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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3dl9BCDVitamin D 25-hydroxylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3dl9BCDVitamin D 25-hydroxylase/1.000
4ejmNAPPutative zinc-binding dehydrogenase/0.514
3k4vROCGag-Pol polyprotein3.4.23.160.490
2q9fC3SCholesterol 24-hydroxylase/0.481
2c0cNAPProstaglandin reductase 310.480
2om9AJAPeroxisome proliferator-activated receptor gamma/0.480
3d3wNAPL-xylulose reductase1.1.1.100.475
1e3eNAIAlcohol dehydrogenase 41.1.1.10.474
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.474
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.473
3lu8IQXSerum albumin/0.473
3ndtROCGag-Pol polyprotein3.4.23.160.472
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.471
1rl8RITGag-Pol polyprotein3.4.23.160.469
3a1nNADNDP-sugar epimerase/0.469
3crzFADFerredoxin--NADP+ reductase/0.469
1hetNADAlcohol dehydrogenase E chain1.1.1.10.468
1tehNADAlcohol dehydrogenase class-31.1.1.10.468
2aazCB3Thymidylate synthase2.1.1.450.468
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.467
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.467
3b70NAPEnoyl reductase LovC10.467
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.467
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.466
1jioDEB6-deoxyerythronolide B hydroxylase/0.465
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.465
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.465
1kziTHGThymidylate synthase/0.464
1njsKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.464
2gqtFADUDP-N-acetylenolpyruvoylglucosamine reductase/0.464
2igoFADPyranose 2-oxidase/0.464
4n9iPCGCatabolite expression activator/0.464
1b16NAQAlcohol dehydrogenase1.1.1.10.463
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.463
1mg5NAIAlcohol dehydrogenase1.1.1.10.463
1vikBAYGag-Pol polyprotein/0.463
2nnkROCProtease/0.463
2wmqZYQSerine/threonine-protein kinase Chk12.7.11.10.463
1k6tXN1Gag-Pol polyprotein3.4.23.160.462
1kzjCB3Thymidylate synthase/0.462
2w4qCBWProstaglandin reductase 21.3.1.480.462
4l8u9AZSerum albumin/0.462
4xumIMNPeroxisome proliferator-activated receptor gamma/0.462
1trgCB3Thymidylate synthase/0.461
1yb5NAPQuinone oxidoreductase1.6.5.50.461
3ox4NADAlcohol dehydrogenase 21.1.1.10.461
3zuyTCHTransporter/0.461
1xddAAYIntegrin alpha-L/0.460
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.460
1ot7CHCBile acid receptor/0.459
2zb3NDPProstaglandin reductase 21.3.1.480.459
3oibFDAPutative acyl-CoA dehydrogenase/0.459
4g7gVFVLanosterol 14-alpha-demethylase/0.459
1ppjANYCytochrome b/0.458
1zx9FADMercuric reductase1.16.1.10.458
3e5rNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.458
4o59NADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.458
4xldBRLPeroxisome proliferator-activated receptor gamma/0.458
4yaiNAIC alpha-dehydrogenase/0.458
2gsdNADFormate dehydrogenase/0.457
2ignFADPyranose 2-oxidase/0.457
3ijoB4DGlutamate receptor 2/0.457
3qwbNDPProbable quinone oxidoreductase1.6.5.50.457
3sa4F72Protease/0.457
3tqhNDPQuinone oxidoreductase/0.457
1rbmKT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.456
1rdt570Peroxisome proliferator-activated receptor gamma/0.456
3nduROCGag-Pol polyprotein3.4.23.160.456
4jjiNADAlcohol dehydrogenase class-3/0.456
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.455
1psa0ZLPepsin A3.4.23.10.455
2ath3EAPeroxisome proliferator-activated receptor gamma/0.455
3ol5SAWCamphor 5-monooxygenase1.14.15.10.455
4q72FADBifunctional protein PutA/0.455
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.454
1ma0NADAlcohol dehydrogenase class-31.1.1.10.454
2q4wFADCytokinin dehydrogenase 71.5.99.120.454
3idsNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.454
3sn6P0GBeta-2 adrenergic receptor/0.454
1iyzNDPProbable quinone oxidoreductase/0.453
1kceCB3Thymidylate synthase/0.453
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.453
3i59N6RCRP-like cAMP-activated global transcriptional regulator/0.453
3jzdNADMaleylacetate reductase/0.453
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.453
4fn4NADShort chain dehydrogenase/0.453
4irnFADAnaB/0.453
4knzCB3Thymidylate synthase/0.453
4l9q9TPSerum albumin/0.453
5fs7FADApoptosis-inducing factor 1, mitochondrial1.1.10.453
5kgjACOPredicted acetyltransferase/0.453
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1wntNAPL-xylulose reductase1.1.1.100.452
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
1a7kNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.451
1t2cNAIL-lactate dehydrogenase1.1.1.270.451
2ejvNADL-threonine 3-dehydrogenase/0.451
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.451
2g78REACellular retinoic acid-binding protein 2/0.451
2rc6NAPFerredoxin--NADP reductase/0.451
3d7zGK5Mitogen-activated protein kinase 14/0.451
3oc4FADOxidoreductase, pyridine nucleotide-disulfide family/0.451
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.451
1fm9570Peroxisome proliferator-activated receptor gamma/0.450
1k74544Peroxisome proliferator-activated receptor gamma/0.450
1z1hHBBGag-Pol polyprotein3.4.23.160.450
2belCBOCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
2gtk208Peroxisome proliferator-activated receptor gamma/0.450
3gbuATPUncharacterized sugar kinase PH14592.7.10.450
3p8z36AGenome polyprotein2.1.1.560.450
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.450
3vrwYS5Vitamin D3 receptor/0.450
3zc3NAPFerredoxin--NADP reductase1.18.1.20.450
4o1mNADEnoyl-acyl carrier reductase/0.450
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.450
1cbrREACellular retinoic acid-binding protein 1/0.449
1hf3NADAlcohol dehydrogenase E chain1.1.1.10.449
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.449
3dmtNADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal1.2.1.120.449
3umvFADDeoxyribodipyrimidine photo-lyase4.1.99.30.449
4fhi0S4Vitamin D3 receptor A/0.449
4q71FADBifunctional protein PutA/0.449
5k2cZMAAdenosine receptor A2a/0.449
1j3kNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
1k6pXN3Gag-Pol polyprotein3.4.23.160.448
1kkq471Peroxisome proliferator-activated receptor alpha/0.448
1obnASVIsopenicillin N synthase1.21.3.10.448
2bbqPFGThymidylate synthase/0.448
2c0tL3GTyrosine-protein kinase HCK2.7.10.20.448
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.448
3d1yROCGag-Pol polyprotein3.4.23.160.448
4fr4STUSerine/threonine-protein kinase 32A2.7.11.10.448
4ia3BIVVitamin D3 receptor A/0.448
4l9kEHFSerum albumin/0.448
4yntFDAGlucose oxidase, putative/0.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
1difA85Gag-Pol polyprotein/0.447
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.447
1i3mUD1UDP-glucose 4-epimerase/0.447
1jpaANPEphrin type-B receptor 22.7.10.10.447
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.447
1nzdUPGDNA beta-glucosyltransferase/0.447
1vrwNAIEnoyl-ACP reductase/0.447
1xq6NAPUncharacterized protein At5g02240/0.447
2nu9COASuccinate--CoA ligase [ADP-forming] subunit alpha6.2.1.50.447
2pnuENMAndrogen receptor/0.447
3a9wNADNDP-sugar epimerase/0.447
3k9vCPS1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial/0.447
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.447
3lzs017Gag-Pol polyprotein3.4.23.160.447
3owaFADAcyl-CoA dehydrogenase/0.447
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4oh4ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.447
4wxlBB2Peptide deformylase/0.447
4xguADPPutative pachytene checkpoint protein 2/0.447
4yagNAIC alpha-dehydrogenase/0.447
1b15NAEAlcohol dehydrogenase1.1.1.10.446
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1ivp1ZKGag-Pol polyprotein/0.446
1jld0PPGag-Pol polyprotein/0.446
1mp0NADAlcohol dehydrogenase class-31.1.1.10.446
1v4sMRKGlucokinase2.7.1.20.446
2q4bNAPUncharacterized protein At5g02240/0.446
2xgs44PUncharacterized protein/0.446
3b6zCO7Enoyl reductase LovC10.446
3cbsR12Cellular retinoic acid-binding protein 2/0.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3gobHXXDdmC/0.446
3pwrROCGag-Pol polyprotein3.4.23.160.446
3qlsNDPDihydrofolate reductase1.5.1.30.446
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.446
4g3jVNTLanosterol 14-alpha-demethylase/0.446
4jx1CAHCamphor 5-monooxygenase1.14.15.10.446
4o7uTHFThymidylate synthase/0.446
4wboANWRhodopsin kinase/0.446
4y8wSTRSteroid 21-hydroxylase/0.446
1blzACVIsopenicillin N synthase1.21.3.10.445
1qvnFRIInterleukin-2/0.445
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.445
2ym7YM7Serine/threonine-protein kinase Chk12.7.11.10.445
3fhyATPPyridoxal kinase2.7.1.350.445
3ggaGGWGag-Pol polyprotein/0.445
3hl0NADMaleylacetate reductase/0.445
3o3pGDDGlycosyl transferase, family 2/0.445
3r5zF42Uncharacterized protein/0.445
3ttp017Gag-Pol polyprotein3.4.23.160.445
3uwlFOZThymidylate synthase/0.445
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.445
4ips1G4Mycocyclosin synthase1.14.21.90.445
4isk1JYThymidylate synthase/0.445
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.445
1hvjA78Gag-Pol polyprotein/0.444
1k6cMK1Gag-Pol polyprotein3.4.23.160.444
1oc1ASVIsopenicillin N synthase1.21.3.10.444
2vnkFADNADPH:ferredoxin reductase/0.444
3p6nDSOCamphor 5-monooxygenase1.14.15.10.444
3p6pA6BCamphor 5-monooxygenase1.14.15.10.444
3qrwNDPPutative ketoacyl reductase1.3.10.444
3r5yF42Uncharacterized protein/0.444
3toxNAPPutative oxidoreductase/0.444
4e5yNDPGDP-L-fucose synthase1.1.1.2710.444
4i7fNVEGag-Pol polyprotein2.7.7.490.444
4nmdFDABifunctional protein PutA/0.444
1bq1CB3Thymidylate synthase/0.443
1qy5NECEndoplasmin/0.443
1zmdNAIDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.443
2qo9ANPEphrin type-A receptor 32.7.10.10.443
3bgxMEFThymidylate synthase/0.443
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.443
3gqvNAPEnoyl reductase LovC10.443
3iaeD7KBenzaldehyde lyase/0.443
3ko8NADNAD-dependent epimerase/dehydratase/0.443
3nwxKVSGag-Pol polyprotein3.4.23.160.443
3r3sNADPutative oxidoreductase/0.443
3stxBKAMethylketone synthase I/0.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4mlhVO2Glucokinase2.7.1.20.443
1b14NADAlcohol dehydrogenase1.1.1.10.442
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.442
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.442
1s7gNADNAD-dependent protein deacylase 2/0.442
1sguMK1Gag-Pol polyprotein3.4.23.160.442
2eeqSAHDiphthine synthase/0.442
2izrBRKCasein kinase I isoform gamma-32.7.11.10.442
2ou2ACOHistone acetyltransferase KAT5/0.442
2owuSAHDiphthine synthase/0.442
2q641UNGag-Pol polyprotein3.4.23.160.442
2wdzNADGalactitol dehydrogenase/0.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3d3eD3ECorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3el4ROCGag-Pol polyprotein3.4.23.160.442
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3hjaNADGlyceraldehyde-3-phosphate dehydrogenase/0.442
3qlrNDPDihydrofolate reductase1.5.1.30.442
4e5nNADPhosphonate dehydrogenase1.20.1.10.442
4gl4NAIAlcohol dehydrogenase class-3/0.442
4i6gFADCryptochrome-2/0.442
4i8zG08Gag-Pol polyprotein3.4.23.160.442
4nieNBHNuclear receptor ROR-gamma/0.442
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4qi4FADCellobiose dehydrogenase/0.442
4y93746Tyrosine-protein kinase/0.442
5kjcNAJAlcohol dehydrogenase E chain1.1.1.10.442
1k7l544Peroxisome proliferator-activated receptor alpha/0.441
1kvrNADUDP-glucose 4-epimerase5.1.3.20.441
1tysDHFThymidylate synthase/0.441
2bd0NAPSepiapterin reductase/0.441
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.441
2f3kRO1Protease/0.441
2r9zFADGlutathione amide reductase/0.441
2znnS44Peroxisome proliferator-activated receptor alpha/0.441
3dckKVIProtease/0.441
3nww3NWMitogen-activated protein kinase 14/0.441
3qtwX3ACyclin-dependent kinase 22.7.11.220.441
3tneRITCandidapepsin-13.4.23.240.441
3vqsJT1Genome polyprotein/0.441
3w33W19Epidermal growth factor receptor2.7.10.10.441
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.441
4xgiNADGlutamate dehydrogenase/0.441
5dp2NAPCurF/0.441
1pyxANPGlycogen synthase kinase-3 beta2.7.11.260.440
1zk7FADMercuric reductase1.16.1.10.440
2hj3FADFAD-linked sulfhydryl oxidase ERV1/0.440
2i4qUA4Renin3.4.23.150.440
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2q3kMUWGag-Pol polyprotein/0.440
3cifNADGlyceraldehyde-3-phosphate dehydrogenase/0.440
3l0lHC3Nuclear receptor ROR-gamma/0.440
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
3w0iO11Vitamin D3 receptor/0.440
4c58824Cyclin-G-associated kinase2.7.11.10.440
4dbzNDPPutative ketoacyl reductase1.3.10.440
4dplNAPMalonyl-CoA reductase1.2.1.750.440
4qxr1YEStimulator of interferon genes protein/0.440
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4uymVOR14-alpha sterol demethylase Cyp51B/0.440
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
5fs8FADApoptosis-inducing factor 1, mitochondrial1.1.10.440