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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
3uvvREARetinoic acid receptor RXR-alpha

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3uvvREARetinoic acid receptor RXR-alpha/1.000
4k4j1O8Retinoic acid receptor RXR-alpha/0.619
1fm69CRRetinoic acid receptor RXR-alpha/0.607
1fbyREARetinoic acid receptor RXR-alpha/0.605
3oapREARetinoic acid receptor RXR-alpha/0.603
1uhlMEIRetinoic acid receptor RXR-beta/0.602
1fm99CRRetinoic acid receptor RXR-alpha/0.601
1xlsREARetinoic acid receptor RXR-alpha/0.590
2p1v5TNRetinoic acid receptor RXR-alpha/0.582
1k749CRRetinoic acid receptor RXR-alpha/0.580
4m8e29VRetinoic acid receptor RXR-alpha/0.575
2p1u4TNRetinoic acid receptor RXR-alpha/0.569
1mznBM6Retinoic acid receptor RXR-alpha/0.566
1xiuREARetinoic acid receptor RXR/0.564
2aclREARetinoic acid receptor RXR-alpha/0.563
4k6i9RARetinoic acid receptor RXR-alpha/0.563
1rdtL79Retinoic acid receptor RXR-alpha/0.562
4m8hR4MRetinoic acid receptor RXR-alpha/0.557
1mvcBM6Retinoic acid receptor RXR-alpha/0.553
3fc6REARetinoic acid receptor RXR-alpha/0.548
3falREARetinoic acid receptor RXR-alpha/0.540
2p1t3TNRetinoic acid receptor RXR-alpha/0.538
3pwhZMAAdenosine receptor A2a/0.510
2bxmIMNSerum albumin/0.508
2bxqIMNSerum albumin/0.496
2xvw9NRSerum albumin/0.492
2xvv9DNSerum albumin/0.491
3cseN22Uncharacterized protein/0.489
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.488
3uzcT4EAdenosine receptor A2a/0.487
1pkfEPDEpothilone C/D epoxidase1.140.486
2fziDH3Dihydrofolate reductase1.5.1.30.485
3lfcZ86Mitogen-activated protein kinase 14/0.483
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.482
3qly55VUncharacterized protein/0.482
4cd2FOLDihydrofolate reductase1.5.1.30.482
1cd2FOLDihydrofolate reductase1.5.1.30.481
1fmjRTLRetinol dehydratase/0.481
4g210VPVitamin D3 receptor A/0.481
3njoPYVAbscisic acid receptor PYR1/0.480
4j6bPLOCytochrome P450 monooxygenase/0.479
2ydoADNAdenosine receptor A2a/0.478
3d75NBBPheromone-binding protein ASP1/0.478
1ia1TQ3Dihydrofolate reductase1.5.1.30.477
4ejh0QACytochrome P450 2A131.14.14.10.476
4j6cSTRCytochrome P450 monooxygenase/0.476
4p6wMOFGlucocorticoid receptor/0.475
2p15EZTEstrogen receptor/0.474
3b9lAZZSerum albumin/0.474
3ctj320Hepatocyte growth factor receptor2.7.10.10.474
4jbtASDCytochrome P450 monooxygenase/0.474
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.471
1ysx4EBSerum albumin/0.471
2acwUPGGlycosyltransferase/0.471
1ia3TQ5Dihydrofolate reductase1.5.1.30.470
4j6dTESCytochrome P450 monooxygenase/0.470
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.469
1vj3TABDihydrofolate reductase1.5.1.30.468
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.468
4iui1GQEstrogen receptor/0.468
5akk1P8Bifunctional epoxide hydrolase 23.1.3.760.468
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.467
3d84NDPDihydrofolate reductase1.5.1.30.466
3eel53TUncharacterized protein/0.466
3irxUDRGag-Pol polyprotein2.7.7.490.466
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.466
4equG6ISerine/threonine-protein kinase 102.7.11.10.466
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.466
3bfb9ODPheromone-binding protein ASP1/0.465
3jsuKA5Bifunctional dihydrofolate reductase-thymidylate synthase/0.465
3td8D2RDihydrofolate reductase1.5.1.30.465
4ek1CAMCamphor 5-monooxygenase1.14.15.10.465
3emlZMAAdenosine receptor A2a/0.465
1db1VDXVitamin D3 receptor/0.464
1ie8KH1Vitamin D3 receptor/0.464
1m7aMQUDihydrofolate reductase1.5.1.30.464
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.464
5uviZMAAdenosine receptor A2a/0.464
1uzwCDHIsopenicillin N synthase1.21.3.10.463
3ar7TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.463
3gwfNAPCyclohexanone monooxygenase/0.463
4dscA8SAbscisic acid receptor PYL3/0.463
5d7pAR6NAD-dependent protein deacetylase sirtuin-23.5.10.463
5k2aZMAAdenosine receptor A2a/0.463
3rfmCFFAdenosine receptor A2a/0.463
1ia4TQ6Dihydrofolate reductase1.5.1.30.462
1x8lOXRRetinol dehydratase/0.462
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
3lalKRVGag-Pol polyprotein2.7.7.490.462
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
3qlrNDPDihydrofolate reductase1.5.1.30.462
4ia1BIVVitamin D3 receptor A/0.462
1fmlRTLRetinol dehydratase/0.461
3bjhNBBOdorant binding protein ASP1/0.461
3clbTMQBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
3qm4PN0Cytochrome P450 2D6/0.461
4bfwZVWPantothenate kinase2.7.1.330.461
5k2bZMAAdenosine receptor A2a/0.461
1m79MQ1Dihydrofolate reductase1.5.1.30.460
1og5SWFCytochrome P450 2C9/0.460
1x2hLPALipoate-protein ligase A6.3.1.200.460
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
3bfa9ODOdorant binding protein ASP1/0.460
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
3l8sBFFMitogen-activated protein kinase 14/0.460
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.460
3qls55VDihydrofolate reductase1.5.1.30.460
4ddrMMVDihydrofolate reductase1.5.1.30.460
1j3iWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.459
2z97CAMCamphor 5-monooxygenase1.14.15.10.459
3qlwN22Dihydrofolate reductase1.5.1.30.459
3t3q9PLCytochrome P450 2A61.14.130.459
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.459
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
4gg70J8Hepatocyte growth factor receptor2.7.10.10.459
4h9614QDihydrofolate reductase1.5.1.30.459
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.458
1sr7MOFProgesterone receptor/0.458
1uy7PU4Heat shock protein HSP 90-alpha/0.458
2cd2FOLDihydrofolate reductase1.5.1.30.458
2jfz003Glutamate racemase/0.458
3is9AC7Gag-Pol polyprotein2.7.7.490.458
3p9tTCLRepressor/0.458
3qlzQLZUncharacterized protein/0.458
3w5p4OAVitamin D3 receptor/0.458
4ia2BIVVitamin D3 receptor A/0.458
4j03FVSBifunctional epoxide hydrolase 23.1.3.760.458
4qa0SHHHistone deacetylase 83.5.1.980.458
2qd5CHDFerrochelatase, mitochondrial4.99.1.10.457
3dgaRJ1Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.457
3l6jZ90Alr2278 protein/0.457
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.457
3vt5YI2Vitamin D3 receptor/0.457
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.457
2dqsTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.456
3qgtCP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.456
3ue4DB8Tyrosine-protein kinase ABL12.7.10.20.456
4l4bCAMCamphor 5-monooxygenase1.14.15.10.456
1cjkFOKAdenylate cyclase type 2/0.455
1cjkFOKAdenylate cyclase type 5/0.455
1dz6CAMCamphor 5-monooxygenase1.14.15.10.455
2pujHPZ2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase3.7.1.80.455
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.455
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.455
4jnc1LFBifunctional epoxide hydrolase 23.1.3.760.455
4l49CAMCamphor 5-monooxygenase1.14.15.10.455
4q0a4OAVitamin D3 receptor A/0.455
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.454
3cd2MTXDihydrofolate reductase1.5.1.30.454
3h1jSMACytochrome b/0.454
3vrwYS5Vitamin D3 receptor/0.454
4iq71G9Mycocyclosin synthase1.14.21.90.454
4ktl1CQCytochrome P450/0.454
4nc3ERM5-hydroxytryptamine receptor 2B/0.454
1e7aPFLSerum albumin/0.453
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.453
2hw2RFPRifampin ADP-ribosyl transferase/0.453
3ar5TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.453
3koo24DBifunctional epoxide hydrolase 23.3.2.100.453
3um81CYBifunctional dihydrofolate reductase-thymidylate synthase/0.453
3vt7VDXVitamin D3 receptor/0.453
4dvi2IWTankyrase-12.4.2.300.453
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4iae1DXAlr2278 protein/0.453
5k2cZMAAdenosine receptor A2a/0.453
1ai9NDPDihydrofolate reductase1.5.1.30.452
1kyoSMACytochrome b/0.452
1l2jETCEstrogen receptor beta/0.452
1mc5AHEAlcohol dehydrogenase class-31.1.1.10.452
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.452
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
2hc4VDXVitamin D3 receptor A/0.452
2rhtC1E2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase3.7.1.80.452
3eek53SUncharacterized protein/0.452
3h0a9RARetinoic acid receptor RXR-alpha/0.452
3vi7CBDHematopoietic prostaglandin D synthase/0.452
3vtcTK3Vitamin D3 receptor/0.452
4jv81M1Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.452
1kzjCB3Thymidylate synthase/0.451
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
2agvTG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.451
2fzhDH1Dihydrofolate reductase1.5.1.30.451
2m56CAMCamphor 5-monooxygenase1.14.15.10.451
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.451
3eon341Glutaryl-CoA dehydrogenase/0.451
3h1vTK1Glucokinase2.7.1.20.451
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.451
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
4g1z0VPVitamin D3 receptor A/0.451
4g47TZFMycocyclosin synthase1.14.21.90.451
4ia7BIVVitamin D3 receptor A/0.451
4ib4ERM5-hydroxytryptamine receptor 2B/0.451
4nb6444Nuclear receptor ROR-gamma/0.451
1g3mPCQEstrogen sulfotransferase2.8.2.40.450
1hfqMOTDihydrofolate reductase1.5.1.30.450
1rkgVD1Vitamin D3 receptor/0.450
2a1nCAMCamphor 5-monooxygenase1.14.15.10.450
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.450
3csdEMOPutative ketoacyl reductase1.3.10.450
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
3eem53VUncharacterized protein/0.450
3ijdC2FMethylenetetrahydrofolate reductase/0.450
4eevL1XHepatocyte growth factor receptor2.7.10.10.450
4g2gTDHMycocyclosin synthase1.14.21.90.450
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.449
1m78CLZDihydrofolate reductase1.5.1.30.449
1q5dEPBEpothilone C/D epoxidase1.140.449
1vruAAPGag-Pol polyprotein2.7.7.490.449
3invC50Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3vt65YIVitamin D3 receptor/0.449
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4jqh1MFAlr2278 protein/0.449
4ktkKTKCytochrome P450/0.449
3reyXACAdenosine receptor A2a/0.449
1dz4CAMCamphor 5-monooxygenase1.14.15.10.448
1nhz486Glucocorticoid receptor/0.448
1s19MC9Vitamin D3 receptor/0.448
1s9qOHTEstrogen-related receptor gamma/0.448
2e9aB28Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.448
2y30SM8Putative repressor SimReg2/0.448
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
4ejgNCTCytochrome P450 2A131.14.14.10.448
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.448
4kbn25UDihydrofolate reductase1.5.1.30.448
1dajMOTDihydrofolate reductase1.5.1.30.447
1gebCAMCamphor 5-monooxygenase1.14.15.10.447
1l0lFMXCytochrome b/0.447
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.447
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.447
2feuCAMCamphor 5-monooxygenase1.14.15.10.447
2jedLG8Protein kinase C theta type2.7.11.130.447
2wi72KLHeat shock protein HSP 90-alpha/0.447
3tk3CPZCytochrome P450 2B41.14.14.10.447
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.447
4g1y0VOVitamin D3 receptor A/0.447
4y6gF6FTryptophan synthase alpha chain/0.447
5k2dZMAAdenosine receptor A2a/0.447
2zlaVDBVitamin D3 receptor/0.446
3d78NBBPheromone-binding protein ASP1/0.446
3dxjNE6DNA-directed RNA polymerase subunit beta/0.446
3dxjNE6DNA-directed RNA polymerase subunit beta'/0.446
3lakKR1Gag-Pol polyprotein2.7.7.490.446
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.446
4fhh0U3Vitamin D3 receptor A/0.446
4fnyI3KALK tyrosine kinase receptor2.7.10.10.446
4h9506UDihydrofolate reductase1.5.1.30.446
4hw219HInduced myeloid leukemia cell differentiation protein Mcl-1/0.446
4m2xTMQDihydrofolate reductase1.5.1.30.446
1dg5TOPDihydrofolate reductase1.5.1.30.445
1sqvUHDCytochrome b/0.445
1wrlTFPTroponin C, slow skeletal and cardiac muscles/0.445
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.445
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
4pnmNU1Tankyrase-22.4.2.300.445
5i2hAGIO-methyltransferase family 2/0.445
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.444
1uymPU3Heat shock protein HSP 90-beta/0.444
1yrcCAMCamphor 5-monooxygenase1.14.15.10.444
2gpvOHTEstrogen-related receptor gamma/0.444
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.444
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3l71AZOCytochrome b/0.444
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3negPYVAbscisic acid receptor PYL1/0.444
4ia3BIVVitamin D3 receptor A/0.444
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.444
1ia2TQ4Dihydrofolate reductase1.5.1.30.443
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.443
1t87CAMCamphor 5-monooxygenase1.14.15.10.443
2chw039Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
2hasC3OVitamin D3 receptor/0.443
2jkcFADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.443
3a0iAJIGlucokinase2.7.1.20.443
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.443
3vtdTKDVitamin D3 receptor/0.443
4l4aCAMCamphor 5-monooxygenase1.14.15.10.443
4y8wSTRSteroid 21-hydroxylase/0.443
1klkPMDDihydrofolate reductase1.5.1.30.442
1s6qTPBGag-Pol polyprotein2.7.7.490.442
1t86CAMCamphor 5-monooxygenase1.14.15.10.442
1zidZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.442
2p7zOHTEstrogen-related receptor gamma/0.442
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.442
2yee2ECHeat shock protein HSP 90-alpha/0.442
2zl9VDAVitamin D3 receptor/0.442
2zlcVDXVitamin D3 receptor/0.442
3antS82Bifunctional epoxide hydrolase 23.3.2.100.442
3f0aACOSpermidine N(1)-acetyltransferase/0.442
3gwfFADCyclohexanone monooxygenase/0.442
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
3vrvYSDVitamin D3 receptor/0.442
3w5q3KLVitamin D3 receptor/0.442
4apuA2KProgesterone receptor/0.442
4dp3MMVBifunctional dihydrofolate reductase-thymidylate synthase/0.442
4g95OAGDihydrofolate reductase1.5.1.30.442
4rupH97Vitamin D3 receptor A/0.442
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.441
1s3yTQTDihydrofolate reductase1.5.1.30.441
2dw4FADLysine-specific histone demethylase 1A10.441
2gjlFMNNitronate monooxygenase1.13.12.160.441
2hamC33Vitamin D3 receptor/0.441
2vrbNAPTriphenylmethane reductase/0.441
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3e5aVX6Aurora kinase A2.7.11.10.441
3eej53RUncharacterized protein/0.441
3fhxPXLPyridoxal kinase2.7.1.350.441
3fu9KIBLaccase-11.10.3.20.441
3gcq1BUMitogen-activated protein kinase 14/0.441
3k47D09Dihydrofolate reductase1.5.1.30.441
3kpzZNEVitamin D3 receptor/0.441
3nefPYVAbscisic acid receptor PYL1/0.441
3qlxQLRUncharacterized protein/0.441
3vg9ZMAAdenosine receptor A2a/0.441
4bfpSWYTankyrase-22.4.2.300.441
4h9814QUncharacterized protein/0.441
4iah1DXAlr2278 protein/0.441
4itmATPTetraacyldisaccharide 4'-kinase/0.441
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
1blzACVIsopenicillin N synthase1.21.3.10.440
1ezvSMACytochrome b/0.440
1ie9VDXVitamin D3 receptor/0.440
1yrdCAMCamphor 5-monooxygenase1.14.15.10.440
2fwyH64Heat shock protein HSP 90-alpha/0.440
2hb7O1CVitamin D3 receptor/0.440
2hcdBIVVitamin D3 receptor A/0.440
2ovhAS0Progesterone receptor/0.440
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.440
3dg8RJ6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
3hf6LX0Tryptophan 5-hydroxylase 11.14.16.40.440
3hz142CHeat shock protein HSP 90-alpha/0.440
3pqbVGPPutative oxidoreductase/0.440
3w5tLHPVitamin D3 receptor/0.440
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
4iteTEYVitamin D3 receptor/0.440
5g53NECAdenosine receptor A2a/0.440
5iu86DZAdenosine receptor A2a/0.440