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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
1n5sADLActVA 6 protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1n5sADLActVA 6 protein/1.000
1n5tOALActVA 6 protein/0.800
1n5qTNCActVA 6 protein/0.619
1n5vNOMActVA 6 protein/0.500
3vtdTKDVitamin D3 receptor/0.496
3zy3GDPGDP-fucose protein O-fucosyltransferase 12.4.1.2210.494
4cavMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.489
4zasTYDCalS13/0.486
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.484
1vbiNADMalate/L-lactate dehydrogenase family protein/0.484
3gyaCOAGCN5-related N-acetyltransferase/0.484
5a02NAPGlucose-fructose oxidoreductase/0.482
1d3gBREDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.480
3zy5GFBGDP-fucose protein O-fucosyltransferase 12.4.1.2210.479
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.479
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.478
2y60M8FIsopenicillin N synthase1.21.3.10.478
1wklATPNucleoside diphosphate kinase/0.477
2dw4FADLysine-specific histone demethylase 1A10.477
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.477
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.477
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.477
3mb714ICasein kinase II subunit alpha2.7.11.10.476
4bfxZVXPantothenate kinase2.7.1.330.476
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.473
1rk3VDXVitamin D3 receptor/0.472
1w06W05Isopenicillin N synthase1.21.3.10.472
4h03LARActin, alpha skeletal muscle/0.472
2ydoADNAdenosine receptor A2a/0.471
5iqhGNPBifunctional AAC/APH2.3.10.471
2imkGTXAGAP009194-PA/0.470
1bk0ACVIsopenicillin N synthase1.21.3.10.469
1hb1OCVIsopenicillin N synthase1.21.3.10.469
2z3uCRRCytochrome P450/0.469
1n0hCIEAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.468
4l5b1UXDeoxycytidine kinase2.7.1.740.468
4rkdKETAminotransferase/0.468
1rywEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.467
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.467
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.467
3p8iFMNPentaerythritol tetranitrate reductase/0.467
4l17DNQGlutamate receptor 2/0.467
5bqfNAPProbable hydroxyacid dehydrogenase protein/0.467
1rftPXMPyridoxal kinase2.7.1.350.466
3w0c6DSVitamin D3 receptor/0.466
4yv1S4MSpermidine synthase, putative/0.466
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.466
3vw7VPXProteinase-activated receptor 1/0.466
2yg5FADPutrescine oxidase/0.465
3l0lHC3Nuclear receptor ROR-gamma/0.465
4nzoANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.465
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
2vpyMGDThiosulfate reductase/0.464
3qh23NMThiazole tautomerase/0.464
1opbRETRetinol-binding protein 2/0.463
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.463
3zkyWT4Isopenicillin N synthase1.21.3.10.463
4f48C2EUncharacterized protein/0.463
4xybNDPFormate dehydrogenase/0.463
5dozNDPJamJ/0.463
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.462
1crbRTLRetinol-binding protein 1/0.462
1pnqNDPNAD(P) transhydrogenase subunit beta1.6.1.20.462
1rkgVD1Vitamin D3 receptor/0.462
1t9a1TBAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.462
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.462
3jpuTY4Transcriptional activator protein LasR/0.462
1akaPLPAspartate aminotransferase, mitochondrial2.6.1.10.461
1aoeGW3Dihydrofolate reductase1.5.1.30.461
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.461
3b7dCNIGlutamate receptor 2/0.461
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3w78CBDFMN-dependent NADH-azoreductase/0.461
4i8vBHFCytochrome P450 1A11.14.14.10.461
4xbfFADLysine-specific histone demethylase 1A10.461
1qiqACCIsopenicillin N synthase1.21.3.10.460
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.460
2hkoFADLysine-specific histone demethylase 1A10.460
2x9dITCTetracycline repressor protein class D/0.460
4r7uUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.460
4tmcFMNOld yellow enzyme/0.460
1xagNAD3-dehydroquinate synthase/0.459
2zevIPEGeranylgeranyl pyrophosphate synthase/0.459
3jynNDPQuinone oxidoreductase/0.459
3r8814FAnthranilate phosphoribosyltransferase/0.459
4f1yCNIGlutamate receptor 3/0.459
4g1y0VOVitamin D3 receptor A/0.459
1dghNDPCatalase1.11.1.60.458
1egcCO8Medium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.458
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
1z6tADPApoptotic protease-activating factor 1/0.458
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.458
4dvi2IWTankyrase-12.4.2.300.458
1h36R88Squalene--hopene cyclase4.2.1.1290.457
2lbvEB4Extracellular fatty acid-binding protein/0.457
3te4ACODopamine N-acetyltransferase/0.457
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.457
4rjeFNRLactate oxidase/0.457
1akcPPEAspartate aminotransferase, mitochondrial2.6.1.10.456
2j9lATPH(+)/Cl(-) exchange transporter 5/0.456
2xvw9NRSerum albumin/0.456
3c3dFO12-phospho-L-lactate transferase/0.456
3p23ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.456
3pqbVGPPutative oxidoreductase/0.456
3vrvYSDVitamin D3 receptor/0.456
4do30LAFatty-acid amide hydrolase 13.5.1.990.456
4es5MGTPolymerase basic protein 2/0.456
5kgpACOPredicted acetyltransferase/0.456
5k2dZMAAdenosine receptor A2a/0.456
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1qjfACSIsopenicillin N synthase1.21.3.10.455
1qnfFADDeoxyribodipyrimidine photo-lyase4.1.99.30.455
1sepBIOSepiapterin reductase1.1.1.1530.455
2zseACPPantothenate kinase2.7.1.330.455
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.455
4ifn12OKelch-like ECH-associated protein 1/0.455
1h35R01Squalene--hopene cyclase4.2.1.1290.454
1i7lATPSynapsin-2/0.454
1mxfMTXPutative pteridine reductase 2/0.454
1p8dCO1Oxysterols receptor LXR-beta/0.454
1x2hLPALipoate-protein ligase A6.3.1.200.454
3cvuFADRE11660p/0.454
3dfrMTXDihydrofolate reductase1.5.1.30.454
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
1bwlFMNNADPH dehydrogenase 11.6.99.10.453
1cm0COAHistone acetyltransferase KAT2B2.3.1.480.453
1dgbNDPCatalase1.11.1.60.453
1ig1ANPDeath-associated protein kinase 12.7.11.10.453
1kqwRTLCellular retinol-binding protein type II/0.453
1qorNDPQuinone oxidoreductase 1/0.453
1ykdCMPAdenylate cyclase/0.453
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.453
3sjzGNPTranslation initiation factor 2 subunit gamma/0.453
4qzuRTLRetinol-binding protein 2/0.453
1ay0TPPTransketolase 12.2.1.10.452
1cq6PY4Aspartate aminotransferase2.6.1.10.452
1e2nRCAThymidine kinase/0.452
3c3xNAPEugenol synthase 11.1.1.3180.452
3zoiM2WIsopenicillin N synthase1.21.3.10.452
4bfsZVSPantothenate kinase2.7.1.330.452
4lt63ATPoly(A) polymerase gamma2.7.7.190.452
1ia1TQ3Dihydrofolate reductase1.5.1.30.451
1q4xG24Thyroid hormone receptor beta/0.451
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.451
1tezFADDeoxyribodipyrimidine photo-lyase4.1.99.30.451
1w83L11Mitogen-activated protein kinase 14/0.451
1yc2NADNAD-dependent protein deacylase 2/0.451
2fknNADUrocanate hydratase4.2.1.490.451
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.451
2j7t274Serine/threonine-protein kinase 102.7.11.10.451
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.451
2r6jNDPEugenol synthase 11.1.1.3180.451
4co4ATPNitrogen regulatory protein P-II 1/0.451
4g1z0VPVitamin D3 receptor A/0.451
4qm6GTPMetallophosphoesterase/0.451
5k2cZMAAdenosine receptor A2a/0.451
1mtcGPRGlutathione S-transferase Mu 12.5.1.180.450
1nasASESepiapterin reductase1.1.1.1530.450
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.450
1swtBTNStreptavidin/0.450
3nbzGTPGTP-binding nuclear protein Ran/0.450
3vruYS3Vitamin D3 receptor/0.450
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.450
4e2bFMNDehydrogenase/0.450
4eyb0WOMetallo-beta-lactamase type 2/0.450
4pmjNAPPutative oxidoreductase/0.450
1os1ATPPhosphoenolpyruvate carboxykinase (ATP)/0.449
1p0pBCHCholinesterase3.1.1.80.449
2a8sGTPU8 snoRNA-decapping enzyme/0.449
2o2yTCLEnoyl-ACP reductase/0.449
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4b4w9L9Bifunctional protein FolD/0.449
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.449
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.449
4ii5ADPCyclin-dependent kinase 22.7.11.220.449
5iqeGNPBifunctional AAC/APH2.3.10.449
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.448
1x8b824Wee1-like protein kinase2.7.10.20.448
2iviACWIsopenicillin N synthase1.21.3.10.448
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.448
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.448
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3o153NMThiamine-phosphate synthase/0.448
3tzaTZGGlutamate receptor 2/0.448
3vtcTK3Vitamin D3 receptor/0.448
4iarERM5-hydroxytryptamine receptor 1B/0.448
4jvlESTEstrogen sulfotransferase2.8.2.40.448
4q0a4OAVitamin D3 receptor A/0.448
5a04NDPGlucose-fructose oxidoreductase/0.448
5c7hNDPPutative oxidoreductase/0.448
5pahLDPPhenylalanine-4-hydroxylase1.14.16.10.448
7catNDPCatalase1.11.1.60.448
3sn6P0GBeta-2 adrenergic receptor/0.448
3emlZMAAdenosine receptor A2a/0.448
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
1ly4COQDihydrofolate reductase1.5.1.30.447
1ygjRMCPyridoxal kinase2.7.1.350.447
1yqj6NPMitogen-activated protein kinase 14/0.447
2ay95PVAromatic-amino-acid aminotransferase2.6.1.570.447
2i9pNAD3-hydroxyisobutyrate dehydrogenase, mitochondrial1.1.1.310.447
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.447
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3lanKBTGag-Pol polyprotein2.7.7.490.447
3nwlNDPCatalase1.11.1.60.447
3vtbTKAVitamin D3 receptor/0.447
3w5p4OAVitamin D3 receptor/0.447
4cdmFO1Deoxyribodipyrimidine photolyase/0.447
4ho2THMGlucose-1-phosphate thymidylyltransferase/0.447
4hsuFADLysine-specific histone demethylase 1B10.447
4jqh1MFAlr2278 protein/0.447
4n4v2GYTankyrase-12.4.2.300.447
5agyGTBTau class glutathione S-transferase/0.447
5kghACOPredicted acetyltransferase/0.447
1dgfNDPCatalase1.11.1.60.446
1lb9DNQGlutamate receptor 2/0.446
1osvCHCBile acid receptor/0.446
2cfcKPC2-(R)-hydroxypropyl-CoM dehydrogenase1.1.1.2680.446
2nomDUTPoly(A) polymerase, putative/0.446
2ym1NAPPhenylacetone monooxygenase1.14.13.920.446
3cneFMNPutative protease I/0.446
3e6eDCSAlanine racemase/0.446
3fo7IMNPhospholipase A2 VRV-PL-VIIIa/0.446
3iw1ASDSteroid C26-monooxygenase1.14.13.1410.446
3ix3OHNTranscriptional activator protein LasR/0.446
3pahXDEPhenylalanine-4-hydroxylase1.14.16.10.446
3poz03PEpidermal growth factor receptor2.7.10.10.446
4b66FADL-ornithine N(5)-monooxygenase/0.446
4giu636Anthranilate phosphoribosyltransferase/0.446
4isuIKMGlutamate receptor 2/0.446
5l8lADPAurora kinase A2.7.11.10.446
1b2lNDCAlcohol dehydrogenase1.1.1.10.445
1nhgTCLEnoyl-ACP reductase/0.445
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.445
2zl9VDAVitamin D3 receptor/0.445
3c3ySAHO-methyltransferase/0.445
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.445
4mv1ADPBiotin carboxylase6.3.4.140.445
4rpgFADUDP-galactopyranose mutase5.4.99.90.445
4y95746Tyrosine-protein kinase/0.445
1adfTADAlcohol dehydrogenase E chain1.1.1.10.444
1bwkFMNNADPH dehydrogenase 11.6.99.10.444
1hb3SCVIsopenicillin N synthase1.21.3.10.444
1mezGDPAdenylosuccinate synthetase isozyme 1/0.444
2bxoOPBSerum albumin/0.444
2r0pK2CPutative FAD-monooxygenase/0.444
2uxoTACHTH-type transcriptional regulator TtgR/0.444
2z4y252Geranylgeranyl pyrophosphate synthase/0.444
3c74ANUUridine phosphorylase2.4.2.30.444
3kb6NADD-lactate dehydrogenase/0.444
3oiaA31Camphor 5-monooxygenase1.14.15.10.444
3vcyUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.444
3w3zGTPGTP-binding nuclear protein Ran/0.444
3zp4TSAChorismate mutase AroH5.4.99.50.444
4z0pNDPNAD-dependent dehydrogenase/0.444
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.444
5jadFB2Platelet-activating factor acetylhydrolase3.1.1.470.444
5kf8ACOPredicted acetyltransferase/0.444
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.443
1pagFMPAntiviral protein I3.2.2.220.443
2bxmIMNSerum albumin/0.443
2g78REACellular retinoic acid-binding protein 2/0.443
2lfoGCHFatty acid-binding protein, liver/0.443
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
2xpwOTCTetracycline repressor protein class D/0.443
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.443
3dr1C5DVitamin D3 receptor A/0.443
3hub469Mitogen-activated protein kinase 14/0.443
3jzdNADMaleylacetate reductase/0.443
3oqkS52Renin3.4.23.150.443
3qly55VUncharacterized protein/0.443
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.443
3w0yDS4Vitamin D3 receptor/0.443
4cnzADPNitrogen regulatory protein P-II 1/0.443
4ryvZEAProtein LlR18A/0.443
4xz3COAAcyl-CoA synthetase (NDP forming)/0.443
5c1gGDUHisto-blood group ABO system transferase/0.443
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.442
1e2jTHMThymidine kinase/0.442
1ftlDNQGlutamate receptor 2/0.442
1t9b1CSAcetolactate synthase catalytic subunit, mitochondrial2.2.1.60.442
3jq3ADPLombricine kinase/0.442
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.442
3p6mDSOCamphor 5-monooxygenase1.14.15.10.442
3r3f4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.442
3td8D2RDihydrofolate reductase1.5.1.30.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4cb629RPolymerase basic protein 2/0.442
4kxjP34Nucleoprotein/0.442
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.442
4ng2OHNTranscriptional activator protein LasR/0.442
4oztP1AEcdysone receptor, putative/0.442
5fm7ADPRuvB-like helicase/0.442
1kt3RTLRetinol-binding protein 4/0.441
1tvrTB9Gag-Pol polyprotein2.7.7.490.441
2a4nCOAAac(6')-Ii protein/0.441
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.441
2zevB71Geranylgeranyl pyrophosphate synthase/0.441
3b9lAZZSerum albumin/0.441
3ds6A17Mitogen-activated protein kinase 14/0.441
3hk1B64Fatty acid-binding protein, adipocyte/0.441
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.441
3up3XCAaceDAF-12/0.441
4dw60MNHTH-type transcriptional regulator EthR/0.441
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.441
4kq2U5PGlycogen [starch] synthase isoform 22.4.1.110.441
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.441
4ztvTA7Anthranilate phosphoribosyltransferase/0.441
5bylGCPBifunctional AAC/APH2.3.10.441
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.441
5k2bZMAAdenosine receptor A2a/0.441
1n83CLRNuclear receptor ROR-alpha/0.440
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.440
1wuuANPGalactokinase2.7.1.60.440
1xxjUNCUricase1.7.3.30.440
2bfmTOPPteridine reductase 11.5.1.330.440
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2ewaSB2Mitogen-activated protein kinase 14/0.440
2f59INI6,7-dimethyl-8-ribityllumazine synthase 1/0.440
2gevCOKPantothenate kinase2.7.1.330.440
2gu8796cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2q4bNAPUncharacterized protein At5g02240/0.440
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3ixp834Ecdysone receptor/0.440
3junAKDPhenazine biosynthesis protein A/B/0.440
3kpzZNEVitamin D3 receptor/0.440
3pdqKC6Lysine-specific demethylase 4A1.14.110.440
3rhaFDAPutrescine oxidase/0.440
4bfuZVUPantothenate kinase2.7.1.330.440
4c1fX8ZMetallo-beta-lactamase type 2/0.440
4g20484Vitamin D3 receptor A/0.440
4kxn6K62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.440
8catNDPCatalase1.11.1.60.440