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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
1r6g442Thyroid hormone receptor beta

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1r6g442Thyroid hormone receptor beta/1.000
1q4xG24Thyroid hormone receptor beta/0.584
1nq14HYThyroid hormone receptor beta/0.533
3vtdTKDVitamin D3 receptor/0.503
2pin4HYThyroid hormone receptor beta/0.496
3w0c6DSVitamin D3 receptor/0.496
4ia3BIVVitamin D3 receptor A/0.491
3vt3VDXVitamin D3 receptor/0.486
4ryvZEAProtein LlR18A/0.485
2q9fC3SCholesterol 24-hydroxylase/0.483
3tqhNDPQuinone oxidoreductase/0.482
3d574HYThyroid hormone receptor beta/0.481
3vt8YI3Vitamin D3 receptor/0.481
3w0aDS5Vitamin D3 receptor/0.481
4fhi0S4Vitamin D3 receptor A/0.481
4g20484Vitamin D3 receptor A/0.481
4ia1BIVVitamin D3 receptor A/0.480
2z6jTUI2-nitropropane dioxygenase/0.479
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.477
1osvCHCBile acid receptor/0.476
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.476
3vt5YI2Vitamin D3 receptor/0.476
3vt65YIVitamin D3 receptor/0.476
3vt45YIVitamin D3 receptor/0.475
4g210VPVitamin D3 receptor A/0.475
3vrwYS5Vitamin D3 receptor/0.474
3vt7VDXVitamin D3 receptor/0.474
3vtcTK3Vitamin D3 receptor/0.473
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.472
3w0yDS4Vitamin D3 receptor/0.472
4f9mFCMPeroxisome proliferator-activated receptor gamma/0.472
4g1d0VKVitamin D3 receptor A/0.471
1kkq471Peroxisome proliferator-activated receptor alpha/0.470
2harOCCVitamin D3 receptor/0.470
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.470
4itfTFYVitamin D3 receptor/0.470
4ruoBIVVitamin D3 receptor A/0.470
1rk3VDXVitamin D3 receptor/0.469
2hfpNSIPeroxisome proliferator-activated receptor gamma/0.469
3s55NADPutative short-chain dehydrogenase/reductase/0.469
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.469
4qe6JN3Bile acid receptor/0.469
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.468
4fhh0U3Vitamin D3 receptor A/0.468
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.467
2zbzVDXVitamin D3 dihydroxylase/0.467
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.467
4a8v2ANMajor pollen allergen Bet v 1-J/0.467
4g1z0VPVitamin D3 receptor A/0.467
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.467
1w06W05Isopenicillin N synthase1.21.3.10.466
2hcdBIVVitamin D3 receptor A/0.466
2zl9VDAVitamin D3 receptor/0.466
3w0jT08Vitamin D3 receptor/0.466
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.465
2j5xGSPADP-ribosylation factor 6/0.465
2q59240Peroxisome proliferator-activated receptor gamma/0.465
4i8vBHFCytochrome P450 1A11.14.14.10.465
4l4cCAMCamphor 5-monooxygenase1.14.15.10.465
4tuvCPZCytochrome P450 1191.140.465
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.465
1db1VDXVitamin D3 receptor/0.464
1q4t4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.464
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.464
3vspEK8Peroxisome proliferator-activated receptor gamma/0.464
1ie8KH1Vitamin D3 receptor/0.463
3w5tLHPVitamin D3 receptor/0.463
4cdmFO1Deoxyribodipyrimidine photolyase/0.463
4enhFVXCholesterol 24-hydroxylase/0.463
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.462
1rkgVD1Vitamin D3 receptor/0.462
3da24MDCarbonic anhydrase 134.2.1.10.462
3vruYS3Vitamin D3 receptor/0.462
4ia7BIVVitamin D3 receptor A/0.462
4jazSTLPeroxisome proliferator-activated receptor gamma/0.462
4ure1PSCyclohexanol dehydrogenase/0.462
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.462
1phgMYTCamphor 5-monooxygenase1.14.15.10.461
1u4dDBQActivated CDC42 kinase 1/0.461
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.461
3mdvCL6Cholesterol 24-hydroxylase/0.461
3sp9IL2Peroxisome proliferator-activated receptor delta/0.461
3w5p4OAVitamin D3 receptor/0.461
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.460
2hbhXE4Vitamin D3 receptor A/0.460
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.460
2zlcVDXVitamin D3 receptor/0.460
3mg3ECHOrange carotenoid-binding protein/0.460
4i3vNADAldehyde dehydrogenase (NAD+)/0.460
4nb6444Nuclear receptor ROR-gamma/0.460
4uyaAGSMitogen-activated protein kinase kinase kinase 212.7.11.250.460
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
1n5dNDPCarbonyl reductase [NADPH] 1/0.459
1olmVTQSEC14-like protein 2/0.459
1ot7CHCBile acid receptor/0.459
2dteNAIGlucose 1-dehydrogenase related protein/0.459
2hc4VDXVitamin D3 receptor A/0.459
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
3inxJZCHeat shock protein HSP 90-alpha/0.459
4lxhC1EAlpha/beta hydrolase fold/0.459
2ftoCB3Thymidylate synthase/0.458
2hb7O1CVitamin D3 receptor/0.458
3cyz9ODPheromone-binding protein ASP1/0.458
3kpzZNEVitamin D3 receptor/0.458
3pm0BHFCytochrome P450 1B1/0.458
3vtbTKAVitamin D3 receptor/0.458
4g2i0VQVitamin D3 receptor/0.458
1dz6CAMCamphor 5-monooxygenase1.14.15.10.457
1fmlRTLRetinol dehydratase/0.457
1nq24HYThyroid hormone receptor beta/0.457
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
1txiTX5Vitamin D3 receptor/0.457
2c0cNAPProstaglandin reductase 310.457
2fzwNADAlcohol dehydrogenase class-31.1.1.10.457
2o4rVD5Vitamin D3 receptor/0.457
3cukFADD-amino-acid oxidase1.4.3.30.457
3drcMTXDihydrofolate reductase1.5.1.30.457
3r7cFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.457
3v9y24LPeroxisome proliferator-activated receptor gamma/0.457
3w0hW12Vitamin D3 receptor/0.457
5k2bZMAAdenosine receptor A2a/0.457
1a72PADAlcohol dehydrogenase E chain1.1.1.10.456
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1y4lSVRBasic phospholipase A2 homolog 2/0.456
2nq8ZIDEnoyl-ACP reductase/0.456
2om9AJAPeroxisome proliferator-activated receptor gamma/0.456
2p4yC03Peroxisome proliferator-activated receptor gamma/0.456
3ielU5PRibonuclease TTHA02523.10.456
3vrvYSDVitamin D3 receptor/0.456
3w0gW07Vitamin D3 receptor/0.456
3w0iO11Vitamin D3 receptor/0.456
4iteTEYVitamin D3 receptor/0.456
4l98LRGPeroxisome proliferator-activated receptor gamma/0.456
4y8wSTRSteroid 21-hydroxylase/0.456
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.455
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.455
2c7xNRBCytochrome P450 monooxygenase PikC/0.455
3gbk2PQPeroxisome proliferator-activated receptor gamma/0.455
3gggNADPrephenate dehydrogenase/0.455
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.455
3stv3HOMethylketone synthase I/0.455
3wmxNADNAD dependent epimerase/dehydratase/0.455
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.455
4j6dTESCytochrome P450 monooxygenase/0.455
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
1uyrD1LAcetyl-CoA carboxylase/0.454
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.454
2zlaVDBVitamin D3 receptor/0.454
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.454
3p99LNPLanosterol 14-alpha-demethylase/0.454
3ukuC69Actin-related protein 3/0.454
3uleC69Actin-related protein 3/0.454
4l4xNDPAmphI/0.454
1cbqRE9Cellular retinoic acid-binding protein 2/0.453
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
3oquA8SAbscisic acid receptor PYL9/0.453
3w5rLOAVitamin D3 receptor/0.453
3zk5Z18Cytochrome P450 monooxygenase PikC/0.453
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.453
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.453
1dkfBMSRetinoic acid receptor alpha/0.452
1ie9VDXVitamin D3 receptor/0.452
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1q4u4CA4-hydroxybenzoyl-CoA thioesterase3.1.2.230.452
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.452
2aibERGBeta-elicitin cinnamomin/0.452
2hasC3OVitamin D3 receptor/0.452
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.452
2zb45OPProstaglandin reductase 21.3.1.480.452
3vt9YI4Vitamin D3 receptor/0.452
4awq592Heat shock protein HSP 90-alpha/0.452
4ejgNCTCytochrome P450 2A131.14.14.10.452
1iyzNDPProbable quinone oxidoreductase/0.451
1naxIH5Thyroid hormone receptor beta/0.451
1y0s331Peroxisome proliferator-activated receptor delta/0.451
3gwfFADCyclohexanone monooxygenase/0.451
3m7rVDXVitamin D3 receptor/0.451
4h50NAPBiphenyl dioxygenase ferredoxin reductase subunit/0.451
4ia2BIVVitamin D3 receptor A/0.451
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.451
4l8u9AZSerum albumin/0.451
1hdrNADDihydropteridine reductase1.5.1.340.450
1iepSTITyrosine-protein kinase ABL12.7.10.20.450
2uxiG50HTH-type transcriptional regulator TtgR/0.450
2xvv9DNSerum albumin/0.450
2znnS44Peroxisome proliferator-activated receptor alpha/0.450
3b6zCO7Enoyl reductase LovC10.450
3dr1C5DVitamin D3 receptor A/0.450
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.450
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.450
3tea4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.450
3tk3CPZCytochrome P450 2B41.14.14.10.450
4bb3KKAIsopenicillin N synthase1.21.3.10.450
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.450
4l4dCAMCamphor 5-monooxygenase1.14.15.10.450
4l9q9TPSerum albumin/0.450
1eioGCHGastrotropin/0.449
1rszDIHPurine nucleoside phosphorylase2.4.2.10.449
1uyuCAMCamphor 5-monooxygenase1.14.15.10.449
1x2hLPALipoate-protein ligase A6.3.1.200.449
2q61SF1Peroxisome proliferator-activated receptor gamma/0.449
2yfeYFEPeroxisome proliferator-activated receptor gamma/0.449
3bgqVX2Serine/threonine-protein kinase pim-12.7.11.10.449
3fwjCAMCamphor 5-monooxygenase1.14.15.10.449
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.449
4xybNDPFormate dehydrogenase/0.449
1g67TZPThiamine-phosphate synthase/0.448
1lriCLRBeta-elicitin cryptogein/0.448
1lwlDSOCamphor 5-monooxygenase1.14.15.10.448
1poxFADPyruvate oxidase1.2.3.30.448
1sozVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.448
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.448
2iviACWIsopenicillin N synthase1.21.3.10.448
2xvw9NRSerum albumin/0.448
3a783EVVitamin D3 receptor/0.448
3aw9NADNAD-dependent epimerase/dehydratase/0.448
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.448
3kytHC2Nuclear receptor ROR-gamma/0.448
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
4gkvNADAlcohol dehydrogenase, propanol-preferring1.1.1.10.448
4iui1GQEstrogen receptor/0.448
4q72FADBifunctional protein PutA/0.448
4q73FADBifunctional protein PutA/0.448
1f4fTP3Thymidylate synthase/0.447
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.447
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.447
2jb4A14Isopenicillin N synthase1.21.3.10.447
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.447
2q5p241Peroxisome proliferator-activated receptor gamma/0.447
2w3bNDPDihydrofolate reductase1.5.1.30.447
3ii43IIDihydrolipoyl dehydrogenase1.8.1.40.447
3pj8404Cyclin-dependent kinase 22.7.11.220.447
3r324CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.447
3uwlFOZThymidylate synthase/0.447
4kkyCAMCamphor 5-monooxygenase1.14.15.10.447
4rrxLURProstaglandin G/H synthase 21.14.99.10.447
5cccDDFDihydrofolate reductase1.5.1.30.447
6cp4CAMCamphor 5-monooxygenase1.14.15.10.447
1navIH5Thyroid hormone receptor alpha/0.446
1upw444Oxysterols receptor LXR-beta/0.446
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
2cig1DGDihydrofolate reductase1.5.1.30.446
2hamC33Vitamin D3 receptor/0.446
2o4jVD4Vitamin D3 receptor/0.446
3cy2MB9Serine/threonine-protein kinase pim-12.7.11.10.446
3iaeD7KBenzaldehyde lyase/0.446
3inwJZBHeat shock protein HSP 90-alpha/0.446
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.446
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.446
4iah1DXAlr2278 protein/0.446
4neuQ1AReceptor-interacting serine/threonine-protein kinase 12.7.11.10.446
4zowCLMMultidrug transporter MdfA/0.446
5idwNAPShort-chain dehydrogenase/reductase SDR/0.446
1draMTXDihydrofolate reductase1.5.1.30.445
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.445
2q6sPLBPeroxisome proliferator-activated receptor gamma/0.445
3cgoJNOMitogen-activated protein kinase 102.7.11.240.445
3d7kD7KBenzaldehyde lyase/0.445
3ey9TDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.445
3l8p0CEAngiopoietin-1 receptor2.7.10.10.445
3t2zFADSulfide-quinone reductase/0.445
3ua506XCytochrome P450 2B61.14.130.445
3w33W19Epidermal growth factor receptor2.7.10.10.445
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.445
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.445
5iu86DZAdenosine receptor A2a/0.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1n83CLRNuclear receptor ROR-alpha/0.444
1powFADPyruvate oxidase1.2.3.30.444
2ca0PXICytochrome P450 monooxygenase PikC/0.444
2hb8MVDVitamin D3 receptor/0.444
2hnzPC0Gag-Pol polyprotein2.7.7.490.444
2p33J07Mitogen-activated protein kinase 102.7.11.240.444
2r7b2533-phosphoinositide-dependent protein kinase 12.7.11.10.444
2vzmNRBCytochrome P450 monooxygenase PikC/0.444
2z97CAMCamphor 5-monooxygenase1.14.15.10.444
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3lanKBTGag-Pol polyprotein2.7.7.490.444
3tmz06XCytochrome P450 2B41.14.14.10.444
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
3up3XCAaceDAF-12/0.444
4a4wYFBPeroxisome proliferator-activated receptor gamma/0.444
4b7dQLECytochrome P450 monooxygenase PikC/0.444
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.444
4ez8DHFThymidylate synthase2.1.1.450.444
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
4q0a4OAVitamin D3 receptor A/0.444
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.444
1e7aPFLSerum albumin/0.443
1jpaANPEphrin type-B receptor 22.7.10.10.443
1jutLYDThymidylate synthase/0.443
1zhzERGOxysterol-binding protein homolog 4/0.443
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.443
2znq401Peroxisome proliferator-activated receptor delta/0.443
3n7uNADFormate dehydrogenase, chloroplastic/mitochondrial/0.443
3w5q3KLVitamin D3 receptor/0.443
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.443
3zoiM2WIsopenicillin N synthase1.21.3.10.443
3zsi52PMitogen-activated protein kinase 14/0.443
4b7sQLECytochrome P450 monooxygenase PikC/0.443
4g1y0VOVitamin D3 receptor A/0.443
4l4fCAMCamphor 5-monooxygenase1.14.15.10.443
1heuNADAlcohol dehydrogenase E chain1.1.1.10.442
1iwjCAMCamphor 5-monooxygenase1.14.15.10.442
1ml6GBXGlutathione S-transferase A22.5.1.180.442
3cxw7CPSerine/threonine-protein kinase pim-12.7.11.10.442
3cz09ODPheromone-binding protein ASP1/0.442
3lqfNADGalactitol dehydrogenase/0.442
3vrtYS2Vitamin D3 receptor/0.442
4cp4CAMCamphor 5-monooxygenase1.14.15.10.442
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4eh9IRGMitogen-activated protein kinase 14/0.442
1bk0ACVIsopenicillin N synthase1.21.3.10.441
1jioDEB6-deoxyerythronolide B hydroxylase/0.441
1n46PFAThyroid hormone receptor beta/0.441
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.441
1s19MC9Vitamin D3 receptor/0.441
1zeoC01Peroxisome proliferator-activated receptor gamma/0.441
2dshSAHDiphthine synthase/0.441
2y9qANPMitogen-activated protein kinase 12.7.11.240.441
3anlNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.441
3hv5R24Mitogen-activated protein kinase 14/0.441
3vev0H4Glucokinase2.7.1.20.441
4i5eNAPAlclohol dehydrogenase/short-chain dehydrogenase/0.441
4id71G0Activated CDC42 kinase 1/0.441
4jufTPPBenzoylformate decarboxylase4.1.1.70.441
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.441
1b16NAQAlcohol dehydrogenase1.1.1.10.440
1eupASD6-deoxyerythronolide B hydroxylase/0.440
1hvyD16Thymidylate synthase2.1.1.450.440
1ia4TQ6Dihydrofolate reductase1.5.1.30.440
1ot7IU5Bile acid receptor/0.440
1r0eDFNGlycogen synthase kinase-3 beta2.7.11.260.440
1re9DSOCamphor 5-monooxygenase1.14.15.10.440
1sn5T3Transthyretin/0.440
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.440
2qo9ANPEphrin type-A receptor 32.7.10.10.440
3koo24DBifunctional epoxide hydrolase 23.3.2.100.440
3p3zP3ZPutative cytochrome P450/0.440
3q7dNPXProstaglandin G/H synthase 21.14.99.10.440
3v9v21LPeroxisome proliferator-activated receptor gamma/0.440
4a81DXCMajor pollen allergen Bet v 1-A/0.440
4b1fKRHGlutamate racemase/0.440
4g3e0WCMitogen-activated protein kinase kinase kinase 142.7.11.250.440
4j6cSTRCytochrome P450 monooxygenase/0.440
4lva20MNicotinamide phosphoribosyltransferase2.4.2.120.440
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.440
4rupH97Vitamin D3 receptor A/0.440