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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
3s41S41Glucokinase2.7.1.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3s41S41Glucokinase2.7.1.21.000
4dhyS41Glucokinase2.7.1.20.929
3vf60H6Glucokinase2.7.1.20.600
3vev0H4Glucokinase2.7.1.20.594
4ixc1JDGlucokinase2.7.1.20.576
4iwv1J9Glucokinase2.7.1.20.575
4dch4DCGlucokinase2.7.1.20.544
1xddAAYIntegrin alpha-L/0.517
5ab7MLCNonspecific lipid-transfer protein, putative/0.506
3bsyACOUDP-N-acetylbacillosamine N-acetyltransferase2.3.1.2030.505
3nxyD2HDihydrofolate reductase1.5.1.30.498
3l0lHC3Nuclear receptor ROR-gamma/0.494
4isg1FYGlucokinase2.7.1.20.491
1h36R88Squalene--hopene cyclase4.2.1.1290.484
4r20AERCytochrome P450 family 17 polypeptide 2/0.484
5ab6CAANonspecific lipid-transfer protein, putative/0.484
2b01TUDPhospholipase A2, major isoenzyme3.1.1.40.480
4iarERM5-hydroxytryptamine receptor 1B/0.480
1ndzFR5Adenosine deaminase3.5.4.40.478
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.478
5dhgDGVNociceptin receptor/0.478
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.477
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.477
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.475
2e0nSAHPrecorrin-2 C20-methyltransferase/0.475
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.475
1ry0PG2Aldo-keto reductase family 1 member C3/0.474
4l4xNDPAmphI/0.474
1o6qR17Squalene--hopene cyclase4.2.1.1290.473
4bfyZVYPantothenate kinase2.7.1.330.473
1rftPXMPyridoxal kinase2.7.1.350.472
3t8xT8XT-cell surface glycoprotein CD1b/0.471
4ddrMMVDihydrofolate reductase1.5.1.30.471
4xbfFADLysine-specific histone demethylase 1A10.471
1gky5GPGuanylate kinase2.7.4.80.470
3l6jZ90Alr2278 protein/0.470
4g48PZBMycocyclosin synthase1.14.21.90.470
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.470
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.469
2z7gEH9Adenosine deaminase3.5.4.40.469
2bf7HBIPteridine reductase 11.5.1.330.468
4l8u9AZSerum albumin/0.466
5g53NECAdenosine receptor A2a/0.466
1pz1NAPGeneral stress protein 69/0.465
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.465
5d7qAR6NAD-dependent protein deacetylase sirtuin-23.5.10.465
3iktNADRedox-sensing transcriptional repressor Rex/0.464
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.464
3ds6A17Mitogen-activated protein kinase 14/0.463
3gncQQQGlutaryl-CoA dehydrogenase/0.463
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.463
4iae1DXAlr2278 protein/0.463
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
1mczRMNBenzoylformate decarboxylase4.1.1.70.462
2wd8VGFPteridine reductase/0.462
3g70A5TRenin3.4.23.150.462
4iah1DXAlr2278 protein/0.462
4qa2SHHHistone deacetylase 83.5.1.980.462
4zm6ACON-acetyl-beta-D glucosaminidase/0.462
1umlFR4Adenosine deaminase3.5.4.40.461
1x2hLPALipoate-protein ligase A6.3.1.200.461
3p3zP3ZPutative cytochrome P450/0.461
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.461
1cqp803Integrin alpha-L/0.460
1fd0254Retinoic acid receptor gamma/0.460
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2xvw9NRSerum albumin/0.460
3p99LNPLanosterol 14-alpha-demethylase/0.460
4n4t2GVTankyrase-12.4.2.300.460
4ea30NNNociceptin receptor/0.460
1icqOPD12-oxophytodienoate reductase 11.3.1.420.459
1o5rFR9Adenosine deaminase3.5.4.40.459
1ygjRMCPyridoxal kinase2.7.1.350.459
2c29NAPDihydroflavonol 4-reductase/0.459
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.459
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
2gjlFMNNitronate monooxygenase1.13.12.160.458
2rkuR78Serine/threonine-protein kinase PLK12.7.11.210.458
3c3xNAPEugenol synthase 11.1.1.3180.458
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.457
1xuoLA1Integrin alpha-L/0.457
2p15EZTEstrogen receptor/0.457
3up0D7SaceDAF-12/0.457
3wv9FEGHmd co-occurring protein HcgE/0.457
1yhjR6CPyridoxal kinase2.7.1.350.456
2bxqIMNSerum albumin/0.456
2zevIPEGeranylgeranyl pyrophosphate synthase/0.456
3elm24FCollagenase 33.4.240.456
3up3XCAaceDAF-12/0.456
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.456
4fwjFADLysine-specific histone demethylase 1B10.456
4g47TZFMycocyclosin synthase1.14.21.90.456
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.456
4jqh1MFAlr2278 protein/0.456
4ktkKTKCytochrome P450/0.456
5hs1VORLanosterol 14-alpha demethylase/0.456
1h35R01Squalene--hopene cyclase4.2.1.1290.455
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.455
1t7o152Carnitine O-acetyltransferase2.3.1.70.455
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.455
4k9oTPPBenzoylformate decarboxylase4.1.1.70.455
1kruIPTGalactoside O-acetyltransferase2.3.1.180.454
2a9z26AAdenosine kinase2.7.1.200.454
2hk9NAPShikimate dehydrogenase (NADP(+))/0.454
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.454
2po7CHDFerrochelatase, mitochondrial4.99.1.10.454
3e5aVX6Aurora kinase A2.7.11.10.454
4bfxZVXPantothenate kinase2.7.1.330.454
5c8d5ADProbable transcriptional regulator/0.454
1lkdBP6Biphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.453
2fs4PZ1Renin3.4.23.150.453
4h9506UDihydrofolate reductase1.5.1.30.453
4iaq2GM5-hydroxytryptamine receptor 1B/0.453
4ktf1TMCytochrome P450/0.453
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1mczTDPBenzoylformate decarboxylase4.1.1.70.452
1synF89Thymidylate synthase/0.452
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.452
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.452
2xkdT3MSerine/threonine-protein kinase Nek22.7.11.10.452
3eanFADThioredoxin reductase 1, cytoplasmic1.8.1.90.452
3fnfJPMEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
3oadLPORenin3.4.23.150.452
3p9tTCLRepressor/0.452
3tm5SFGUncharacterized protein/0.452
4ap1NAPSteroid monooxygenase/0.452
4ktl1CQCytochrome P450/0.452
4lb2DM5Serum albumin/0.452
4mprTPPBenzoylformate decarboxylase4.1.1.70.452
1diuBDMDihydrofolate reductase1.5.1.30.451
1puaCOAHAT A1/0.451
1ygkRRCPyridoxal kinase2.7.1.350.451
2c31ADPOxalyl-CoA decarboxylase4.1.1.80.451
2psjCEIRenilla-luciferin 2-monooxygenase1.13.12.50.451
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
4a4l939Serine/threonine-protein kinase PLK12.7.11.210.451
4bfpSWYTankyrase-22.4.2.300.451
4g1nNZTPyruvate kinase PKM2.7.1.400.451
4uugPXGBranched-chain amino acid aminotransferase, putative/0.451
1jomFFODihydrofolate reductase1.5.1.30.450
1v7aFRCAdenosine deaminase3.5.4.40.450
1zq5E04Aldo-keto reductase family 1 member C3/0.450
2d29FADAcyl-CoA dehydrogenase/0.450
2obxINI6,7-dimethyl-8-ribityllumazine synthase 22.5.1.780.450
2ociTYCValacyclovir hydrolase3.10.450
3gkjHC3Niemann-Pick C1 protein/0.450
3hl0NADMaleylacetate reductase/0.450
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.450
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
5kf2ACOPredicted acetyltransferase/0.450
3emlZMAAdenosine receptor A2a/0.450
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.449
1exa394Retinoic acid receptor gamma/0.449
3phiNDPShikimate dehydrogenase (NADP(+))/0.449
3vo2FADFerredoxin--NADP reductase/0.449
3w0uHPWLactoylglutathione lyase4.4.1.50.449
4ea2RWZDehydrosqualene synthase/0.449
4j6cSTRCytochrome P450 monooxygenase/0.449
1jf2CZHObelin/0.448
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.448
1yw8A75Methionine aminopeptidase 2/0.448
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.448
4bftZVTPantothenate kinase2.7.1.330.448
4ixd1HVIntegrin alpha-L/0.448
4uymVOR14-alpha sterol demethylase Cyp51B/0.448
1pqc444Oxysterols receptor LXR-beta/0.447
2ea2F77Methionine aminopeptidase 2/0.447
2pnuENMAndrogen receptor/0.447
2z3uCRRCytochrome P450/0.447
3gieACPSensor histidine kinase DesK2.7.13.30.447
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.447
3vtbTKAVitamin D3 receptor/0.447
4a83DXCMajor pollen allergen Bet v 1-A/0.447
4q71FADBifunctional protein PutA/0.447
1fmjRTLRetinol dehydratase/0.446
1krv147Galactoside O-acetyltransferase2.3.1.180.446
1x1aSAMC-20 methyltransferase/0.446
1yc2NADNAD-dependent protein deacylase 2/0.446
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.446
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.446
3a1l2CCCytochrome P450/0.446
3ntgD72Prostaglandin G/H synthase 21.14.99.10.446
3u8dU8DPhospholipase A2, membrane associated/0.446
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.446
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.445
1fm4DXCMajor pollen allergen Bet v 1-L/0.445
1ia4TQ6Dihydrofolate reductase1.5.1.30.445
1p33MTXPteridine reductase 11.5.1.330.445
2jblSMAReaction center protein L chain/0.445
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.445
3h18PMSEsterase/lipase/0.445
3kytHC2Nuclear receptor ROR-gamma/0.445
3n0hTOPDihydrofolate reductase1.5.1.30.445
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
4dnaFADProbable glutathione reductase/0.445
4lsl1YQGag-Pol polyprotein2.7.7.490.445
4mv1ADPBiotin carboxylase6.3.4.140.445
5k2cZMAAdenosine receptor A2a/0.445
1u1d181Uridine phosphorylase2.4.2.30.444
1wxyFRKAdenosine deaminase3.5.4.40.444
2lbdREARetinoic acid receptor gamma/0.444
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.444
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.444
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.444
4isf1FXGlucokinase2.7.1.20.444
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1cdeDZFPhosphoribosylglycinamide formyltransferase/0.443
1o6rR19Squalene--hopene cyclase4.2.1.1290.443
1oj4CDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.443
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.443
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2bfaCB3Pteridine reductase 11.5.1.330.443
2bxoOPBSerum albumin/0.443
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.443
2xvv9DNSerum albumin/0.443
3bhrTHGThymidylate synthase/0.443
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3njoPYVAbscisic acid receptor PYR1/0.443
3otwCOAPhosphopantetheine adenylyltransferase/0.443
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4nc3ERM5-hydroxytryptamine receptor 2B/0.443
4zj8SUVOrexin receptor type 1/0.443
1s36CEIObelin/0.442
1zprCB3Thymidylate synthase/0.442
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.442
2jedLG8Protein kinase C theta type2.7.11.130.442
3oagLPQRenin3.4.23.150.442
3tl1JROPutative polyketide cyclase/0.442
3zg6APRNAD-dependent protein deacetylase sirtuin-63.5.10.442
4zhiADPKinesin-like protein KIF11/0.442
1hfqMOTDihydrofolate reductase1.5.1.30.441
1nm6L86Prothrombin3.4.21.50.441
1qtqQSIGlutamine--tRNA ligase6.1.1.180.441
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.441
2mm3CHOGastrotropin/0.441
2p1t3TNRetinoic acid receptor RXR-alpha/0.441
2z4y252Geranylgeranyl pyrophosphate synthase/0.441
3fkoFKOMitogen-activated protein kinase 14/0.441
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.441
4bfuZVUPantothenate kinase2.7.1.330.441
4fhd0TTSpore photoproduct lyase/0.441
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.441
4ise1FWGlucokinase2.7.1.20.441
4k4fK4FTankyrase-12.4.2.300.441
4l5b1UXDeoxycytidine kinase2.7.1.740.441
1crbRTLRetinol-binding protein 1/0.440
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.440
2ewaSB2Mitogen-activated protein kinase 14/0.440
2yac937Serine/threonine-protein kinase PLK12.7.11.210.440
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.440
3p2oNADBifunctional protein FolD/0.440
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.440
4at0FADPossible succinate dehydrogenase/0.440
4n4v2GYTankyrase-12.4.2.300.440
4qa0SHHHistone deacetylase 83.5.1.980.440
4zqcF6FTryptophan synthase alpha chain/0.440
5dhhDGWNociceptin receptor/0.440