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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
4fwfFADLysine-specific histone demethylase 1B1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4fwfFADLysine-specific histone demethylase 1B11.000
4gusFADLysine-specific histone demethylase 1B10.548
4hsuFADLysine-specific histone demethylase 1B10.531
4fweFADLysine-specific histone demethylase 1B10.501
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.500
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.494
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.494
3fhxPLPPyridoxal kinase2.7.1.350.491
3s1dZIRCytokinin dehydrogenase 11.5.99.120.487
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.485
2znq401Peroxisome proliferator-activated receptor delta/0.484
3nmpPYVAbscisic acid receptor PYL2/0.476
4l4xNDPAmphI/0.475
3kb6NADD-lactate dehydrogenase/0.473
1x2hLPALipoate-protein ligase A6.3.1.200.472
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.472
3pqbVGPPutative oxidoreductase/0.472
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.471
3wfjNAD2-dehydropantoate 2-reductase/0.470
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.470
3cppCAMCamphor 5-monooxygenase1.14.15.10.468
2bxmIMNSerum albumin/0.467
2g1n1IGRenin3.4.23.150.467
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.467
4yntFDAGlucose oxidase, putative/0.467
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
4zohFADPutative oxidoreductase FAD-binding subunit/0.466
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.465
1qoqIGPTryptophan synthase alpha chain/0.465
1xe55FEPlasmepsin-23.4.23.390.465
4kwi1TJReductase homolog/0.465
4xbfFADLysine-specific histone demethylase 1A10.465
1a72PADAlcohol dehydrogenase E chain1.1.1.10.464
4nvk2NYPeroxidase/0.464
4ea30NNNociceptin receptor/0.464
3gb4D3MDdmC/0.463
4fxy0W2Neurolysin, mitochondrial3.4.24.160.463
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.463
5kghACOPredicted acetyltransferase/0.463
1mjbACOHistone acetyltransferase ESA1/0.462
2rqfJH3Hemolymph juvenile hormone binding protein/0.462
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
1ia4TQ6Dihydrofolate reductase1.5.1.30.461
3fhxPXLPyridoxal kinase2.7.1.350.461
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
1fy7COAHistone acetyltransferase ESA1/0.459
2z4sADPChromosomal replication initiator protein DnaA/0.459
4fmxCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.459
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.458
2yeiXQIHeat shock protein HSP 90-alpha/0.458
3fwjCAMCamphor 5-monooxygenase1.14.15.10.458
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.458
3qlrNDPDihydrofolate reductase1.5.1.30.458
1dhrNADDihydropteridine reductase1.5.1.340.457
1nvqUCNSerine/threonine-protein kinase Chk12.7.11.10.457
1obnASVIsopenicillin N synthase1.21.3.10.457
2c27ACOMycothiol acetyltransferase2.3.1.1890.457
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.457
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.457
2yejZZ3Heat shock protein HSP 90-alpha/0.457
2c29NAPDihydroflavonol 4-reductase/0.456
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.456
4l4eCAMCamphor 5-monooxygenase1.14.15.10.456
5c88COAN-alpha-acetyltransferase/0.456
1yrcCAMCamphor 5-monooxygenase1.14.15.10.455
2g8yNADHydroxycarboxylate dehydrogenase B/0.455
2xvw9NRSerum albumin/0.455
1ia3TQ5Dihydrofolate reductase1.5.1.30.454
2vcmM11Isopenicillin N synthase1.21.3.10.454
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
2yejXQKHeat shock protein HSP 90-alpha/0.454
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4gurFADLysine-specific histone demethylase 1B10.454
4kgkGTPUncharacterized protein/0.454
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.453
1xddAAYIntegrin alpha-L/0.453
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.453
2dvlFADAcyl-CoA dehydrogenase/0.453
2x7hPFNProstaglandin reductase 310.453
2xvv9DNSerum albumin/0.453
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.453
5k5zANPUncharacterized protein/0.453
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.452
2yk2YJWHeat shock protein HSP 90-alpha/0.452
3fwiCAMCamphor 5-monooxygenase1.14.15.10.452
3h6vNS6Glutamate receptor 2/0.452
4a8v2ANMajor pollen allergen Bet v 1-J/0.452
5dhgDGVNociceptin receptor/0.452
1ra3MTXDihydrofolate reductase1.5.1.30.451
2bxqIMNSerum albumin/0.451
2dw4FADLysine-specific histone demethylase 1A10.451
2feuCAMCamphor 5-monooxygenase1.14.15.10.451
2qa2FADPolyketide oxygenase CabE/0.451
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3l63CAMCamphor 5-monooxygenase1.14.15.10.451
4boeCLRJapanin/0.451
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.451
4hxyNDPPlm1/0.451
3b05IPEIsopentenyl-diphosphate delta-isomerase/0.450
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.450
4l4fCAMCamphor 5-monooxygenase1.14.15.10.450
1kfbIGPTryptophan synthase alpha chain/0.449
1me6IVSPlasmepsin-23.4.23.390.449
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.449
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.449
2vz6FEFCalcium/calmodulin-dependent protein kinase type II subunit alpha2.7.11.170.449
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4bdcODHSerine/threonine-protein kinase Chk22.7.11.10.449
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.449
4ejmNAPPutative zinc-binding dehydrogenase/0.449
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.449
4ftt6HKSerine/threonine-protein kinase Chk12.7.11.10.449
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.449
4rrrA3TThreonine--tRNA ligase6.1.1.30.449
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2a94AP0L-lactate dehydrogenase1.1.1.270.448
2qg2A91Heat shock protein HSP 90-alpha/0.448
3i0aDBHNeutrophil gelatinase-associated lipocalin/0.448
4fv7E94Mitogen-activated protein kinase 12.7.11.240.448
4r1lADPPhenylacetate-coenzyme A ligase/0.448
5k2dZMAAdenosine receptor A2a/0.448
1xelUPGUDP-glucose 4-epimerase5.1.3.20.447
3ih0ANPUncharacterized sugar kinase PH14592.7.10.447
3w32W32Epidermal growth factor receptor2.7.10.10.447
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.447
4l3q926Glucokinase2.7.1.20.447
4relKMPGlycosyltransferase/0.447
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.446
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
2wo7ASVIsopenicillin N synthase1.21.3.10.446
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3nx2FERFerulic acid decarboxylase/0.446
3p8jFMNPentaerythritol tetranitrate reductase/0.446
3wrlCAMCamphor 5-monooxygenase1.14.15.10.446
4jb1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.446
4l4cCAMCamphor 5-monooxygenase1.14.15.10.446
4zs2FLUAlpha-ketoglutarate-dependent dioxygenase FTO/0.446
1phePIYCamphor 5-monooxygenase1.14.15.10.445
1ykdCMPAdenylate cyclase/0.445
2a1oCAMCamphor 5-monooxygenase1.14.15.10.445
3bi6396Wee1-like protein kinase2.7.10.20.445
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3ha5SFGHydroxymycolate synthase MmaA42.1.10.445
3q5kD1UHeat shock protein 83-1/0.445
4g1d0VKVitamin D3 receptor A/0.445
4m4922YL-lactate dehydrogenase A chain1.1.1.270.445
4y1bNAPAntE/0.445
5a3bAPRSIR2 family protein/0.445
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.445
1gpeFADGlucose oxidase1.1.3.40.444
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.444
1uxjNADMalate dehydrogenase/0.444
2a1nCAMCamphor 5-monooxygenase1.14.15.10.444
2v2zADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.444
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3d84NDPDihydrofolate reductase1.5.1.30.444
3phiNDPShikimate dehydrogenase (NADP(+))/0.444
3t8vBTJM1 family aminopeptidase3.4.110.444
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.444
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.443
1kl2FONSerine hydroxymethyltransferase/0.443
2hxzH7JCathepsin S3.4.22.270.443
3fql79ZGenome polyprotein2.7.7.480.443
3gobHXXDdmC/0.443
3gtsD3MDdmC/0.443
3pe2E1BCasein kinase II subunit alpha2.7.11.10.443
3sp9IL2Peroxisome proliferator-activated receptor delta/0.443
4d5gFADCyclohexane-1,2-dione hydrolase3.7.1.110.443
4du82P0Mevalonate diphosphate decarboxylase/0.443
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.443
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.443
4l4bCAMCamphor 5-monooxygenase1.14.15.10.443
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
5k2bZMAAdenosine receptor A2a/0.443
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.442
1mezGDPAdenylosuccinate synthetase isozyme 1/0.442
1pd9CO4Dihydrofolate reductase1.5.1.30.442
1tj0FADBifunctional protein PutA1.5.5.20.442
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.442
2eb3ANPEpidermal growth factor receptor2.7.10.10.442
2q4bNAPUncharacterized protein At5g02240/0.442
2w3bNDPDihydrofolate reductase1.5.1.30.442
2x8hFADThioredoxin glutathione reductase/0.442
3b9lAZZSerum albumin/0.442
3bi5FADPolyamine oxidase FMS1/0.442
3gviADPMalate dehydrogenase/0.442
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.442
4a802ANMajor pollen allergen Bet v 1-A/0.442
4eji0QACytochrome P450 2A131.14.14.10.442
4g1z0VPVitamin D3 receptor A/0.442
4hw219HInduced myeloid leukemia cell differentiation protein Mcl-1/0.442
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.442
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.442
4jr3KJREpidermal growth factor receptor2.7.10.10.442
4kne1CYDihydrofolate reductase1.5.1.30.442
4tuvCPZCytochrome P450 1191.140.442
1iwjCAMCamphor 5-monooxygenase1.14.15.10.441
1kqwRTLCellular retinol-binding protein type II/0.441
1t88CAMCamphor 5-monooxygenase1.14.15.10.441
2g78REACellular retinoic acid-binding protein 2/0.441
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
2wmuZYUSerine/threonine-protein kinase Chk12.7.11.10.441
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.441
2yk2YJXHeat shock protein HSP 90-alpha/0.441
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.441
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.441
3mfrANPPeripheral plasma membrane protein CASK2.7.11.10.441
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4bfxZVXPantothenate kinase2.7.1.330.441
4l0qNADAlcohol dehydrogenase class-3/0.441
4nmdFDABifunctional protein PutA/0.441
1adfTADAlcohol dehydrogenase E chain1.1.1.10.440
1cs4FOKAdenylate cyclase type 2/0.440
1cs4FOKAdenylate cyclase type 5/0.440
1el4CTZObelin/0.440
1k7l544Peroxisome proliferator-activated receptor alpha/0.440
1ke6LS2Cyclin-dependent kinase 22.7.11.220.440
1m78NDPDihydrofolate reductase1.5.1.30.440
2bjfDXCCholoylglycine hydrolase3.5.1.240.440
2cppCAMCamphor 5-monooxygenase1.14.15.10.440
2ivuZD6Proto-oncogene tyrosine-protein kinase receptor Ret2.7.10.10.440
3elm24FCollagenase 33.4.240.440
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.440
3nyrMLCPutative fatty acid synthase/0.440
4bfzZVZPantothenate kinase2.7.1.330.440
4c02TAKActivin receptor type-12.7.11.300.440
4gs4ACOAlpha-tubulin N-acetyltransferase 1/0.440
4k6fNAPPutative Acetoacetyl-CoA reductase/0.440
4k9oTPPBenzoylformate decarboxylase4.1.1.70.440
4kcfAKMFAD-dependent oxidoreductase/0.440
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.440
4qysPLRTryptophan synthase beta chain 24.2.1.200.440
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.440
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.440