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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
1f5fDHTSex hormone-binding globulin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1f5fDHTSex hormone-binding globulin/1.000
1d2sDHTSex hormone-binding globulin/0.593
1lhvNOGSex hormone-binding globulin/0.505
3w5p4OAVitamin D3 receptor/0.496
3vt3VDXVitamin D3 receptor/0.495
3w0gW07Vitamin D3 receptor/0.495
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.493
3h3t16HCollagen type IV alpha-3-binding protein/0.490
1lhoAOMSex hormone-binding globulin/0.488
3vrtYS2Vitamin D3 receptor/0.488
3atzFMNProstaglandin F2a synthase/0.486
3kpzZNEVitamin D3 receptor/0.484
2hamC33Vitamin D3 receptor/0.482
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.481
3w5rLOAVitamin D3 receptor/0.480
3d84NDPDihydrofolate reductase1.5.1.30.479
3koo24DBifunctional epoxide hydrolase 23.3.2.100.479
3vt65YIVitamin D3 receptor/0.479
1txiTX5Vitamin D3 receptor/0.477
3a783EVVitamin D3 receptor/0.477
3oafOAGDihydrofolate reductase1.5.1.30.477
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.476
1s19MC9Vitamin D3 receptor/0.475
2vbpVB1Isopenicillin N synthase1.21.3.10.475
2nq8ZIDEnoyl-ACP reductase/0.474
4ia3BIVVitamin D3 receptor A/0.474
3w0hW12Vitamin D3 receptor/0.473
2hb7O1CVitamin D3 receptor/0.472
3atyFMNProstaglandin F2a synthase/0.472
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.472
3w5tLHPVitamin D3 receptor/0.472
3vrwYS5Vitamin D3 receptor/0.471
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.470
3vt45YIVitamin D3 receptor/0.470
3vt5YI2Vitamin D3 receptor/0.470
3zoiM2WIsopenicillin N synthase1.21.3.10.470
2y6fM9FIsopenicillin N synthase1.21.3.10.469
2zl9VDAVitamin D3 receptor/0.469
4q0a4OAVitamin D3 receptor A/0.469
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
3w0aDS5Vitamin D3 receptor/0.468
1db1VDXVitamin D3 receptor/0.467
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.467
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.467
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.467
1blzACVIsopenicillin N synthase1.21.3.10.466
2hc4VDXVitamin D3 receptor A/0.466
3gwfFADCyclohexanone monooxygenase/0.466
3h3r14HCollagen type IV alpha-3-binding protein/0.466
3qlrNDPDihydrofolate reductase1.5.1.30.466
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.466
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.465
3vt8YI3Vitamin D3 receptor/0.465
4g95OAGDihydrofolate reductase1.5.1.30.465
1mp0NADAlcohol dehydrogenase class-31.1.1.10.464
1rd4L08Integrin alpha-L/0.464
1rkhVD2Vitamin D3 receptor/0.464
2hasC3OVitamin D3 receptor/0.464
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.464
2q59240Peroxisome proliferator-activated receptor gamma/0.464
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.464
4a8v2ANMajor pollen allergen Bet v 1-J/0.464
4r20AERCytochrome P450 family 17 polypeptide 2/0.464
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.464
1rjkVDZVitamin D3 receptor/0.463
1rx1NAPDihydrofolate reductase1.5.1.30.463
2hcdBIVVitamin D3 receptor A/0.463
3sx2NADUncharacterized protein/0.463
1oc1ASVIsopenicillin N synthase1.21.3.10.462
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.462
3vtbTKAVitamin D3 receptor/0.462
3w0iO11Vitamin D3 receptor/0.462
3w8eNAD3-hydroxybutyrate dehydrogenase/0.462
3zkyWT4Isopenicillin N synthase1.21.3.10.462
4q71FADBifunctional protein PutA/0.462
1ie9VDXVitamin D3 receptor/0.461
1upw444Oxysterols receptor LXR-beta/0.461
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.461
2zlcVDXVitamin D3 receptor/0.461
3w0yDS4Vitamin D3 receptor/0.461
4ia1BIVVitamin D3 receptor A/0.461
4z9g1Q5Corticotropin-releasing factor receptor 1/0.461
3oq13OQCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3v49PK0Androgen receptor/0.460
4iteTEYVitamin D3 receptor/0.460
1db48INPhospholipase A2, membrane associated/0.459
1rk3VDXVitamin D3 receptor/0.459
2vzzSCAPutative succinyl-CoA transferase Rv0802c2.8.30.459
2znnS44Peroxisome proliferator-activated receptor alpha/0.459
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.459
3w0c6DSVitamin D3 receptor/0.459
3w0jT08Vitamin D3 receptor/0.459
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
5eccNAPDehydrofolate reductase type I/0.459
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
1s0zEB1Vitamin D3 receptor/0.458
2iltNN1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
3nxxNDPDihydrofolate reductase1.5.1.30.458
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.458
4q73FADBifunctional protein PutA/0.458
5dcyNAPIridoid synthase1.3.1.990.458
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
1r2jFADFkbI/0.457
2aibERGBeta-elicitin cinnamomin/0.457
2xviFADPutative flavin-containing monooxygenase/0.457
2zlaVDBVitamin D3 receptor/0.457
4rupH97Vitamin D3 receptor A/0.457
1bk0ACVIsopenicillin N synthase1.21.3.10.456
2bxqIMNSerum albumin/0.456
2o4rVD5Vitamin D3 receptor/0.456
2z97CAMCamphor 5-monooxygenase1.14.15.10.456
3gw9VNILanosterol 14-alpha-demethylase/0.456
3own3OWRenin3.4.23.150.456
3vrvYSDVitamin D3 receptor/0.456
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
1rkgVD1Vitamin D3 receptor/0.455
2wo7ASVIsopenicillin N synthase1.21.3.10.455
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.455
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
4g1y0VOVitamin D3 receptor A/0.455
1hb1OCVIsopenicillin N synthase1.21.3.10.454
2bu9HFVIsopenicillin N synthase1.21.3.10.454
3oibFDAPutative acyl-CoA dehydrogenase/0.454
3w5q3KLVitamin D3 receptor/0.454
3zuyTCHTransporter/0.454
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
1ia1NDPDihydrofolate reductase1.5.1.30.453
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.453
2o4jVD4Vitamin D3 receptor/0.453
3cgcCOACoenzyme A disulfide reductase/0.453
3qlsNDPDihydrofolate reductase1.5.1.30.453
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.453
4e2bFMNDehydrogenase/0.453
4ftiH7KSerine/threonine-protein kinase Chk12.7.11.10.453
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
2iviACWIsopenicillin N synthase1.21.3.10.452
2zbaZBATrichothecene 3-O-acetyltransferase/0.452
3gwfNAPCyclohexanone monooxygenase/0.452
3vruYS3Vitamin D3 receptor/0.452
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.452
4dbzNDPPutative ketoacyl reductase1.3.10.452
4e2dFMNDehydrogenase/0.452
4g1d0VKVitamin D3 receptor A/0.452
4g1z0VPVitamin D3 receptor A/0.452
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
4r87COASpermidine N(1)-acetyltransferase/0.452
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1obnASVIsopenicillin N synthase1.21.3.10.451
3cobADPKinesin heavy chain-like protein/0.451
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.451
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.451
4a33MYAGlycylpeptide N-tetradecanoyltransferase/0.451
4g20484Vitamin D3 receptor A/0.451
4kfn1QRNicotinamide phosphoribosyltransferase2.4.2.120.451
1bsvNDPGDP-L-fucose synthase/0.450
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1fm4DXCMajor pollen allergen Bet v 1-L/0.450
2hbhXE4Vitamin D3 receptor A/0.450
3vt7VDXVitamin D3 receptor/0.450
4bb3KKAIsopenicillin N synthase1.21.3.10.450
4ienCOAPutative acyl-CoA hydrolase/0.450
2ie0ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2ztlNADD(-)-3-hydroxybutyrate dehydrogenase/0.449
3h3sH15Collagen type IV alpha-3-binding protein/0.449
3vtcTK3Vitamin D3 receptor/0.449
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.449
4fhh0U3Vitamin D3 receptor A/0.449
4itfTFYVitamin D3 receptor/0.449
4l9q9TPSerum albumin/0.449
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.448
1rx8NAPDihydrofolate reductase1.5.1.30.448
1w06W05Isopenicillin N synthase1.21.3.10.448
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.448
2harOCCVitamin D3 receptor/0.448
2p5uNADUDP-glucose 4-epimerase/0.448
3lu8IQXSerum albumin/0.448
3s1dZIRCytokinin dehydrogenase 11.5.99.120.448
3tqaNDPDihydrofolate reductase/0.448
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.448
4ruoBIVVitamin D3 receptor A/0.448
1pdhFASp-hydroxybenzoate hydroxylase/0.447
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
2zynBCDPeriplasmic binding protein/0.447
3w6hAZMCarbonic anhydrase 14.2.1.10.447
5fsxADPUncharacterized protein/0.447
1cf3FADGlucose oxidase1.1.3.40.446
1diuBDMDihydrofolate reductase1.5.1.30.446
1kkq471Peroxisome proliferator-activated receptor alpha/0.446
2hb8MVDVitamin D3 receptor/0.446
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.446
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.446
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
3m7rVDXVitamin D3 receptor/0.446
3vt9YI4Vitamin D3 receptor/0.446
4ez8DHFThymidylate synthase2.1.1.450.446
4lxhC1EAlpha/beta hydrolase fold/0.446
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.446
4xymCOAAcyl-CoA synthetase (NDP forming)/0.446
1ia4TQ6Dihydrofolate reductase1.5.1.30.445
1ie8KH1Vitamin D3 receptor/0.445
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.445
1n83CLRNuclear receptor ROR-alpha/0.445
1pq944BOxysterols receptor LXR-beta/0.445
1s3vTQDDihydrofolate reductase1.5.1.30.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.445
3nr4PYVAbscisic acid receptor PYL2/0.445
4o63NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.445
4r21STRCytochrome P450 family 17 polypeptide 2/0.445
4rrrA3TThreonine--tRNA ligase6.1.1.30.445
1dr2TAPDihydrofolate reductase1.5.1.30.444
1drhNAPDihydrofolate reductase1.5.1.30.444
1qjfACSIsopenicillin N synthase1.21.3.10.444
1rx8FOLDihydrofolate reductase1.5.1.30.444
1u33LM2Pancreatic alpha-amylase/0.444
2w71L23Biotin carboxylase6.3.4.140.444
3h1vTK1Glucokinase2.7.1.20.444
3kytHC2Nuclear receptor ROR-gamma/0.444
3lqfNADGalactitol dehydrogenase/0.444
3v3m0ENReplicase polyprotein 1a3.4.19.120.444
4fhi0S4Vitamin D3 receptor A/0.444
4gl4NAIAlcohol dehydrogenase class-3/0.444
4i0h1BLBeta-secretase 13.4.23.460.444
4ltsLTSNicotinamide phosphoribosyltransferase2.4.2.120.444
5cp4CAMCamphor 5-monooxygenase1.14.15.10.444
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.444
1ai9NDPDihydrofolate reductase1.5.1.30.443
1ddrMTXDihydrofolate reductase1.5.1.30.443
1m78NDPDihydrofolate reductase1.5.1.30.443
1ma0NADAlcohol dehydrogenase class-31.1.1.10.443
1pq6965Oxysterols receptor LXR-beta/0.443
2ahrNAPPyrroline-5-carboxylate reductase/0.443
2j9gANPBiotin carboxylase6.3.4.140.443
2o7pNAPRiboflavin biosynthesis protein RibD/0.443
2po7CHDFerrochelatase, mitochondrial4.99.1.10.443
2vbdV10Isopenicillin N synthase1.21.3.10.443
2xaaNADSecondary alcohol dehydrogenase/0.443
3ey9TDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.443
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
4ceqQCHIntegrase/0.443
4g210VPVitamin D3 receptor A/0.443
4l4xNDPAmphI/0.443
4q72FADBifunctional protein PutA/0.443
4xz3COAAcyl-CoA synthetase (NDP forming)/0.443
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.443
5fm7ADPRuvB-like helicase/0.443
5jy1NADPutative short-chain dehydrogenase/reductase/0.443
1f4fTP3Thymidylate synthase/0.442
1ju6LYAThymidylate synthase2.1.1.450.442
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1uzwCDHIsopenicillin N synthase1.21.3.10.442
2a1nCAMCamphor 5-monooxygenase1.14.15.10.442
2pg0FADAcyl-CoA dehydrogenase/0.442
2qbmCAMCamphor 5-monooxygenase1.14.15.10.442
2xvw9NRSerum albumin/0.442
3u9eCOALmo1369 protein/0.442
4lb2DM5Serum albumin/0.442
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.442
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
1dhiMTXDihydrofolate reductase1.5.1.30.441
1dr3TAPDihydrofolate reductase1.5.1.30.441
1f0qEMOCasein kinase II subunit alpha2.7.11.10.441
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
1f4gTP4Thymidylate synthase/0.441
1kdmDHTSex hormone-binding globulin/0.441
1p0hCOAMycothiol acetyltransferase2.3.1.1890.441
1u3vNADAlcohol dehydrogenase 1B1.1.1.10.441
1xs7MMIBeta-secretase 13.4.23.460.441
2bx8AZQSerum albumin/0.441
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.441
3oquA8SAbscisic acid receptor PYL9/0.441
3p3zP3ZPutative cytochrome P450/0.441
3vdqNAD3-hydroxybutyrate dehydrogenase/0.441
3vtdTKDVitamin D3 receptor/0.441
4dl9NADS-(hydroxymethyl)glutathione dehydrogenase/0.441
4ffrATPUncharacterized protein/0.441
4h6rFDAProline dehydrogenase/0.441
4l8u9AZSerum albumin/0.441
4mv1ADPBiotin carboxylase6.3.4.140.441
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.441
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.441
5kjePFBAlcohol dehydrogenase E chain1.1.1.10.441
1dtpAPUDiphtheria toxin/0.440
1p8dCO1Oxysterols receptor LXR-beta/0.440
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.440
1xe65FPPlasmepsin-23.4.23.390.440
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.440
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3p62FMNPentaerythritol tetranitrate reductase/0.440
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3znqSS8D-amino-acid oxidase1.4.3.30.440
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
4h9753SDihydrofolate reductase1.5.1.30.440
5ag7MYAGlycylpeptide N-tetradecanoyltransferase/0.440