Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
4y17LAETranscriptional regulator of ftsQAZ gene cluster

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4y17LAETranscriptional regulator of ftsQAZ gene cluster/1.000
2avxHTFRegulatory protein SdiA/0.556
2cekN8TAcetylcholinesterase3.1.1.70.524
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.495
1jwtBLIProthrombin3.4.21.50.494
4a802ANMajor pollen allergen Bet v 1-A/0.494
1umaIN2Prothrombin3.4.21.50.491
3rbqGLY_ALA_GLY_DAOProtein unc-119 homolog A/0.488
1ut6A8NAcetylcholinesterase3.1.1.70.487
1nzq162Prothrombin3.4.21.50.486
2xufTZ4Acetylcholinesterase3.1.1.70.486
1odcA8BAcetylcholinesterase3.1.1.70.483
1vbiNADMalate/L-lactate dehydrogenase family protein/0.483
1zgbA1EAcetylcholinesterase3.1.1.70.483
2flhZEACytokinin-specific binding protein/0.483
2bxqIMNSerum albumin/0.482
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.481
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.481
4a862ANMajor pollen allergen Bet v 1-A/0.481
3rsv3RSBeta-secretase 13.4.23.460.480
1gj5130Prothrombin3.4.21.50.478
2xugTZ4Acetylcholinesterase3.1.1.70.478
3h3qH13Collagen type IV alpha-3-binding protein/0.478
3qj0QI3Botulinum neurotoxin type A3.4.24.690.477
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.477
5cmx0G6Prothrombin3.4.21.50.476
2rqfJH3Hemolymph juvenile hormone binding protein/0.475
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
1x1aSAMC-20 methyltransferase/0.474
2xupTZ5Acetylcholinesterase3.1.1.70.474
2xvw9NRSerum albumin/0.474
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
3l6jZ90Alr2278 protein/0.474
1xddAAYIntegrin alpha-L/0.473
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.473
1qrsATPGlutamine--tRNA ligase6.1.1.180.472
4q0kGA3Phytohormone-binding protein/0.472
1zgcA2EAcetylcholinesterase3.1.1.70.471
2whqHI6Acetylcholinesterase3.1.1.70.471
4arbC57Acetylcholinesterase3.1.1.70.471
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.471
1eveE20Acetylcholinesterase3.1.1.70.470
2jf0HBPAcetylcholinesterase3.1.1.70.470
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
4iae1DXAlr2278 protein/0.470
4a8v2ANMajor pollen allergen Bet v 1-J/0.469
4bfzZVZPantothenate kinase2.7.1.330.469
4eqxFADCoenzyme A disulfide reductase/0.469
1x1bSAHC-20 methyltransferase/0.468
4a81DXCMajor pollen allergen Bet v 1-A/0.468
4a87NARMajor pollen allergen Bet v 1-A/0.468
1o5gCR9Prothrombin3.4.21.50.467
1rz1NADPhenol 2-hydroxylase component B/0.467
1ypeUIPProthrombin3.4.21.50.467
1yplRA8Prothrombin3.4.21.50.466
3kkzSAMUncharacterized protein/0.466
4m0f1YKAcetylcholinesterase3.1.1.70.466
1ry0PG2Aldo-keto reductase family 1 member C3/0.465
3ix4TX1Transcriptional activator protein LasR/0.465
1w6rGNTAcetylcholinesterase3.1.1.70.464
2g8yNADHydroxycarboxylate dehydrogenase B/0.464
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.464
2uuk897Prothrombin3.4.21.50.464
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
4psbGA3Cytokinin-specific binding protein/0.464
1t4v14AProthrombin3.4.21.50.463
1votHUPAcetylcholinesterase3.1.1.70.463
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.463
3r1kCOAN-acetyltransferase Eis/0.463
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.463
4a83DXCMajor pollen allergen Bet v 1-A/0.463
4jqh1MFAlr2278 protein/0.463
1acjTHAAcetylcholinesterase3.1.1.70.462
3c1kT15Prothrombin3.4.21.50.462
4u140HKMuscarinic acetylcholine receptor M3/0.462
1qtiGNTAcetylcholinesterase3.1.1.70.461
2jl1NAPTriphenylmethane reductase/0.461
2psjCEIRenilla-luciferin 2-monooxygenase1.13.12.50.461
2r2mI50Prothrombin3.4.21.50.461
2xuhTZ4Acetylcholinesterase3.1.1.70.461
4tjy3GNTankyrase-22.4.2.300.461
4xbjIN5Alanine racemase, biosynthetic/0.461
1h22E10Acetylcholinesterase3.1.1.70.460
1rsgFADPolyamine oxidase FMS1/0.460
2ckmAA7Acetylcholinesterase3.1.1.70.460
2dxiATPGlutamate--tRNA ligase6.1.1.170.460
3mauPLRPutative sphingosine-1-phosphate lyase/0.460
4b7zQ4QAcetylcholinesterase3.1.1.70.460
4ey6GNTAcetylcholinesterase3.1.1.70.460
4gm4TZDBenzoylformate decarboxylase4.1.1.70.460
4iah1DXAlr2278 protein/0.460
1e66HUXAcetylcholinesterase3.1.1.70.459
2xi4AFTAcetylcholinesterase3.1.1.70.459
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3gncQQQGlutaryl-CoA dehydrogenase/0.459
4fam0SZAldo-keto reductase family 1 member C3/0.459
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.459
1fxuGU7Purine nucleoside phosphorylase2.4.2.10.458
1gw2FERPeroxidase C1A1.11.1.70.458
1xe65FPPlasmepsin-23.4.23.390.458
2g1r3IGRenin3.4.23.150.458
2gv8NDPThiol-specific monooxygenase1.14.130.458
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.458
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.458
2pnuENMAndrogen receptor/0.458
2po7CHDFerrochelatase, mitochondrial4.99.1.10.458
2stdCRPScytalone dehydratase4.2.1.940.458
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.458
1gpnHUBAcetylcholinesterase3.1.1.70.457
1h60STRPentaerythritol tetranitrate reductase/0.457
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2g1y5IGRenin3.4.23.150.457
2qw034Z4-chlorobenzoyl CoA ligase/0.457
2x8gFADThioredoxin glutathione reductase/0.457
1ypgUIRProthrombin3.4.21.50.456
2zhf49UProthrombin3.4.21.50.456
3zv7NHGAcetylcholinesterase3.1.1.70.456
5d6lCAUBeta-2 adrenergic receptor/0.456
1dx6GNTAcetylcholinesterase3.1.1.70.455
1u65CP0Acetylcholinesterase3.1.1.70.455
2w6cBM4Acetylcholinesterase3.1.1.70.455
2zhe13UProthrombin3.4.21.50.455
3b9lAZZSerum albumin/0.455
4ax9N5NProthrombin3.4.21.50.455
1d3pBT3Prothrombin3.4.21.50.454
1x2hLPALipoate-protein ligase A6.3.1.200.454
1x8lOXRRetinol dehydratase/0.454
2fxuBIDActin, alpha skeletal muscle/0.454
2j3qTFLAcetylcholinesterase3.1.1.70.454
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.454
4b4w9L9Bifunctional protein FolD/0.454
1bwlFMNNADPH dehydrogenase 11.6.99.10.453
1if5FBTCarbonic anhydrase 24.2.1.10.453
2xujTZ5Acetylcholinesterase3.1.1.70.453
3fhxPLPPyridoxal kinase2.7.1.350.453
1c4uIH1Prothrombin3.4.21.50.452
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1o6qR17Squalene--hopene cyclase4.2.1.1290.452
1qjfACSIsopenicillin N synthase1.21.3.10.452
2dvlFADAcyl-CoA dehydrogenase/0.452
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3own3OWRenin3.4.23.150.452
3uayADNPurine nucleoside phosphorylase DeoD-type/0.452
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.452
4b1e6T6Beta-secretase 13.4.23.460.452
4q36CO8Uncharacterized protein/0.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1jqdSAHHistamine N-methyltransferase2.1.1.80.451
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.451
3fsjD7KBenzoylformate decarboxylase4.1.1.70.451
3junAJDPhenazine biosynthesis protein A/B/0.451
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.451
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4n3r2GUTankyrase-12.4.2.300.451
5c1gGDUHisto-blood group ABO system transferase/0.451
3uonQNBMuscarinic acetylcholine receptor M2/0.451
1ddtAPUDiphtheria toxin/0.450
1dtpAPUDiphtheria toxin/0.450
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.450
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.450
2cv2GSUGlutamate--tRNA ligase6.1.1.170.450
3burTES3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3cb2GDPTubulin gamma-1 chain/0.450
3qiyQI1Botulinum neurotoxin type A3.4.24.690.450
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.450
4jicFMNGTN Reductase/0.450
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.450
4zu44TGWxcM-like protein/0.450
5c8d5ADProbable transcriptional regulator/0.450
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.449
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.449
2g1n1IGRenin3.4.23.150.449
3pchCHBProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.449
3pfhT3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.449
3rgaILDEpoxide hydrolase LasB5.5.10.449
3sxjSAMPutative methyltransferase/0.449
4araC56Acetylcholinesterase3.1.1.70.449
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.449
5bqfNAPProbable hydroxyacid dehydrogenase protein/0.449
1nm6L86Prothrombin3.4.21.50.448
1pq944BOxysterols receptor LXR-beta/0.448
1x1dSAHC-20 methyltransferase/0.448
1ygjRMCPyridoxal kinase2.7.1.350.448
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.448
2zbaZBATrichothecene 3-O-acetyltransferase/0.448
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.448
3qp8HL0Transcriptional activator, LuxR/UhpA family of regulators/0.448
3zoiM2WIsopenicillin N synthase1.21.3.10.448
4boeCLRJapanin/0.448
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4ey7E20Acetylcholinesterase3.1.1.70.448
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.448
4h380YXDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.448
1d6w00RProthrombin3.4.21.50.447
1fm4DXCMajor pollen allergen Bet v 1-L/0.447
1je1GMPPurine nucleoside phosphorylase/0.447
1m13HYFNuclear receptor subfamily 1 group I member 2/0.447
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.447
1rxjBNIStreptavidin/0.447
1wuaAP8Actin, alpha skeletal muscle/0.447
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.447
2op18PCEnoyl-ACP reductase/0.447
2x06NADL-sulfolactate dehydrogenase/0.447
2zsaADPPantothenate kinase2.7.1.330.447
3h3t16HCollagen type IV alpha-3-binding protein/0.447
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3pm1ETHTH-type transcriptional regulator QacR/0.447
4iarERM5-hydroxytryptamine receptor 1B/0.447
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4nieNBHNuclear receptor ROR-gamma/0.447
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.447
1d3dBZTProthrombin3.4.21.50.446
1mu6CDAProthrombin3.4.21.50.446
1rszDIHPurine nucleoside phosphorylase2.4.2.10.446
1vf3GDNGlutathione S-transferase 32.5.1.180.446
2qimZEAClass 10 plant pathogenesis-related protein/0.446
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.446
2tplHPPTyrosine phenol-lyase4.1.99.20.446
2xuiTZ5Acetylcholinesterase3.1.1.70.446
2xvv9DNSerum albumin/0.446
3e6eDCSAlanine racemase/0.446
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.446
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.446
3h3r14HCollagen type IV alpha-3-binding protein/0.446
3iktNADRedox-sensing transcriptional repressor Rex/0.446
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3w0uHPWLactoylglutathione lyase4.4.1.50.446
3zvmADPBifunctional polynucleotide phosphatase/kinase2.7.1.780.446
4bftZVTPantothenate kinase2.7.1.330.446
4bfuZVUPantothenate kinase2.7.1.330.446
1h36R88Squalene--hopene cyclase4.2.1.1290.445
1me6IVSPlasmepsin-23.4.23.390.445
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.445
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.445
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.445
1ay0TPPTransketolase 12.2.1.10.444
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.444
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.444
1q83TZ5Acetylcholinesterase3.1.1.70.444
1z6tADPApoptotic protease-activating factor 1/0.444
1zji2PG2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.444
2jj8AZZDeoxynucleoside kinase/0.444
2lbvEB4Extracellular fatty acid-binding protein/0.444
2rehFADNitroalkane oxidase1.7.3.10.444
3c1oNAPEugenol synthase/0.444
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.444
3pn1IVHDNA ligase/0.444
3wqmB29Diterpene synthase3.1.7.80.444
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.444
4bfyZVYPantothenate kinase2.7.1.330.444
4do30LAFatty-acid amide hydrolase 13.5.1.990.444
1gky5GPGuanylate kinase2.7.4.80.443
1w4lGL8Acetylcholinesterase3.1.1.70.443
2gyuHI6Acetylcholinesterase3.1.1.70.443
2yp0OVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
2zc922UProthrombin3.4.21.50.443
3mjrAC2Deoxycytidine kinase2.7.1.740.443
4gddNAIUDP-galactopyranose mutase/0.443
4zj8SUVOrexin receptor type 1/0.443
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.442
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
2nr4FMNConserved protein/0.442
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.442
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.442
4dc0NDPPutative ketoacyl reductase1.3.10.442
4eqrCOACoenzyme A disulfide reductase/0.442
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.442
4rtbSAMPutative thiazole biosynthesis protein ThiH/0.442
4xbfFADLysine-specific histone demethylase 1A10.442
5stdUNNScytalone dehydratase4.2.1.940.442
1el4CTZObelin/0.441
1icsFMN12-oxophytodienoate reductase 11.3.1.420.441
1qtqQSIGlutamine--tRNA ligase6.1.1.180.441
2h3wCOACarnitine O-acetyltransferase2.3.1.70.441
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.441
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3fktSIIBeta-secretase 13.4.23.460.441
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.441
3imeBZ2Pantothenate synthetase6.3.2.10.441
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.441
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.441
3nmpPYVAbscisic acid receptor PYL2/0.441
3nu03TUDihydrofolate reductase1.5.1.30.441
3px3T3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.441
5choFADFlavin reductase/0.441
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.440
1h50FMNPentaerythritol tetranitrate reductase/0.440
1hfqMOTDihydrofolate reductase1.5.1.30.440
1o2g696Prothrombin3.4.21.50.440
1r5hAO2Methionine aminopeptidase 2/0.440
2fk8SAMHydroxymycolate synthase MmaA42.1.10.440
2gs9SAHUncharacterized protein/0.440
2lfoGCHFatty acid-binding protein, liver/0.440
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.440
2rd2QSIGlutamine--tRNA ligase6.1.1.180.440
2zsdCOAPantothenate kinase2.7.1.330.440
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.440
3ha7B32Hydroxymycolate synthase MmaA42.1.10.440
3i0pNADMalate dehydrogenase, putative/0.440
3q43D66M1 family aminopeptidase3.4.110.440
3r7kFDAProbable acyl CoA dehydrogenase/0.440
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.440
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.440
3vtdTKDVitamin D3 receptor/0.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440