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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
2o4jVD4Vitamin D3 receptor

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2o4jVD4Vitamin D3 receptor/1.000
1rkhVD2Vitamin D3 receptor/0.884
2o4rVD5Vitamin D3 receptor/0.836
3vruYS3Vitamin D3 receptor/0.750
1rkgVD1Vitamin D3 receptor/0.726
2hb7O1CVitamin D3 receptor/0.717
1rjkVDZVitamin D3 receptor/0.708
2hasC3OVitamin D3 receptor/0.708
3vrvYSDVitamin D3 receptor/0.706
3vrwYS5Vitamin D3 receptor/0.700
1s0zEB1Vitamin D3 receptor/0.697
2hc4VDXVitamin D3 receptor A/0.695
4g1z0VPVitamin D3 receptor A/0.695
2hamC33Vitamin D3 receptor/0.694
2harOCCVitamin D3 receptor/0.692
2zlcVDXVitamin D3 receptor/0.692
2zl9VDAVitamin D3 receptor/0.691
1ie8KH1Vitamin D3 receptor/0.690
1s19MC9Vitamin D3 receptor/0.690
1txiTX5Vitamin D3 receptor/0.690
4g1d0VKVitamin D3 receptor A/0.689
4iteTEYVitamin D3 receptor/0.689
3w0jT08Vitamin D3 receptor/0.688
4rupH97Vitamin D3 receptor A/0.688
2hb8MVDVitamin D3 receptor/0.687
1db1VDXVitamin D3 receptor/0.684
4g20484Vitamin D3 receptor A/0.684
4fhh0U3Vitamin D3 receptor A/0.683
4ia3BIVVitamin D3 receptor A/0.681
3kpzZNEVitamin D3 receptor/0.676
1ie9VDXVitamin D3 receptor/0.675
1rk3VDXVitamin D3 receptor/0.674
3a783EVVitamin D3 receptor/0.673
3vt5YI2Vitamin D3 receptor/0.673
4g210VPVitamin D3 receptor A/0.672
3w0aDS5Vitamin D3 receptor/0.671
2zlaVDBVitamin D3 receptor/0.670
3vt3VDXVitamin D3 receptor/0.670
4rujVDXVitamin D3 receptor A/0.670
3dr1C5DVitamin D3 receptor A/0.667
3vt45YIVitamin D3 receptor/0.667
3vt65YIVitamin D3 receptor/0.667
4ia7BIVVitamin D3 receptor A/0.667
4itfTFYVitamin D3 receptor/0.667
3vtbTKAVitamin D3 receptor/0.665
3w0yDS4Vitamin D3 receptor/0.665
4fhi0S4Vitamin D3 receptor A/0.665
4g1y0VOVitamin D3 receptor A/0.664
2hbhXE4Vitamin D3 receptor A/0.662
3w0iO11Vitamin D3 receptor/0.659
3vtcTK3Vitamin D3 receptor/0.658
4g2h0VQVitamin D3 receptor A/0.657
2hcdBIVVitamin D3 receptor A/0.654
3vrtYS2Vitamin D3 receptor/0.654
4ia1BIVVitamin D3 receptor A/0.654
4ruoBIVVitamin D3 receptor A/0.653
3vtdTKDVitamin D3 receptor/0.651
3vt8YI3Vitamin D3 receptor/0.650
3w0c6DSVitamin D3 receptor/0.647
3vt7VDXVitamin D3 receptor/0.645
3w0hW12Vitamin D3 receptor/0.644
3vt9YI4Vitamin D3 receptor/0.642
4q0a4OAVitamin D3 receptor A/0.640
3m7rVDXVitamin D3 receptor/0.638
3w0gW07Vitamin D3 receptor/0.637
3w5tLHPVitamin D3 receptor/0.626
3w5q3KLVitamin D3 receptor/0.622
3w5p4OAVitamin D3 receptor/0.620
3w5rLOAVitamin D3 receptor/0.615
4g2i0VQVitamin D3 receptor/0.521
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.508
1lcoPPYCytochrome b2, mitochondrial1.1.2.30.489
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.489
2q9fC3SCholesterol 24-hydroxylase/0.485
2z97CAMCamphor 5-monooxygenase1.14.15.10.483
4ia2BIVVitamin D3 receptor A/0.483
3d5fL41Peroxisome proliferator-activated receptor delta/0.482
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.481
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.479
3bejMUFBile acid receptor/0.476
3up0D7SaceDAF-12/0.476
1blzACVIsopenicillin N synthase1.21.3.10.475
3l0lHC3Nuclear receptor ROR-gamma/0.474
4a83DXCMajor pollen allergen Bet v 1-A/0.473
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.472
1upw444Oxysterols receptor LXR-beta/0.472
2ev9NAPShikimate dehydrogenase (NADP(+))/0.472
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.472
2ykjYKJHeat shock protein HSP 90-alpha/0.472
3qm4PN0Cytochrome P450 2D6/0.472
5eccNAPDehydrofolate reductase type I/0.470
1f5fDHTSex hormone-binding globulin/0.468
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.468
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.468
1p8dCO1Oxysterols receptor LXR-beta/0.467
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.467
2zb45OPProstaglandin reductase 21.3.1.480.467
4r20AERCytochrome P450 family 17 polypeptide 2/0.467
4j6dTESCytochrome P450 monooxygenase/0.466
3gggNADPrephenate dehydrogenase/0.465
3zuxTCHTransporter/0.465
1dz6CAMCamphor 5-monooxygenase1.14.15.10.464
1eioGCHGastrotropin/0.464
1uyfPU1Heat shock protein HSP 90-alpha/0.464
4iah1DXAlr2278 protein/0.464
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
3cgeCOACoenzyme A disulfide reductase/0.463
1vrwNAIEnoyl-ACP reductase/0.462
2jn3JN3Fatty acid-binding protein, liver/0.462
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.462
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.461
3c14FOKAdenylate cyclase type 2/0.461
3c14FOKAdenylate cyclase type 5/0.461
3nr4PYVAbscisic acid receptor PYL2/0.461
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
4iui1GQEstrogen receptor/0.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
3p6nDSOCamphor 5-monooxygenase1.14.15.10.460
4dc0NDPPutative ketoacyl reductase1.3.10.460
4j6cSTRCytochrome P450 monooxygenase/0.460
4jvb1M0Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.460
4kxn6K62'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.460
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
5akk1P8Bifunctional epoxide hydrolase 23.1.3.760.460
1z6tADPApoptotic protease-activating factor 1/0.459
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.459
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.459
3up3XCAaceDAF-12/0.459
4dhyS41Glucokinase2.7.1.20.459
4l9q9TPSerum albumin/0.459
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.458
2z3uCRRCytochrome P450/0.458
3nj0PYVAbscisic acid receptor PYL2/0.458
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.457
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.457
1uzwCDHIsopenicillin N synthase1.21.3.10.457
4nb6444Nuclear receptor ROR-gamma/0.457
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.457
3mnrSD1Heat shock protein HSP 90-alpha/0.456
4ead0NPThymidine phosphorylase2.4.2.40.456
1cjkFOKAdenylate cyclase type 2/0.455
1cjkFOKAdenylate cyclase type 5/0.455
2ykcYKCHeat shock protein HSP 90-alpha/0.455
1dhjMTXDihydrofolate reductase1.5.1.30.454
1lhvNOGSex hormone-binding globulin/0.454
1nytNAPShikimate dehydrogenase (NADP(+))/0.454
1osvCHCBile acid receptor/0.454
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3h3r14HCollagen type IV alpha-3-binding protein/0.454
4a9mP9MBromodomain-containing protein 2/0.454
4iarERM5-hydroxytryptamine receptor 1B/0.454
2yk2YJXHeat shock protein HSP 90-alpha/0.453
2ykeYKEHeat shock protein HSP 90-alpha/0.453
3fpjSAMUncharacterized protein/0.453
4h6rFDAProline dehydrogenase/0.453
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1uyePU9Heat shock protein HSP 90-alpha/0.452
2aibERGBeta-elicitin cinnamomin/0.452
2rhrEMOPutative ketoacyl reductase1.3.10.452
3h3sH15Collagen type IV alpha-3-binding protein/0.452
3lkhLT6Genome polyprotein2.7.7.480.452
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.452
3a1l2CCCytochrome P450/0.451
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3hz5Z64Heat shock protein HSP 90-alpha/0.451
3wd7COAAcridone synthase/0.451
4l9kEHFSerum albumin/0.451
4okt198Androgen receptor/0.451
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.450
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.450
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
2vn0TDZCytochrome P450 2C8/0.450
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.450
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.450
3a0iAJIGlucokinase2.7.1.20.450
3csdEMOPutative ketoacyl reductase1.3.10.450
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
3gwfFADCyclohexanone monooxygenase/0.450
3koo24DBifunctional epoxide hydrolase 23.3.2.100.450
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
1dr3TAPDihydrofolate reductase1.5.1.30.449
1rf9DBRCamphor 5-monooxygenase1.14.15.10.449
1uy8PU5Heat shock protein HSP 90-alpha/0.449
2bu9HFVIsopenicillin N synthase1.21.3.10.449
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.449
3ijdC2FMethylenetetrahydrofolate reductase/0.449
4a862ANMajor pollen allergen Bet v 1-A/0.449
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.449
4q73FADBifunctional protein PutA/0.449
5k2bZMAAdenosine receptor A2a/0.449
1cf3FADGlucose oxidase1.1.3.40.448
1nq7ARLNuclear receptor ROR-beta/0.448
1uydPU8Heat shock protein HSP 90-alpha/0.448
2qblCAMCamphor 5-monooxygenase1.14.15.10.448
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.448
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.448
4tuvCPZCytochrome P450 1191.140.448
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.448
4uymVOR14-alpha sterol demethylase Cyp51B/0.448
1heuNADAlcohol dehydrogenase E chain1.1.1.10.447
1re9DSOCamphor 5-monooxygenase1.14.15.10.447
1sn5T3Transthyretin/0.447
1t86CAMCamphor 5-monooxygenase1.14.15.10.447
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
2qboCAMCamphor 5-monooxygenase1.14.15.10.447
2vd5BI8Myotonin-protein kinase2.7.11.10.447
2zgzGNPPlasmid segregation protein ParM/0.447
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.447
3jynNDPQuinone oxidoreductase/0.447
4a802ANMajor pollen allergen Bet v 1-A/0.447
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.447
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
4q71FADBifunctional protein PutA/0.447
1o6qR17Squalene--hopene cyclase4.2.1.1290.446
1qiqACCIsopenicillin N synthase1.21.3.10.446
1qxlFR8Adenosine deaminase3.5.4.40.446
2o7pNAPRiboflavin biosynthesis protein RibD/0.446
2p5uNADUDP-glucose 4-epimerase/0.446
2vbpVB1Isopenicillin N synthase1.21.3.10.446
3nxxNDPDihydrofolate reductase1.5.1.30.446
3o0iP54Heat shock protein HSP 90-alpha/0.446
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.446
4ejgNCTCytochrome P450 2A131.14.14.10.446
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
5eypLOCTubulin beta chain/0.446
1m13HYFNuclear receptor subfamily 1 group I member 2/0.445
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.445
2w6oOA3Biotin carboxylase6.3.4.140.445
2ykbYKBHeat shock protein HSP 90-alpha/0.445
3a25SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.445
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
3mdvCL6Cholesterol 24-hydroxylase/0.445
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4ly91YYGlucokinase regulatory protein/0.445
5cp4CAMCamphor 5-monooxygenase1.14.15.10.445
5ifyUMPGlucose-1-phosphate thymidylyltransferase/0.445
1hetNADAlcohol dehydrogenase E chain1.1.1.10.444
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
2ovhAS0Progesterone receptor/0.444
2y60M8FIsopenicillin N synthase1.21.3.10.444
3bzuA21Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3h3t16HCollagen type IV alpha-3-binding protein/0.444
3tnlNADShikimate dehydrogenase (NADP(+))/0.444
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.444
1culFOKAdenylate cyclase type 2/0.443
1culFOKAdenylate cyclase type 5/0.443
1og5SWFCytochrome P450 2C9/0.443
1opbRETRetinol-binding protein 2/0.443
1phgMYTCamphor 5-monooxygenase1.14.15.10.443
1uykPUXHeat shock protein HSP 90-alpha/0.443
2wotZZGTGF-beta receptor type-12.7.11.300.443
2zawCAMCamphor 5-monooxygenase1.14.15.10.443
3d75NBBPheromone-binding protein ASP1/0.443
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3l8sBFFMitogen-activated protein kinase 14/0.443
3um61CYBifunctional dihydrofolate reductase-thymidylate synthase/0.443
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.443
4l0qNADAlcohol dehydrogenase class-3/0.443
4m11MXMProstaglandin G/H synthase 21.14.99.10.443
1cs4FOKAdenylate cyclase type 2/0.442
1cs4FOKAdenylate cyclase type 5/0.442
1d2sDHTSex hormone-binding globulin/0.442
1ju6LYAThymidylate synthase2.1.1.450.442
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
3d84NDPDihydrofolate reductase1.5.1.30.442
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.442
3gwfNAPCyclohexanone monooxygenase/0.442
3oquA8SAbscisic acid receptor PYL9/0.442
4h9506UDihydrofolate reductase1.5.1.30.442
4imfSI3N-acetylneuraminate lyase/0.442
4jv618FRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.442
4kl9NDPDihydrofolate reductase1.5.1.30.442
5kjcPFBAlcohol dehydrogenase E chain1.1.1.10.442
1eupASD6-deoxyerythronolide B hydroxylase/0.441
1h35R01Squalene--hopene cyclase4.2.1.1290.441
2ftoCB3Thymidylate synthase/0.441
2vcmM11Isopenicillin N synthase1.21.3.10.441
3gkjHC3Niemann-Pick C1 protein/0.441
3p6oETGCamphor 5-monooxygenase1.14.15.10.441
3ukuC69Actin-related protein 3/0.441
4kne1CYDihydrofolate reductase1.5.1.30.441
4nh82LCHeat shock protein HSP 90-alpha/0.441
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1dr3HBIDihydrofolate reductase1.5.1.30.440
1jioDEB6-deoxyerythronolide B hydroxylase/0.440
1n83CLRNuclear receptor ROR-alpha/0.440
1qknRALEstrogen receptor beta/0.440
1uyhPU0Heat shock protein HSP 90-alpha/0.440
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.440
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
2zynBCDPeriplasmic binding protein/0.440
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3inwJZBHeat shock protein HSP 90-alpha/0.440
3oafOAGDihydrofolate reductase1.5.1.30.440
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3um5CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.440
3zep1NXTyrosine-protein kinase JAK32.7.10.20.440
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4jbtASDCytochrome P450 monooxygenase/0.440
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4l8u9AZSerum albumin/0.440
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.440
5kgpACOPredicted acetyltransferase/0.440