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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
4c66H4CBromodomain-containing protein 4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4c66H4CBromodomain-containing protein 4/1.000
4f3i0S6Bromodomain-containing protein 4/0.726
4lrg1XBBromodomain-containing protein 4/0.665
4j0r1H2Bromodomain-containing protein 4/0.649
4j0s1H3Bromodomain-containing protein 4/0.638
4a9oA9OBromodomain-containing protein 2/0.635
4hxs1A3Bromodomain-containing protein 4/0.628
4aknS5BBromodomain-containing protein 2/0.627
4cfl8DQBromodomain-containing protein 4/0.625
3aqaBYHBromodomain-containing protein 2/0.621
4ogiR78Bromodomain-containing protein 4/0.619
4hxn1A7Bromodomain-containing protein 4/0.617
4nqmY1ZBromodomain-containing protein 4/0.617
4bjx73BBromodomain-containing protein 4/0.615
4o74R78Bromodomain-containing protein 4/0.612
4bw39BMBromodomain-containing protein 4/0.607
4c67L5SBromodomain-containing protein 4/0.599
4hxo1A6Bromodomain-containing protein 4/0.598
4j3i1K0Bromodomain-containing protein 4/0.597
4mr41K0Bromodomain-containing protein 4/0.596
4a9lP9LBromodomain-containing protein 4/0.595
4qzsJQ1Bromodomain-containing protein 4/0.595
4a9nA9NBromodomain-containing protein 2/0.594
4lr61XABromodomain-containing protein 4/0.593
4bw2UTHBromodomain-containing protein 4/0.591
2yelWSHBromodomain-containing protein 4/0.585
4men25KBromodomain-containing protein 4/0.584
4meq25OBromodomain-containing protein 4/0.581
4lyw21QBromodomain-containing protein 4/0.579
4o701QKBromodomain-containing protein 4/0.574
4hxr1A4Bromodomain-containing protein 4/0.572
4flpJQ1Bromodomain testis-specific protein/0.569
4bw1S5BBromodomain-containing protein 4/0.568
4mep24YBromodomain-containing protein 4/0.568
2ydwWSHBromodomain-containing protein 2/0.565
3zyu1GHBromodomain-containing protein 4/0.557
4hby13FBromodomain-containing protein 4/0.557
4alhA9PBromodomain-containing protein 2/0.550
4uyg73BBromodomain-containing protein 2/0.549
4hbw14ZBromodomain-containing protein 4/0.547
4mr61K0Bromodomain-containing protein 2/0.547
4o71CPBBromodomain-containing protein 4/0.541
4j1p1K0Bromodomain-containing protein 2/0.527
2yemWSHBromodomain-containing protein 4/0.525
4alg1GHBromodomain-containing protein 2/0.520
4py6R78Bromodomain protein, putative/0.517
2yekEAMBromodomain-containing protein 2/0.513
5bt42LOBromodomain-containing protein 4/0.513
4bw49B6Bromodomain-containing protein 4/0.512
4nr52LLCREB-binding protein/0.512
4meo25VBromodomain-containing protein 4/0.511
5bt52LOBromodomain-containing protein 2/0.511
4gpj0Q1Bromodomain-containing protein 4/0.510
3h4vNAPPteridine reductase 11.5.1.330.506
4cfkLY2Bromodomain-containing protein 4/0.504
4o78SAVBromodomain-containing protein 4/0.503
4mr51K0Bromodomain-containing protein 2/0.496
2v5aLZLBiotin carboxylase6.3.4.140.494
4e960NSBromodomain-containing protein 4/0.494
3ia4MTXDihydrofolate reductase/0.489
3vt7VDXVitamin D3 receptor/0.489
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.481
2hasC3OVitamin D3 receptor/0.480
3vt9YI4Vitamin D3 receptor/0.480
3b9lAZZSerum albumin/0.479
4cdmFO1Deoxyribodipyrimidine photolyase/0.479
4nra2LWBromodomain adjacent to zinc finger domain protein 2B/0.479
2hb7O1CVitamin D3 receptor/0.478
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.478
3svgODRBromodomain-containing protein 4/0.478
3cgdCOACoenzyme A disulfide reductase/0.477
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.475
4ir5IR5Bromodomain adjacent to zinc finger domain protein 2B/0.475
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.475
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.474
2i40BLZCyclin-dependent kinase 22.7.11.220.473
2rhrEMOPutative ketoacyl reductase1.3.10.473
2w6mOA1Biotin carboxylase6.3.4.140.473
3m7rVDXVitamin D3 receptor/0.473
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.472
2znq401Peroxisome proliferator-activated receptor delta/0.470
4iteTEYVitamin D3 receptor/0.470
2hamC33Vitamin D3 receptor/0.469
2xvv9DNSerum albumin/0.469
2v58LZJBiotin carboxylase6.3.4.140.468
2xlsFADPutative flavin-containing monooxygenase/0.468
3kpzZNEVitamin D3 receptor/0.468
4hxm1A8Bromodomain-containing protein 4/0.468
4ia1BIVVitamin D3 receptor A/0.468
3w0aDS5Vitamin D3 receptor/0.467
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.466
4qa2SHHHistone deacetylase 83.5.1.980.466
4pnmNU1Tankyrase-22.4.2.300.465
5eccNAPDehydrofolate reductase type I/0.465
2a4zBYMPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
2xvw9NRSerum albumin/0.464
4qzuRTLRetinol-binding protein 2/0.464
3emlZMAAdenosine receptor A2a/0.464
2zjwREFCasein kinase II subunit alpha2.7.11.10.463
2wotZZGTGF-beta receptor type-12.7.11.300.462
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.461
3c3eGDP2-phospho-L-lactate transferase/0.461
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.461
4prxADPDNA gyrase subunit B/0.461
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.460
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.459
2harOCCVitamin D3 receptor/0.458
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.458
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.458
3exnACOProbable acetyltransferase/0.458
3srqQ19Dihydrofolate reductase1.5.1.30.458
4nyv15ECREB-binding protein/0.458
1rx8NAPDihydrofolate reductase1.5.1.30.457
2hcdBIVVitamin D3 receptor A/0.457
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.457
3vt8YI3Vitamin D3 receptor/0.457
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.457
4ruoBIVVitamin D3 receptor A/0.457
3fql79ZGenome polyprotein2.7.7.480.456
4ia3BIVVitamin D3 receptor A/0.456
4k9yK9YFocal adhesion kinase 12.7.10.20.456
2w9hTOPDihydrofolate reductase1.5.1.30.455
3vrwYS5Vitamin D3 receptor/0.455
1w4zNAPPutative ketoacyl reductase1.3.10.454
1y4lSVRBasic phospholipase A2 homolog 2/0.454
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.454
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.454
2q5qTPWIndole-3-pyruvate decarboxylase4.1.1.740.454
4c02TAKActivin receptor type-12.7.11.300.454
4iarERM5-hydroxytryptamine receptor 1B/0.454
4mv4ACPBiotin carboxylase6.3.4.140.454
4mv8ACPBiotin carboxylase6.3.4.140.454
4prvADPDNA gyrase subunit B/0.454
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.454
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
2pg0FADAcyl-CoA dehydrogenase/0.453
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.453
3bgqVX2Serine/threonine-protein kinase pim-12.7.11.10.453
3cgbCOACoenzyme A disulfide reductase/0.453
3q3cNADNAD-dependent L-serine dehydrogenase/0.453
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4g2h0VQVitamin D3 receptor A/0.453
4nr82LLBromodomain-containing protein 4/0.453
1blzACVIsopenicillin N synthase1.21.3.10.452
1ppjANYCytochrome b/0.452
2w3vTOPDihydrofolate reductase/0.452
3fznD7KBenzoylformate decarboxylase4.1.1.70.452
3mnrSD1Heat shock protein HSP 90-alpha/0.452
3rmf20ZCyclin-dependent kinase 22.7.11.220.452
4feq0T8Tyrosine-protein kinase receptor TYRO32.7.10.10.452
5kp2COA3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2/0.452
1fmjRTLRetinol dehydratase/0.451
1opbRETRetinol-binding protein 2/0.451
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.451
3cgeCOACoenzyme A disulfide reductase/0.451
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.451
4ez8DHFThymidylate synthase2.1.1.450.451
4kl9NDPDihydrofolate reductase1.5.1.30.451
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.451
4yx6FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.451
2gvcFADThiol-specific monooxygenase1.14.130.450
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.450
2y6o1N1Ephrin type-A receptor 42.7.10.10.450
3cgcCOACoenzyme A disulfide reductase/0.450
3qlrNDPDihydrofolate reductase1.5.1.30.450
4b4oNDPEpimerase family protein SDR39U1/0.450
4m11MXMProstaglandin G/H synthase 21.14.99.10.450
4y1bNAPAntE/0.450
5iu86DZAdenosine receptor A2a/0.450
3sn6P0GBeta-2 adrenergic receptor/0.450
1g28FMNPHY3/0.449
1ndzFR5Adenosine deaminase3.5.4.40.449
1qpdSTUTyrosine-protein kinase Lck2.7.10.20.449
1yqzCOACoenzyme A disulfide reductase/0.449
2vbpVB1Isopenicillin N synthase1.21.3.10.449
3vruYS3Vitamin D3 receptor/0.449
3vt5YI2Vitamin D3 receptor/0.449
4mf129YTyrosine-protein kinase ITK/TSK2.7.10.20.449
4r1lADPPhenylacetate-coenzyme A ligase/0.449
5k2dZMAAdenosine receptor A2a/0.449
1db1VDXVitamin D3 receptor/0.448
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.448
1ia3TQ5Dihydrofolate reductase1.5.1.30.448
1ie9VDXVitamin D3 receptor/0.448
1pl8NADSorbitol dehydrogenase1.1.1.140.448
1rfuADPPyridoxal kinase2.7.1.350.448
2qo9ANPEphrin type-A receptor 32.7.10.10.448
3oquA8SAbscisic acid receptor PYL9/0.448
3sufSUEPolyprotein/0.448
4aoi4K0Hepatocyte growth factor receptor2.7.10.10.448
4awp99AHeat shock protein HSP 90-alpha/0.448
4g1y0VOVitamin D3 receptor A/0.448
4k9pTPPBenzoylformate decarboxylase4.1.1.70.448
4qpmADPMitotic checkpoint serine/threonine-protein kinase BUB12.7.11.10.448
5akk1P8Bifunctional epoxide hydrolase 23.1.3.760.448
1m9k7NINitric oxide synthase, endothelial1.14.13.390.447
1p0hACOMycothiol acetyltransferase2.3.1.1890.447
3c6uM22Gag-Pol polyprotein2.7.7.490.447
3h3r14HCollagen type IV alpha-3-binding protein/0.447
3lqfNADGalactitol dehydrogenase/0.447
3mykANPMyosin-2 heavy chain/0.447
3w0jT08Vitamin D3 receptor/0.447
4asyN5YGlucose-1-phosphate thymidylyltransferase/0.447
4bj9UHBTankyrase-22.4.2.300.447
4ia7BIVVitamin D3 receptor A/0.447
4o761M3Bromodomain-containing protein 4/0.447
4ocvANPAminoglycoside phosphotransferase/0.447
1ke9LS5Cyclin-dependent kinase 22.7.11.220.446
1kzjCB3Thymidylate synthase/0.446
1likADNAdenosine kinase2.7.1.200.446
1uy7PU4Heat shock protein HSP 90-alpha/0.446
2c27ACOMycothiol acetyltransferase2.3.1.1890.446
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.446
2ociTYCValacyclovir hydrolase3.10.446
2vr1ATFBiotin carboxylase6.3.4.140.446
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.446
2zbaZBATrichothecene 3-O-acetyltransferase/0.446
3a783EVVitamin D3 receptor/0.446
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.446
3t3q9PLCytochrome P450 2A61.14.130.446
3w0c6DSVitamin D3 receptor/0.446
4bb432WEphrin type-B receptor 42.7.10.10.446
4mwhATPCasein kinase II subunit alpha2.7.11.10.446
4wkqIREEpidermal growth factor receptor2.7.10.10.446
1fxsNAPGDP-L-fucose synthase/0.445
1ia1NDPDihydrofolate reductase1.5.1.30.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
2vwz7X6Ephrin type-B receptor 42.7.10.10.445
4g2rH1LProbable propionyl-CoA carboxylase beta chain 66.4.1.30.445
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.445
5ahkTPPAcetolactate synthase II, large subunit/0.445
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.445
5e8wSTUTGF-beta receptor type-12.7.11.300.445
1crbRTLRetinol-binding protein 1/0.444
1fwkADPHomoserine kinase2.7.1.390.444
1m78NDPDihydrofolate reductase1.5.1.30.444
1rkhVD2Vitamin D3 receptor/0.444
1rx1NAPDihydrofolate reductase1.5.1.30.444
1s0zEB1Vitamin D3 receptor/0.444
1suoCPZCytochrome P450 2B41.14.14.10.444
1unlRRCCyclin-dependent-like kinase 52.7.11.10.444
2b7aIZATyrosine-protein kinase JAK2/0.444
2vwy7X5Ephrin type-B receptor 42.7.10.10.444
3pe2E1BCasein kinase II subunit alpha2.7.11.10.444
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4do30LAFatty-acid amide hydrolase 13.5.1.990.444
5cvhADPCasein kinase II subunit alpha2.7.11.10.444
5e8xSTUTGF-beta receptor type-12.7.11.300.444
5k2aZMAAdenosine receptor A2a/0.444
1itzTPPTransketolase, chloroplastic2.2.1.10.443
1mczTDPBenzoylformate decarboxylase4.1.1.70.443
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.443
2hc4VDXVitamin D3 receptor A/0.443
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.443
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.443
3a0iAJIGlucokinase2.7.1.20.443
3cseN22Uncharacterized protein/0.443
3hy4N5G5-formyltetrahydrofolate cyclo-ligase6.3.3.20.443
3l8p0CEAngiopoietin-1 receptor2.7.10.10.443
3nga3NGCasein kinase II subunit alpha2.7.11.10.443
3sf6FDAGlutaryl-CoA dehydrogenase/0.443
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
3vrvYSDVitamin D3 receptor/0.443
3vt3VDXVitamin D3 receptor/0.443
4bfvZVVPantothenate kinase2.7.1.330.443
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.443
4rujVDXVitamin D3 receptor A/0.443
4xx0COASuccinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial6.2.1.40.443
4yekTHMThymidine phosphorylase/0.443
5lc1NADL-threonine 3-dehydrogenase/0.443
1jpaANPEphrin type-B receptor 22.7.10.10.442
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.442
1tehNADAlcohol dehydrogenase class-31.1.1.10.442
1uy8PU5Heat shock protein HSP 90-alpha/0.442
1v7aFRCAdenosine deaminase3.5.4.40.442
2acwUPGGlycosyltransferase/0.442
2bxmIMNSerum albumin/0.442
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.442
2e9v85ASerine/threonine-protein kinase Chk12.7.11.10.442
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
2itpAEEEpidermal growth factor receptor2.7.10.10.442
2vx07X7Ephrin type-B receptor 42.7.10.10.442
2zlaVDBVitamin D3 receptor/0.442
3nxxNDPDihydrofolate reductase1.5.1.30.442
3p62FMNPentaerythritol tetranitrate reductase/0.442
3p8jFMNPentaerythritol tetranitrate reductase/0.442
3wv7ADPHmd co-occurring protein HcgE/0.442
4ejh0QACytochrome P450 2A131.14.14.10.442
4nyw2O3CREB-binding protein/0.442
5k2cZMAAdenosine receptor A2a/0.442
5jtbZMAAdenosine receptor A2a/0.442
1ckpPVBCyclin-dependent kinase 22.7.11.220.441
1uyhPU0Heat shock protein HSP 90-alpha/0.441
2bu9HFVIsopenicillin N synthase1.21.3.10.441
2cy2ACOProbable acetyltransferase/0.441
2dwbANPAurora kinase A2.7.11.10.441
2fszOHTEstrogen receptor beta/0.441
2q5oPPYIndole-3-pyruvate decarboxylase4.1.1.740.441
2uxoTACHTH-type transcriptional regulator TtgR/0.441
2zlcVDXVitamin D3 receptor/0.441
3e7iB2Nitric oxide synthase, inducible1.14.13.390.441
3ibqATPPyridoxal kinase/0.441
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
3s79ASDAromatase1.14.14.140.441
3vetADPnebramycin 5' synthase6.1.2.20.441
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.441
3vg9ZMAAdenosine receptor A2a/0.441
4bgg844Activin receptor type-12.7.11.300.441
4bqh9VUUDP-N-acetylglucosamine pyrophosphorylase, putative/0.441
4du82P0Mevalonate diphosphate decarboxylase/0.441
4g210VPVitamin D3 receptor A/0.441
4gk2L66Ephrin type-A receptor 32.7.10.10.441
4k4eK4ETankyrase-12.4.2.300.441
4mf029ZTyrosine-protein kinase ITK/TSK2.7.10.20.441
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.441
1f4fTP3Thymidylate synthase/0.440
1h51FMNPentaerythritol tetranitrate reductase/0.440
1hw5CMPcAMP-activated global transcriptional regulator CRP/0.440
1qxlFR8Adenosine deaminase3.5.4.40.440
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.440
2gjlFMNNitronate monooxygenase1.13.12.160.440
2h94FADLysine-specific histone demethylase 1A10.440
3nmpPYVAbscisic acid receptor PYL2/0.440
3pm9FADPutative oxidoreductase/0.440
3qdd94MHeat shock protein HSP 90-alpha/0.440
3sfeFADSuccinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial/0.440
3tk3CPZCytochrome P450 2B41.14.14.10.440
4fw05KJNitric oxide synthase, brain1.14.13.390.440
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.440
4m6l21VDihydrofolate reductase1.5.1.30.440
4uyf73BBromodomain-containing protein 2/0.440
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.440
5bvw1N1Epithelial discoidin domain-containing receptor 12.7.10.10.440
5uviZMAAdenosine receptor A2a/0.440