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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
4hxm1A8Bromodomain-containing protein 4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4hxm1A8Bromodomain-containing protein 4/1.000
4c67L5SBromodomain-containing protein 4/0.644
4nr82LLBromodomain-containing protein 4/0.641
4hxr1A4Bromodomain-containing protein 4/0.624
4cfkLY2Bromodomain-containing protein 4/0.617
4gpj0Q1Bromodomain-containing protein 4/0.608
4hbw14ZBromodomain-containing protein 4/0.554
4mr41K0Bromodomain-containing protein 4/0.537
4men25KBromodomain-containing protein 4/0.515
5bt52LOBromodomain-containing protein 2/0.506
4meo25VBromodomain-containing protein 4/0.500
4alhA9PBromodomain-containing protein 2/0.498
4mq5TPPBenzoylformate decarboxylase4.1.1.70.497
4aknS5BBromodomain-containing protein 2/0.492
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.491
4e960NSBromodomain-containing protein 4/0.490
2c1zU2FAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.486
4j1p1K0Bromodomain-containing protein 2/0.484
4o78SAVBromodomain-containing protein 4/0.484
3svgODRBromodomain-containing protein 4/0.477
4hxs1A3Bromodomain-containing protein 4/0.476
4mep24YBromodomain-containing protein 4/0.476
1obnASVIsopenicillin N synthase1.21.3.10.475
4ju9TZDBenzoylformate decarboxylase4.1.1.70.474
1bwsNDPGDP-L-fucose synthase/0.472
1cg4IMOAdenylosuccinate synthetase/0.472
2p5uNADUDP-glucose 4-epimerase/0.471
2vhxNADAlanine dehydrogenase1.4.1.10.470
4pnmNU1Tankyrase-22.4.2.300.470
1rx6DDFDihydrofolate reductase1.5.1.30.469
3fznD7KBenzoylformate decarboxylase4.1.1.70.469
2lf1NDPDihydrofolate reductase1.5.1.30.467
4ju8TZDBenzoylformate decarboxylase4.1.1.70.467
3q43D66M1 family aminopeptidase3.4.110.466
4nyw2O3CREB-binding protein/0.465
1jolFFODihydrofolate reductase1.5.1.30.463
2i4qUA4Renin3.4.23.150.463
3sigAR6Uncharacterized protein/0.463
4meq25OBromodomain-containing protein 4/0.463
4j0r1H2Bromodomain-containing protein 4/0.462
4gah0ETAcyl-coenzyme A thioesterase THEM43.1.2.20.460
4mihFADPyranose 2-oxidase1.1.3.100.460
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.458
2drcMTXDihydrofolate reductase1.5.1.30.458
3qlrNDPDihydrofolate reductase1.5.1.30.458
3t37FADPyridoxine 4-oxidase/0.458
4hxn1A7Bromodomain-containing protein 4/0.458
1rd4L08Integrin alpha-L/0.457
3lqfNADGalactitol dehydrogenase/0.457
3qrwNDPPutative ketoacyl reductase1.3.10.457
4xd2NAIAlcohol dehydrogenase E chain1.1.1.10.457
1olmVTQSEC14-like protein 2/0.456
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
4c717RD3-oxoacyl-ACP synthase/0.456
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1rdt570Peroxisome proliferator-activated receptor gamma/0.455
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.455
2ctsCOACitrate synthase, mitochondrial2.3.3.10.455
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.455
4alg1GHBromodomain-containing protein 2/0.455
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.454
1dhfFOLDihydrofolate reductase1.5.1.30.454
4dfrMTXDihydrofolate reductase1.5.1.30.454
1w4zNAPPutative ketoacyl reductase1.3.10.453
1x7dNADPutative ornithine cyclodeaminase/0.453
1xq6NAPUncharacterized protein At5g02240/0.453
3ieuGDPGTPase Era/0.453
3siiA1RUncharacterized protein/0.453
3uxe465Ribosyldihydronicotinamide dehydrogenase [quinone]/0.453
4hby13FBromodomain-containing protein 4/0.453
4hxo1A6Bromodomain-containing protein 4/0.453
1hetNADAlcohol dehydrogenase E chain1.1.1.10.452
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
2y6qI7TTetX family tetracycline inactivation enzyme/0.452
4dc1NDPPutative ketoacyl reductase1.3.10.452
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.452
5cdtPFBAlcohol dehydrogenase E chain1.1.1.10.452
1u7tTDT3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.451
2j5bTYETyrosine--tRNA ligase6.1.1.10.451
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
3opxU5PSuppressor of disruption of TFIIS/0.451
4a9lP9LBromodomain-containing protein 4/0.451
4cfl8DQBromodomain-containing protein 4/0.451
4fn4NADShort chain dehydrogenase/0.451
4z0hNADGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic1.2.1.120.451
1a27ESTEstradiol 17-beta-dehydrogenase 11.1.1.620.450
1dyhDZFDihydrofolate reductase1.5.1.30.450
1gveNAPAflatoxin B1 aldehyde reductase member 310.450
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.450
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2uxoTACHTH-type transcriptional regulator TtgR/0.450
3oqfS51Renin3.4.23.150.450
3pgxNADUncharacterized NAD-dependent oxidoreductase MAP_4146/0.450
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.450
4mzxTZDBenzoylformate decarboxylase4.1.1.70.450
4qelTZDBenzoylformate decarboxylase4.1.1.70.450
1draMTXDihydrofolate reductase1.5.1.30.449
1dyjDDFDihydrofolate reductase1.5.1.30.449
1jzsMRCIsoleucine--tRNA ligase6.1.1.50.449
2oiqSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.449
4bfyZVYPantothenate kinase2.7.1.330.449
4elg52JDihydrofolate reductase/0.449
4m11MXMProstaglandin G/H synthase 21.14.99.10.449
4q71FADBifunctional protein PutA/0.449
5kj1NAJAlcohol dehydrogenase E chain1.1.1.10.449
1bfdTPPBenzoylformate decarboxylase4.1.1.70.448
2rc6NAPFerredoxin--NADP reductase/0.448
2vnaNAPProstaglandin reductase 21.3.1.480.448
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.448
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.448
4o74R78Bromodomain-containing protein 4/0.448
4zvlFADRibosyldihydronicotinamide dehydrogenase [quinone]/0.448
1dhjMTXDihydrofolate reductase1.5.1.30.447
2x7hPFNProstaglandin reductase 310.447
3w8dNAD3-hydroxybutyrate dehydrogenase/0.447
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.447
4lr61XABromodomain-containing protein 4/0.447
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.446
1mr9ACOStreptogramin A acetyltransferase2.3.10.446
2gv8NDPThiol-specific monooxygenase1.14.130.446
2znpK55Peroxisome proliferator-activated receptor delta/0.446
4ryvZEAProtein LlR18A/0.446
4uyg73BBromodomain-containing protein 2/0.446
5emhNAPIridoid synthase1.3.1.990.446
1heuNADAlcohol dehydrogenase E chain1.1.1.10.445
1pr9NAPL-xylulose reductase1.1.1.100.445
2g1s4IGRenin3.4.23.150.445
2g2zCOZMalonyl CoA-acyl carrier protein transacylase2.3.1.390.445
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.445
3s3vTOPDihydrofolate reductase1.5.1.30.445
3wagTYDGlycosyltransferase/0.445
4h1e10JBeta-secretase 13.4.23.460.445
4yuzS4MSpermidine synthase, putative/0.445
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.445
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.445
5hidB1ESerine/threonine-protein kinase B-raf2.7.11.10.445
1hf3NADAlcohol dehydrogenase E chain1.1.1.10.444
1vbiNADMalate/L-lactate dehydrogenase family protein/0.444
2onmADPAldehyde dehydrogenase, mitochondrial1.2.1.30.444
2rewREWPeroxisome proliferator-activated receptor alpha/0.444
3gncQQQGlutaryl-CoA dehydrogenase/0.444
4ele31IDihydrofolate reductase/0.444
4iawLIZNeutrophil gelatinase-associated lipocalin/0.444
4umxNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.444
4xldBRLPeroxisome proliferator-activated receptor gamma/0.444
5cdtNAJAlcohol dehydrogenase E chain1.1.1.10.444
1qmzATPCyclin-dependent kinase 22.7.11.220.443
1tduDURThymidylate synthase/0.443
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.443
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.443
2yelWSHBromodomain-containing protein 4/0.443
3eej53RUncharacterized protein/0.443
4bfxZVXPantothenate kinase2.7.1.330.443
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4i9n1E5L-lactate dehydrogenase A chain1.1.1.270.443
4mr61K0Bromodomain-containing protein 2/0.443
1dfoFFOSerine hydroxymethyltransferase2.1.2.10.442
1dr5NAPDihydrofolate reductase1.5.1.30.442
1mvtDTMDihydrofolate reductase1.5.1.30.442
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.442
1s3vTQDDihydrofolate reductase1.5.1.30.442
1xuoLA1Integrin alpha-L/0.442
3c3xNAPEugenol synthase 11.1.1.3180.442
3grySAMProbable ribosomal RNA small subunit methyltransferase A/0.442
4z24FADPutative GMC-type oxidoreductase R13510.442
1bwkFMNNADPH dehydrogenase 11.6.99.10.441
1qjfACSIsopenicillin N synthase1.21.3.10.441
1x1bSAHC-20 methyltransferase/0.441
2bu9HFVIsopenicillin N synthase1.21.3.10.441
2fwnTDPBenzoylformate decarboxylase4.1.1.70.441
2jb4A14Isopenicillin N synthase1.21.3.10.441
3k9uACOSpermidine N(1)-acetyltransferase/0.441
3oafOAGDihydrofolate reductase1.5.1.30.441
3vr8RQXSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.441
3vr8RQXCytochrome b-large subunit/0.441
3w8eNAD3-hydroxybutyrate dehydrogenase/0.441
4pkl1GHUncharacterized protein/0.441
4r8hSP1cAMP-activated global transcriptional regulator CRP/0.441
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.441
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1hdoNAPFlavin reductase (NADPH)/0.440
1kqfMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.440
2ijgFADCryptochrome DASH, chloroplastic/mitochondrial/0.440
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.440
3wleNAD(R)-specific carbonyl reductase/0.440
3zkyWT4Isopenicillin N synthase1.21.3.10.440
6ctsCICCitrate synthase, mitochondrial2.3.3.10.440