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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
4cbyKEEHistone deacetylase 43.5.1.98

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4cbyKEEHistone deacetylase 43.5.1.981.000
3znrNU9Histone deacetylase 73.5.1.980.605
3znsNU7Histone deacetylase 73.5.1.980.544
2vqjTFGHistone deacetylase 43.5.1.980.530
3c10TSNHistone deacetylase 73.5.1.980.530
3c0zSHHHistone deacetylase 73.5.1.980.491
2puiADPMethylthioribose kinase2.7.1.1000.487
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.486
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.481
3pqbVGPPutative oxidoreductase/0.477
4iae1DXAlr2278 protein/0.476
1oc1ASVIsopenicillin N synthase1.21.3.10.475
3bmqAX5Pteridine reductase/0.475
3zsh469Mitogen-activated protein kinase 14/0.475
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.473
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.473
4iah1DXAlr2278 protein/0.473
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.471
1fmjRTLRetinol dehydratase/0.468
1x8lOXRRetinol dehydratase/0.468
4jlj1NMDeoxycytidine kinase2.7.1.740.468
1kquBR4Phospholipase A2, membrane associated/0.467
2f3815MAldo-keto reductase family 1 member C3/0.467
4jqh1MFAlr2278 protein/0.467
4y9rFADNADPH--cytochrome P450 reductase/0.467
5c1mCLRMu-type opioid receptor/0.467
4daj0HKMuscarinic acetylcholine receptor M3/0.467
3gieACPSensor histidine kinase DesK2.7.13.30.466
3nu03TUDihydrofolate reductase1.5.1.30.466
1dr4HBIDihydrofolate reductase1.5.1.30.465
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.465
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.464
3u8hBHPPhospholipase A2, membrane associated/0.464
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.463
1o5rFR9Adenosine deaminase3.5.4.40.463
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.463
5bn3ADPV-type ATP synthase alpha chain/0.463
5bn3ADPNEQ263/0.463
5kf9ACOPredicted acetyltransferase/0.463
1yc2NADNAD-dependent protein deacylase 2/0.462
2qjpANJCytochrome b/0.462
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.462
4u163C0Muscarinic acetylcholine receptor M3/0.462
2oliIOPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.461
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.461
4bfuZVUPantothenate kinase2.7.1.330.461
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.461
5jr34MUCarminomycin 4-O-methyltransferase DnrK2.1.1.2920.461
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
3aosJH2Hemolymph juvenile hormone binding protein/0.460
3ugrIMNAldo-keto reductase family 1 member C3/0.460
4a83DXCMajor pollen allergen Bet v 1-A/0.460
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.460
1fmlRTLRetinol dehydratase/0.459
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.459
2zevIPEGeranylgeranyl pyrophosphate synthase/0.459
3r7mSUZAldo-keto reductase family 1 member C3/0.459
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
4a86H35Major pollen allergen Bet v 1-A/0.459
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.458
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.458
4mv1ADPBiotin carboxylase6.3.4.140.458
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.457
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.457
3h1vTK1Glucokinase2.7.1.20.457
3htjETEbrA repressor/0.457
3zo7K6HMuconolactone Delta-isomerase/0.457
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.457
5ab6CAANonspecific lipid-transfer protein, putative/0.457
2ejzSAHDiphthine synthase/0.456
3fhxPXLPyridoxal kinase2.7.1.350.456
2ojg19AMitogen-activated protein kinase 12.7.11.240.455
3ewkFADSensory box histidine kinase/response regulator/0.455
3h4vDVPPteridine reductase 11.5.1.330.455
3qeoLLTDeoxycytidine kinase2.7.1.740.455
3vf60H6Glucokinase2.7.1.20.455
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.455
1dgbNDPCatalase1.11.1.60.454
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1u0wSTLChalcone synthase 22.3.1.740.454
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.454
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.454
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.454
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.454
1gt5BZQOdorant-binding protein/0.453
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.453
1odjGMPPurine nucleoside phosphorylase/0.453
1upw444Oxysterols receptor LXR-beta/0.453
2vz0D64Pteridine reductase/0.453
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.453
3d80Q22Dihydrofolate reductase1.5.1.30.453
3frfXCFDihydrofolate reductase1.5.1.30.453
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3zoiM2WIsopenicillin N synthase1.21.3.10.453
4a81DXCMajor pollen allergen Bet v 1-A/0.453
5cc9DDFDihydrofolate reductase1.5.1.30.453
5k2aZMAAdenosine receptor A2a/0.453
1e79ADPATP synthase subunit alpha, mitochondrial/0.452
1e79ADPATP synthase subunit beta, mitochondrial3.6.3.140.452
1kijNOVDNA gyrase subunit B/0.452
1r8qAFBCytohesin-2/0.452
1r8qAFBADP-ribosylation factor 1/0.452
1s2cFLFAldo-keto reductase family 1 member C3/0.452
2bpoFADNADPH--cytochrome P450 reductase/0.452
3qly55VUncharacterized protein/0.452
3zkyWT4Isopenicillin N synthase1.21.3.10.452
4jq2SUZAldo-keto reductase family 1 member C2/0.452
4jtrIZPAldo-keto reductase family 1 member C2/0.452
4li61XOTankyrase-12.4.2.300.452
1umlFR4Adenosine deaminase3.5.4.40.451
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2xk3XK3Serine/threonine-protein kinase Nek22.7.11.10.451
3rgzBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.451
4dhyS41Glucokinase2.7.1.20.451
4iwv1J9Glucokinase2.7.1.20.451
2vcmM11Isopenicillin N synthase1.21.3.10.450
2w3aTOPDihydrofolate reductase1.5.1.30.450
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.450
4ixfIXFDihydrofolate reductase1.5.1.30.450
4jbtASDCytochrome P450 monooxygenase/0.450
4k9yK9YFocal adhesion kinase 12.7.10.20.450
1lhwESMSex hormone-binding globulin/0.449
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.449
3elePLPAminotransferase/0.449
3jqbDX6Pteridine reductase, putative/0.449
3l3rOAGDihydrofolate reductase1.5.1.30.449
3vi7CBDHematopoietic prostaglandin D synthase/0.449
5k2cZMAAdenosine receptor A2a/0.449
1qxlFR8Adenosine deaminase3.5.4.40.448
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.448
1ygjRMCPyridoxal kinase2.7.1.350.448
2pupADPMethylthioribose kinase2.7.1.1000.448
2vbpVB1Isopenicillin N synthase1.21.3.10.448
3szfDCQSulfide-quinone reductase/0.448
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.448
5kghACOPredicted acetyltransferase/0.448
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.447
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2oz57XYUncharacterized protein/0.447
3cth319Hepatocyte growth factor receptor2.7.10.10.447
3k4551PDihydrofolate reductase1.5.1.30.447
3nj0PYVAbscisic acid receptor PYL2/0.447
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3vo2FADFerredoxin--NADP reductase/0.447
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
4bfwZVWPantothenate kinase2.7.1.330.447
4burNADApoptosis-inducing factor 1, mitochondrial1.1.10.447
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.446
2ea4F79Methionine aminopeptidase 2/0.446
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.446
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3gc9B45Mitogen-activated protein kinase 112.7.11.240.446
3nxyD2HDihydrofolate reductase1.5.1.30.446
3vt9YI4Vitamin D3 receptor/0.446
4e0u0MVCyclic dipeptide N-prenyltransferase/0.446
4jq4IMNAldo-keto reductase family 1 member C2/0.446
4kfj1R0Dihydrofolate reductase1.5.1.30.446
4q0kGA3Phytohormone-binding protein/0.446
1akbPPDAspartate aminotransferase, mitochondrial2.6.1.10.445
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.445
2rd2QSIGlutamine--tRNA ligase6.1.1.180.445
2uxoTACHTH-type transcriptional regulator TtgR/0.445
2w6zL21Biotin carboxylase6.3.4.140.445
3bl7DD1m7GpppX diphosphatase3.6.1.590.445
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
4bfxZVXPantothenate kinase2.7.1.330.445
4djx0KQBeta-secretase 13.4.23.460.445
4ia2BIVVitamin D3 receptor A/0.445
4ko8AGSTransitional endoplasmic reticulum ATPase3.6.4.60.445
5kgpACOPredicted acetyltransferase/0.445
1ve3SAMUncharacterized protein/0.444
1yw7A41Methionine aminopeptidase 2/0.444
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.444
2zzcNAPThioredoxin reductase 1, cytoplasmic1.8.1.90.444
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.444
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.444
3btjDEQHTH-type transcriptional regulator QacR/0.444
3l6jZ90Alr2278 protein/0.444
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.444
4djw0KPBeta-secretase 13.4.23.460.444
4hqvQEIQueuine tRNA-ribosyltransferase2.4.2.290.444
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.444
4qa0SHHHistone deacetylase 83.5.1.980.444
1fm4DXCMajor pollen allergen Bet v 1-L/0.443
1h35R01Squalene--hopene cyclase4.2.1.1290.443
1kmyBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.443
1kyyINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1mdlRMNMandelate racemase/0.443
1ry0PG2Aldo-keto reductase family 1 member C3/0.443
1z6tADPApoptotic protease-activating factor 1/0.443
2bfmTOPPteridine reductase 11.5.1.330.443
2bxoOPBSerum albumin/0.443
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2vbvFMNRiboflavin kinase2.7.1.1610.443
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.443
3jx3JI5Nitric oxide synthase, brain1.14.13.390.443
3nwlNDPCatalase1.11.1.60.443
4c6zTLE3-oxoacyl-ACP synthase/0.443
5epvACPBlue-light-activated histidine kinase2.7.13.30.443
1ludTRRDihydrofolate reductase1.5.1.30.442
1s3vTQDDihydrofolate reductase1.5.1.30.442
1vkgCRIHistone deacetylase 83.5.1.980.442
2j0vGDPRac-like GTP-binding protein ARAC7/0.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3jwcEKBDihydrofolate reductase/0.442
3new3NEMitogen-activated protein kinase 14/0.442
3nxrD2DDihydrofolate reductase1.5.1.30.442
3nxvD2FDihydrofolate reductase1.5.1.30.442
3s41S41Glucokinase2.7.1.20.442
3ug8IMNAldo-keto reductase family 1 member C3/0.442
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
3w0uHPWLactoylglutathione lyase4.4.1.50.442
4b2gV1NUncharacterized protein/0.442
4r20AERCytochrome P450 family 17 polypeptide 2/0.442
5bn4ANPV-type ATP synthase alpha chain/0.442
1ej2NADNicotinamide-nucleotide adenylyltransferase2.7.7.10.441
1g63FMNEpidermin decarboxylase4.1.10.441
1ihiIU5Aldo-keto reductase family 1 member C2/0.441
1lgtBP3Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.441
1pkfEPDEpothilone C/D epoxidase1.140.441
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.441
2qhxFE1Pteridine reductase 11.5.1.330.441
3fnfJPMEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
3mjrAC2Deoxycytidine kinase2.7.1.740.441
3otwCOAPhosphopantetheine adenylyltransferase/0.441
3pne8AXNitric oxide synthase, brain1.14.13.390.441
3srsM23Dihydrofolate reductase1.5.1.30.441
3zc3FADFerredoxin--NADP reductase1.18.1.20.441
4hshQEIQueuine tRNA-ribosyltransferase2.4.2.290.441
4o7uTHFThymidylate synthase/0.441
4uthFMNXenobiotic reductase/0.441
1maqPGUAspartate aminotransferase, mitochondrial2.6.1.10.440
1nhz486Glucocorticoid receptor/0.440
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1q6s214Tyrosine-protein phosphatase non-receptor type 13.1.3.480.440
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
1ygkRRCPyridoxal kinase2.7.1.350.440
1yhsSTUSerine/threonine-protein kinase pim-12.7.11.10.440
1yw8A75Methionine aminopeptidase 2/0.440
1zg32HIIsoflavone 4'-O-methyltransferase/0.440
2h42VIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.440
2io6330Wee1-like protein kinase2.7.10.20.440
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.440
2z2w770Wee1-like protein kinase2.7.10.20.440
3i8aN22Dihydrofolate reductase1.5.1.30.440
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.440
3lfcZ86Mitogen-activated protein kinase 14/0.440
3sh25DRDihydrofolate reductase1.5.1.30.440
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.440
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
4xe606UDihydrofolate reductase1.5.1.30.440
5stdUNNScytalone dehydratase4.2.1.940.440
3uzaT4GAdenosine receptor A2a/0.440