate kinase 12.7.1.40

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4hyvPEPPyruvate kinase 12.7.1.401.000
4ddhMS0Pantothenate synthetase6.3.2.10.501
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.496
1n2hPAJPantothenate synthetase6.3.2.10.490
2pz8APCNH(3)-dependent NAD(+) synthetase/0.487
2oapANPType II secretion system protein (GspE-2)/0.483
3ty3GGGHomoisocitrate dehydrogenase1.1.1.870.480
3hyoADPPyridoxal kinase/0.479
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.478
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.473
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.473
2yxuATPPyridoxal kinase2.7.1.350.469
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.467
3ivxFG6Pantothenate synthetase6.3.2.10.467
3ivgFG5Pantothenate synthetase6.3.2.10.466
3fr5I4AFatty acid-binding protein, adipocyte/0.465
5kwvANPPantothenate synthetase/0.465
1nzdUPGDNA beta-glucosyltransferase/0.464
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.464
3apwDP0Alpha-1-acid glycoprotein 2/0.463
3bk2U5PRibonuclease J/0.463
3keuATPPyridoxal kinase2.7.1.350.463
4fduIHSPutative multiple inositol polyphosphate histidine phosphatase 1/0.463
2qjoNADBifunctional NMN adenylyltransferase/Nudix hydrolase2.7.7.10.462
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.462
1rfvADPPyridoxal kinase2.7.1.350.461
1j21ATPArgininosuccinate synthase/0.459
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.459
4fxy0W2Neurolysin, mitochondrial3.4.24.160.459
5hg0SAMPantothenate synthetase/0.459
1xdpATPPolyphosphate kinase/0.458
2bn4FMNNADPH--cytochrome P450 reductase/0.458
2zt5B4PGlycine--tRNA ligase/0.458
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.457
3ibqATPPyridoxal kinase/0.457
2j07HDFDeoxyribodipyrimidine photo-lyase4.1.99.30.456
3q9lATPSeptum site-determining protein MinD/0.456
3qyyC2EResponse regulator/0.456
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.456
1mbbEEBUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.455
1nb6UTPGenome polyprotein2.7.7.480.455
2f3rG5PGuanylate kinase2.7.4.80.455
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.455
2xfsJ01Uncharacterized protein/0.455
3lqsPSZD-alanine aminotransferase2.6.1.210.455
1rfuADPPyridoxal kinase2.7.1.350.454
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.454
3zhyFM61-deoxy-D-xylulose 5-phosphate reductoisomerase/0.454
4rvgTYDD-mycarose 3-C-methyltransferase/0.454
1udcUFMUDP-glucose 4-epimerase5.1.3.20.453
1vhzAPRADP compounds hydrolase NudE3.6.10.453
2dvoITTdITP/XTP pyrophosphatase3.6.1.190.453
3lm9ADPPutative fructokinase2.7.1.40.453
3qt62P0Mevalonate diphosphate decarboxylase/0.453
1n2eAPCPantothenate synthetase6.3.2.10.452
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.452
1n2jPAFPantothenate synthetase6.3.2.10.451
1ytmATPPhosphoenolpyruvate carboxykinase (ATP)/0.451
2dftADPShikimate kinase2.7.1.710.451
1qwjNCCN-acylneuraminate cytidylyltransferase2.7.7.430.450
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.450
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.450
4yqfGDPSeptin-9/0.450
5agaANPDNA polymerase theta/0.450
3ckqUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.449
3enkUPGUDP-glucose 4-epimerase/0.449
1n38U3HRNA-directed RNA polymerase lambda-32.7.7.480.448
2qbuSAHPrecorrin-2 methyltransferase/0.448
2z1mNDPGDP-mannose 4,6-dehydratase/0.448
3tr05GPGuanylate kinase/0.448
4gavFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.448
1n2gAPCPantothenate synthetase6.3.2.10.447
2npxFADNADH peroxidase1.11.1.10.447
3zkiWZVBeta-secretase 23.4.23.450.447
4dptAGSMevalonate diphosphate decarboxylase/0.447
2ilvC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.446
2z95NDPGDP-mannose 4,6-dehydratase/0.446
3b1dPLSBetaC-S lyase/0.446
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.445
1n2bPAFPantothenate synthetase6.3.2.10.445
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.444
1sxjAGSReplication factor C subunit 1/0.444
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.444
3fhyATPPyridoxal kinase2.7.1.350.444
3isjA8DPantothenate synthetase6.3.2.10.444
3ziuLSSLeucyl-tRNA synthetase/0.444
4fryNADPutative signal-transduction protein with CBS domains/0.444
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.443
4df2FMNNADPH dehydrogenase/0.443
1o9bNAIQuinate/shikimate dehydrogenase/0.442
2ylrNAPPhenylacetone monooxygenase1.14.13.920.442
3tjzGNPADP-ribosylation factor 1/0.442
4hn1TYDdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.442
1kh2ATPArgininosuccinate synthase/0.441
1sesAHXSerine--tRNA ligase6.1.1.110.441
2cv2GSUGlutamate--tRNA ligase6.1.1.170.441
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.441
3c8aARG_ARG_GLY_LEU_NH2Botulinum neurotoxin type A3.4.24.690.441
3coy53HPantothenate synthetase6.3.2.10.441
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
4m2bUPGUDP-glucose pyrophosphorylase/0.441
1kh3ANPArgininosuccinate synthase/0.440
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.440
2bxoOPBSerum albumin/0.440
4xr9NADCalS8/0.440