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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
1w88TDPPyruvate dehydrogenase E1 component subunit alpha1.2.4.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1w88TDPPyruvate dehydrogenase E1 component subunit alpha1.2.4.11.000
1w88TDPPyruvate dehydrogenase E1 component subunit beta1.2.4.11.000
4jlm1NNDeoxycytidine kinase2.7.1.740.515
1dnpMHFDeoxyribodipyrimidine photo-lyase4.1.99.30.504
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.502
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.500
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.499
3i1y33NBifunctional epoxide hydrolase 23.3.2.100.492
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.489
2zi53L1Deoxycytidine kinase2.7.1.740.489
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.487
1mrkFMCRibosome-inactivating protein alpha-trichosanthin3.2.2.220.486
1thnADPAnti-sigma F factor/0.482
2b8jADNClass B acid phosphatase3.1.3.20.482
3nx2FERFerulic acid decarboxylase/0.482
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.482
2gyuHI6Acetylcholinesterase3.1.1.70.481
3qeoLLTDeoxycytidine kinase2.7.1.740.481
3c14FOKAdenylate cyclase type 2/0.480
3c14FOKAdenylate cyclase type 5/0.480
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.480
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.480
2pdaTPPPyruvate synthase/0.477
1dfoPLGSerine hydroxymethyltransferase2.1.2.10.476
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.476
1gtrATPGlutamine--tRNA ligase6.1.1.180.475
3bi5FADPolyamine oxidase FMS1/0.475
1m2xMCOMetallo-beta-lactamase type 2/0.474
3bi2FADPolyamine oxidase FMS1/0.474
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.473
1ltzHBIPhenylalanine-4-hydroxylase1.14.16.10.473
1lv89PPPurine nucleoside phosphorylase2.4.2.10.472
1rzuADPGlycogen synthase 12.4.1.210.472
2adaHPRAdenosine deaminase3.5.4.40.472
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.472
4p9dTMPDeoxycytidylate deaminase/0.472
1tilATPAnti-sigma F factor/0.471
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.470
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.470
3biz61EWee1-like protein kinase2.7.10.20.470
3nn6HNK6-hydroxy-L-nicotine oxidase/0.470
2xugTZ4Acetylcholinesterase3.1.1.70.468
2zfq45UProthrombin3.4.21.50.468
2wu4HBPAcetylcholinesterase3.1.1.70.467
3ddcGNPGTPase HRas/0.467
1iayAVG1-aminocyclopropane-1-carboxylate synthase 24.4.1.140.466
2rqfJH3Hemolymph juvenile hormone binding protein/0.466
2vmyFFOSerine hydroxymethyltransferase/0.466
3p0fBAUUridine phosphorylase 22.4.2.30.466
3fhxPLPPyridoxal kinase2.7.1.350.465
2j3qTFLAcetylcholinesterase3.1.1.70.464
3h3qH13Collagen type IV alpha-3-binding protein/0.464
3vv8B02Beta-secretase 13.4.23.460.464
1cbqRE9Cellular retinoic acid-binding protein 2/0.463
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.463
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.463
3t70DU4Deoxyuridine 5'-triphosphate nucleotidohydrolase/0.463
4n4t2GVTankyrase-12.4.2.300.463
2gvdFKPAdenylate cyclase type 2/0.462
2gvdFKPAdenylate cyclase type 5/0.462
3t64DU3Deoxyuridine 5'-triphosphate nucleotidohydrolase/0.462
3vf60H6Glucokinase2.7.1.20.462
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.462
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.461
4iarERM5-hydroxytryptamine receptor 1B/0.461
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3h3t16HCollagen type IV alpha-3-binding protein/0.460
1dljUGAUDP-glucose 6-dehydrogenase/0.459
1kqwRTLCellular retinol-binding protein type II/0.459
1lvu9PPPurine nucleoside phosphorylase2.4.2.10.459
1lwxAZDNucleoside diphosphate kinase, cytosolic2.7.4.60.459
1trkTPPTransketolase 12.2.1.10.459
3ddw055Glycogen phosphorylase, liver form2.4.1.10.459
3lq2TDPPyruvate dehydrogenase E1 component1.2.4.10.459
3zhtTD9Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.459
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.458
2trsPLSTryptophan synthase beta chain4.2.1.200.458
2xtnGTPGTPase IMAP family member 2/0.458
3c3xNAPEugenol synthase 11.1.1.3180.458
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.458
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3keqNADRedox-sensing transcriptional repressor Rex/0.458
3v2uATPProtein GAL3/0.458
4eqrCOACoenzyme A disulfide reductase/0.458
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.458
5epeSAHUncharacterized protein/0.458
1tkcM6TTransketolase 12.2.1.10.457
1toxNADDiphtheria toxin/0.457
2xxvKAIGlutamate receptor ionotropic, kainate 2/0.457
3iogSDFMetallo-beta-lactamase type 2/0.457
3lbhGNPGTPase HRas/0.457
4ubfADPKinesin-like protein KIF2C/0.457
1obnASVIsopenicillin N synthase1.21.3.10.456
1towCRZFatty acid-binding protein, adipocyte/0.456
3ntz3TZDihydrofolate reductase1.5.1.30.456
4f5dC2EStimulator of interferon genes protein/0.456
1digL37C-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.455
1dr4HBIDihydrofolate reductase1.5.1.30.455
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.455
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.455
1wnz2VAIsoleucine--tRNA ligase6.1.1.50.455
2jf0HBPAcetylcholinesterase3.1.1.70.455
3djfBC3Purine nucleoside phosphorylase/0.455
4g2i0VQVitamin D3 receptor/0.455
1a9sNOSPurine nucleoside phosphorylase2.4.2.10.454
1dfoFFOSerine hydroxymethyltransferase2.1.2.10.454
1f20FADNitric oxide synthase, brain1.14.13.390.454
1z6lFADPolyamine oxidase FMS1/0.454
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.454
3nmpPYVAbscisic acid receptor PYL2/0.454
3sn6P0GBeta-2 adrenergic receptor/0.454
1culFOKAdenylate cyclase type 2/0.453
1culFOKAdenylate cyclase type 5/0.453
1tl7ONMAdenylate cyclase type 2/0.453
1tl7ONMAdenylate cyclase type 5/0.453
1tysDHFThymidylate synthase/0.453
2p5uNADUDP-glucose 4-epimerase/0.453
2zi63D1Deoxycytidine kinase2.7.1.740.453
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.453
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.453
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.452
1wklATPNucleoside diphosphate kinase/0.452
2hkoFADLysine-specific histone demethylase 1A10.452
2qe2452Polyprotein/0.452
3ou7SAMSAM-dependent methyltransferase/0.452
3ugrIMNAldo-keto reductase family 1 member C3/0.452
4hyf1AKTankyrase-22.4.2.300.452
1kqnNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.451
1kvkATPMevalonate kinase2.7.1.360.451
2gv8NDPThiol-specific monooxygenase1.14.130.451
2tysPLTTryptophan synthase beta chain4.2.1.200.451
2zscBTNTamavidin2/0.451
3pftFMNFlavin reductase/0.451
4b1hAR6Poly(ADP-ribose) glycohydrolase3.2.1.1430.451
4j21AJ6Tankyrase-22.4.2.300.451
4pkwGM6Lethal factor3.4.24.830.451
4qzuRTLRetinol-binding protein 2/0.451
1rctNOSPurine nucleoside phosphorylase2.4.2.10.450
1swnBTNStreptavidin/0.450
1v48HA1Purine nucleoside phosphorylase2.4.2.10.450
1yryMSGPurine nucleoside phosphorylase2.4.2.10.450
2fzbTOLAldose reductase1.1.1.210.450
3lmhADPMyosin heavy chain kinase A2.7.11.70.450
3nu03TUDihydrofolate reductase1.5.1.30.450
3rykTYDdTDP-4-dehydrorhamnose 3,5-epimerase/0.450
4bfvZVVPantothenate kinase2.7.1.330.450
1fxuGU7Purine nucleoside phosphorylase2.4.2.10.449
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1z4uPH9Polyprotein/0.449
2bfmTOPPteridine reductase 11.5.1.330.449
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.449
3q9bB3NAcetylpolyamine amidohydrolase/0.449
4arbC57Acetylcholinesterase3.1.1.70.449
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.448
2cekN8TAcetylcholinesterase3.1.1.70.448
4a81DXCMajor pollen allergen Bet v 1-A/0.448
4twnB96Ephrin type-A receptor 32.7.10.10.448
5il2SAHN6-adenosine-methyltransferase 70 kDa subunit/0.448
1e92HBIPteridine reductase 11.5.1.330.447
1oc1ASVIsopenicillin N synthase1.21.3.10.447
2g0lFLNNeocarzinostatin/0.447
2vqjTFGHistone deacetylase 43.5.1.980.447
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.447
3ewdMCFAdenosine deaminase, putative/0.447
3ivcFG4Pantothenate synthetase6.3.2.10.447
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.447
1b8oIMHPurine nucleoside phosphorylase2.4.2.10.446
1r2jFADFkbI/0.446
2geuCOKPantothenate kinase2.7.1.330.446
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.446
2x06NADL-sulfolactate dehydrogenase/0.446
3q5pTACMultidrug-efflux transporter 1 regulator/0.446
3rs4GNPGTPase HRas/0.446
4dpy2P0Mevalonate diphosphate decarboxylase/0.446
4kwcSAHMethyltransferase domain family/0.446
1e1qADPATP synthase subunit beta, mitochondrial3.6.3.140.445
1itzTPPTransketolase, chloroplastic2.2.1.10.445
1xuzMMNCapsule biosynthesis protein/0.445
1ygjRMCPyridoxal kinase2.7.1.350.445
2b82ADNClass B acid phosphatase3.1.3.20.445
2clhF19Tryptophan synthase alpha chain/0.445
2in6839Wee1-like protein kinase2.7.10.20.445
3k8q22APurine nucleoside phosphorylase2.4.2.10.445
3oiwGNPGTPase HRas/0.445
3stdMQ0Scytalone dehydratase4.2.1.940.445
3wv9FEGHmd co-occurring protein HcgE/0.445
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.445
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.445
4mk728OGenome polyprotein2.7.7.480.445
5iqbGNPBifunctional AAC/APH2.3.10.445
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.444
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.444
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
2zhw12UProthrombin3.4.21.50.444
3f3y4OABile salt sulfotransferase2.8.2.140.444
3mjrAC2Deoxycytidine kinase2.7.1.740.444
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.444
4dlvGNPGTPase HRas/0.444
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.444
4hlf15ZTankyrase-22.4.2.300.444
4l1xSTRAldo-keto reductase family 1 member C2/0.444
4l33F70Tankyrase-22.4.2.300.444
4ycpFMNtRNA-dihydrouridine(16) synthase/0.444
4zobLGCLin1840 protein/0.444
1p33MTXPteridine reductase 11.5.1.330.443
1t4v14AProthrombin3.4.21.50.443
1t91GTPRas-related protein Rab-7a/0.443
2dw4FADLysine-specific histone demethylase 1A10.443
2ejzSAHDiphthine synthase/0.443
2vczVC3Hematopoietic prostaglandin D synthase/0.443
2xufTZ4Acetylcholinesterase3.1.1.70.443
4fa30SLAldo-keto reductase family 1 member C3/0.443
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
4x5hFOLDihydrofolate reductase1.5.1.30.443
1cs4FOKAdenylate cyclase type 2/0.442
1cs4FOKAdenylate cyclase type 5/0.442
1g63FMNEpidermin decarboxylase4.1.10.442
1tkaN3TTransketolase 12.2.1.10.442
2ffqGSPRas-related protein Rab-6B/0.442
2g78REACellular retinoic acid-binding protein 2/0.442
2gevCOKPantothenate kinase2.7.1.330.442
2p4sDIHAGAP005945-PA/0.442
3mauPLRPutative sphingosine-1-phosphate lyase/0.442
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.442
4a39GEMUncharacterized protein/0.442
4fwnAQPPropionate kinase/0.442
4k37SAMAnaerobic sulfatase-maturating enzyme1.8.980.442
4mk828QGenome polyprotein2.7.7.480.442
4pnmNU1Tankyrase-22.4.2.300.442
1d8fSPIStromelysin-13.4.24.170.441
1efzPRFQueuine tRNA-ribosyltransferase2.4.2.290.441
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.441
1szgFNSCytochrome b2, mitochondrial1.1.2.30.441
2c5lGTPGTPase HRas/0.441
2hxzH7JCathepsin S3.4.22.270.441
2r2mI50Prothrombin3.4.21.50.441
2uz2BTNAvd protein/0.441
3cehAVEGlycogen phosphorylase, liver form2.4.1.10.441
4bjcRPBTankyrase-22.4.2.300.441
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.441
4dh60KNBeta-secretase 13.4.23.460.441
4s1iPLPPyridoxal kinase, putative/0.441
3reyXACAdenosine receptor A2a/0.441
1jdzFMBPurine nucleoside phosphorylase/0.440
1kzjCB3Thymidylate synthase/0.440
1stpBTNStreptavidin/0.440
1ulbGUNPurine nucleoside phosphorylase2.4.2.10.440
2ibuCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.440
2igyA2TPlasmepsin 2/0.440
2xviFADPutative flavin-containing monooxygenase/0.440
3cid318Beta-secretase 13.4.23.460.440
3cr0809Wee1-like protein kinase2.7.10.20.440
3h4vNAPPteridine reductase 11.5.1.330.440
4twpAXITyrosine-protein kinase ABL12.7.10.20.440