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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
3nd1SAHPrecorrin-6A synthase (Deacetylating)

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3nd1SAHPrecorrin-6A synthase (Deacetylating)/1.000
2npnSAMPutative cobalamin synthesis related protein/0.569
3kjm245Cytokinin dehydrogenase 11.5.99.120.489
3ibqATPPyridoxal kinase/0.488
2q9fC3SCholesterol 24-hydroxylase/0.484
5eccNAPDehydrofolate reductase type I/0.484
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.483
2zbaZBATrichothecene 3-O-acetyltransferase/0.481
3rfxNADUronate dehydrogenase/0.481
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.480
2y6o1N1Ephrin type-A receptor 42.7.10.10.480
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.477
3lqfNADGalactitol dehydrogenase/0.476
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.476
4q73FADBifunctional protein PutA/0.476
4tuvCPZCytochrome P450 1191.140.476
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.475
2bdf24AProto-oncogene tyrosine-protein kinase Src2.7.10.20.474
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.474
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.473
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.472
3qt62P0Mevalonate diphosphate decarboxylase/0.471
4g3jVNTLanosterol 14-alpha-demethylase/0.471
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.471
2itqITQEpidermal growth factor receptor2.7.10.10.469
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.469
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.469
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.468
3gwfFADCyclohexanone monooxygenase/0.468
3mdmFJZCholesterol 24-hydroxylase/0.468
3mdvCL6Cholesterol 24-hydroxylase/0.468
3nglNAPBifunctional protein FolD/0.468
4q72FADBifunctional protein PutA/0.467
4r21STRCytochrome P450 family 17 polypeptide 2/0.467
1culFOKAdenylate cyclase type 2/0.466
1culFOKAdenylate cyclase type 5/0.466
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.466
2j5xGSPADP-ribosylation factor 6/0.466
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.466
3zuyTCHTransporter/0.466
4qq3XMPInosine-5'-monophosphate dehydrogenase/0.466
1g6kNADGlucose 1-dehydrogenase1.1.1.470.465
2rkvZBATrichothecene 3-O-acetyltransferase/0.465
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.465
4gk3L87Ephrin type-A receptor 32.7.10.10.465
2bxmIMNSerum albumin/0.464
3pe6ZYHMonoglyceride lipase/0.464
3s1dZIRCytokinin dehydrogenase 11.5.99.120.464
4k28NADShikimate dehydrogenase family protein/0.464
4ktkKTKCytochrome P450/0.464
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.463
2gr1FADFerredoxin reductase/0.462
2p5uNADUDP-glucose 4-epimerase/0.462
3gobHXXDdmC/0.462
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.462
4cd2FOLDihydrofolate reductase1.5.1.30.462
4cukNAID-lactate dehydrogenase/0.462
4g6gFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.462
4jx1CAHCamphor 5-monooxygenase1.14.15.10.462
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.462
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
2ejvNADL-threonine 3-dehydrogenase/0.461
3ns2PYVAbscisic acid receptor PYL2/0.461
4enhFVXCholesterol 24-hydroxylase/0.461
1k6pXN3Gag-Pol polyprotein3.4.23.160.460
2rhrEMOPutative ketoacyl reductase1.3.10.460
2xh9J01Uncharacterized protein/0.460
3cppCAMCamphor 5-monooxygenase1.14.15.10.460
3o8tBMUMitogen-activated protein kinase 14/0.460
3r9uFADThioredoxin reductase/0.460
4dbzNDPPutative ketoacyl reductase1.3.10.460
4fmxCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.460
4g47TZFMycocyclosin synthase1.14.21.90.460
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.460
1bwsNDPGDP-L-fucose synthase/0.459
2cx8SAHRibosomal RNA small subunit methyltransferase E/0.459
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.459
4g48PZBMycocyclosin synthase1.14.21.90.459
4h4qFADBiphenyl dioxygenase ferredoxin reductase subunit/0.459
5a3cNADSIR2 family protein/0.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.458
1k6tXN1Gag-Pol polyprotein3.4.23.160.458
3p74FMNPentaerythritol tetranitrate reductase/0.458
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.458
4g2gTDHMycocyclosin synthase1.14.21.90.458
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.458
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.458
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
2znnS44Peroxisome proliferator-activated receptor alpha/0.457
3kpkFADSulfide-quinone reductase/0.457
3orfNADDihydropteridine reductase1.5.1.340.457
4cp4CAMCamphor 5-monooxygenase1.14.15.10.457
4kl9NDPDihydrofolate reductase1.5.1.30.457
5bsfNADPyrroline-5-carboxylate reductase/0.457
1cjkFOKAdenylate cyclase type 2/0.456
1cjkFOKAdenylate cyclase type 5/0.456
1v35NAIEnoyl-ACP reductase/0.456
3cisATPUniversal stress protein Rv2623/0.456
3drcMTXDihydrofolate reductase1.5.1.30.456
3w8wFADPutative FAD-dependent oxygenase EncM/0.456
1k6vXN2Gag-Pol polyprotein3.4.23.160.455
1nzdUPGDNA beta-glucosyltransferase/0.455
1t2bCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.455
1uu9BI33-phosphoinositide-dependent protein kinase 12.7.11.10.455
2eklNADD-3-phosphoglycerate dehydrogenase/0.455
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.455
3dt1P40Mitogen-activated protein kinase 14/0.455
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.455
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.455
4m87NADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.455
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1zrzBI1Protein kinase C iota type2.7.11.130.454
3lsiFADPyranose 2-oxidase/0.454
4gncASORegucalcin3.1.1.170.454
4nm9FADBifunctional protein PutA/0.454
1c70L75Protease/0.453
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.453
1pjkANPCasein kinase II subunit alpha2.7.11.10.453
2feuCAMCamphor 5-monooxygenase1.14.15.10.453
2xfsJ01Uncharacterized protein/0.453
3iaeD7KBenzaldehyde lyase/0.453
3invC50Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.453
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.453
4l4dCAMCamphor 5-monooxygenase1.14.15.10.453
4q71FADBifunctional protein PutA/0.453
4qmwKS1Serine/threonine-protein kinase 242.7.11.10.453
1xddAAYIntegrin alpha-L/0.452
3a1nNADNDP-sugar epimerase/0.452
4k6fNAPPutative Acetoacetyl-CoA reductase/0.452
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4ure1PSCyclohexanol dehydrogenase/0.452
5dhhDGWNociceptin receptor/0.452
1dz4CAMCamphor 5-monooxygenase1.14.15.10.451
1h51FMNPentaerythritol tetranitrate reductase/0.451
1r2jFADFkbI/0.451
3maaFKPAdenylate cyclase type 2/0.451
3maaFKPAdenylate cyclase type 5/0.451
3p62FMNPentaerythritol tetranitrate reductase/0.451
4a99FADTetX family tetracycline inactivation enzyme/0.451
4dpy2P0Mevalonate diphosphate decarboxylase/0.451
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.451
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.451
5fwnNAPPutative dehydrogenase/0.451
1bsvNDPGDP-L-fucose synthase/0.450
1kkq471Peroxisome proliferator-activated receptor alpha/0.450
1tl7FOKAdenylate cyclase type 2/0.450
1tl7FOKAdenylate cyclase type 5/0.450
1u59STUTyrosine-protein kinase ZAP-702.7.10.20.450
2nq8ZIDEnoyl-ACP reductase/0.450
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.450
2qboCAMCamphor 5-monooxygenase1.14.15.10.450
2rqfJH3Hemolymph juvenile hormone binding protein/0.450
2xyuQ9GEphrin type-A receptor 42.7.10.10.450
3g5hYTTMycocyclosin synthase1.14.21.90.450
3koo24DBifunctional epoxide hydrolase 23.3.2.100.450
3wmxNADNAD dependent epimerase/dehydratase/0.450
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
1cs4FOKAdenylate cyclase type 2/0.449
1cs4FOKAdenylate cyclase type 5/0.449
1jioDEB6-deoxyerythronolide B hydroxylase/0.449
1k6cMK1Gag-Pol polyprotein3.4.23.160.449
1y0s331Peroxisome proliferator-activated receptor delta/0.449
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.449
2cgw3C3Serine/threonine-protein kinase Chk12.7.11.10.449
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.449
2qblCAMCamphor 5-monooxygenase1.14.15.10.449
3antS82Bifunctional epoxide hydrolase 23.3.2.100.449
3kb1ADPIron-sulfur cluster carrier protein/0.449
3nr4PYVAbscisic acid receptor PYL2/0.449
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.449
4bb3KKAIsopenicillin N synthase1.21.3.10.449
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.449
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.449
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
4ly91YYGlucokinase regulatory protein/0.449
1u54ACPActivated CDC42 kinase 1/0.448
2gjlFMNNitronate monooxygenase1.13.12.160.448
2qbmCAMCamphor 5-monooxygenase1.14.15.10.448
3f03FMNPentaerythritol tetranitrate reductase/0.448
3gw9VNILanosterol 14-alpha-demethylase/0.448
4iwq1FVSerine/threonine-protein kinase TBK12.7.11.10.448
4lxhC1EAlpha/beta hydrolase fold/0.448
5hs1VORLanosterol 14-alpha demethylase/0.448
1cjuFOKAdenylate cyclase type 2/0.447
1cjuFOKAdenylate cyclase type 5/0.447
1fm4DXCMajor pollen allergen Bet v 1-L/0.447
1iwjCAMCamphor 5-monooxygenase1.14.15.10.447
1zmdNAIDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.447
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.447
2y3sTIRTamL/0.447
2znpK55Peroxisome proliferator-activated receptor delta/0.447
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.447
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
3t3r9PLCytochrome P450 2A61.14.130.447
4bqh9VUUDP-N-acetylglucosamine pyrophosphorylase, putative/0.447
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4cqlNADEstradiol 17-beta-dehydrogenase 81.1.1.620.447
4ktl1CQCytochrome P450/0.447
4oqyNDP(S)-imine reductase/0.447
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.447
1f4fTP3Thymidylate synthase/0.446
1j39UPGDNA beta-glucosyltransferase/0.446
1l8qADPChromosomal replication initiator protein DnaA/0.446
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.446
2znq401Peroxisome proliferator-activated receptor delta/0.446
3eyaTDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.446
3gwfNAPCyclohexanone monooxygenase/0.446
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.446
3sx2NADUncharacterized protein/0.446
3u9eCOALmo1369 protein/0.446
4gl4NAIAlcohol dehydrogenase class-3/0.446
4m4922YL-lactate dehydrogenase A chain1.1.1.270.446
4v2gITCTetracycline repressor protein class D/0.446
1yrdCAMCamphor 5-monooxygenase1.14.15.10.445
2aa3AP0L-lactate dehydrogenase/0.445
2acxANPG protein-coupled receptor kinase 62.7.11.160.445
2nniMTKCytochrome P450 2C8/0.445
2qo9ANPEphrin type-A receptor 32.7.10.10.445
2z97CAMCamphor 5-monooxygenase1.14.15.10.445
3atzFMNProstaglandin F2a synthase/0.445
3lu1NADUDP-N-acetylglucosamine 4-epimerase/0.445
3lxiCAMCytochrome P450/0.445
3p8jFMNPentaerythritol tetranitrate reductase/0.445
3ziaATPATP synthase subunit alpha, mitochondrial/0.445
3zs7ATPPyridoxine/pyridoxal/pyridoxamine kinase/0.445
4ejmNAPPutative zinc-binding dehydrogenase/0.445
4m83ERYOleandomycin glycosyltransferase2.4.10.445
5e8wSTUTGF-beta receptor type-12.7.11.300.445
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
1og5SWFCytochrome P450 2C9/0.444
2a1nCAMCamphor 5-monooxygenase1.14.15.10.444
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.444
3flwFLWMitogen-activated protein kinase 14/0.444
3k4nFADPyranose 2-oxidase/0.444
3nj0PYVAbscisic acid receptor PYL2/0.444
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
4djaFAD(6-4) photolyase/0.444
4gk2L66Ephrin type-A receptor 32.7.10.10.444
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.444
4l4eCAMCamphor 5-monooxygenase1.14.15.10.444
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.444
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.444
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1o76CAMCamphor 5-monooxygenase1.14.15.10.443
1qnfFADDeoxyribodipyrimidine photo-lyase4.1.99.30.443
1ykdCMPAdenylate cyclase/0.443
1zmcNADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.443
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2cig1DGDihydrofolate reductase1.5.1.30.443
2y4gTIRTamL/0.443
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.443
3d8vUD1Bifunctional protein GlmU/0.443
3l63CAMCamphor 5-monooxygenase1.14.15.10.443
3mvqNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.443
3r2b05BMAP kinase-activated protein kinase 22.7.11.10.443
4e2bFMNDehydrogenase/0.443
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.443
4ienCOAPutative acyl-CoA hydrolase/0.443
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.443
4r20AERCytochrome P450 family 17 polypeptide 2/0.443
1dhiMTXDihydrofolate reductase1.5.1.30.442
1g4tFTPThiamine-phosphate synthase/0.442
1jolFFODihydrofolate reductase1.5.1.30.442
1rx1NAPDihydrofolate reductase1.5.1.30.442
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.442
1zk7FADMercuric reductase1.16.1.10.442
2dfvNADL-threonine 3-dehydrogenase/0.442
2drcMTXDihydrofolate reductase1.5.1.30.442
2g1n1IGRenin3.4.23.150.442
2iw94SPCyclin-dependent kinase 22.7.11.220.442
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.442
2x0iNAIMalate dehydrogenase/0.442
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.442
4du82P0Mevalonate diphosphate decarboxylase/0.442
4g7gVFVLanosterol 14-alpha-demethylase/0.442
4hgs15GCasein kinase I isoform gamma-32.7.11.10.442
1dz6CAMCamphor 5-monooxygenase1.14.15.10.441
1v9aSAHUncharacterized protein/0.441
2a1oCAMCamphor 5-monooxygenase1.14.15.10.441
2acwUPGGlycosyltransferase/0.441
2br1PFPSerine/threonine-protein kinase Chk12.7.11.10.441
2hog710Serine/threonine-protein kinase Chk12.7.11.10.441
2rh9IGPTryptophan synthase alpha chain/0.441
2vn0TDZCytochrome P450 2C8/0.441
2vwqNAPGlucose 1-dehydrogenase/0.441
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.441
3dagFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.441
3triNAPPyrroline-5-carboxylate reductase/0.441
5a3bAPRSIR2 family protein/0.441
5dt3ATPAurora kinase A2.7.11.10.441
1fxsNAPGDP-L-fucose synthase/0.440
1nhhANPDNA mismatch repair protein MutL/0.440
2eq6FADDihydrolipoyl dehydrogenase/0.440
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.440
2q5g1FAPeroxisome proliferator-activated receptor delta/0.440
2xpuTDCTetracycline repressor protein class D/0.440
2y3rTRKTamL/0.440
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
3kb6NADD-lactate dehydrogenase/0.440
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.440
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.440
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4a8v2ANMajor pollen allergen Bet v 1-J/0.440
4c9pCAMCytochrome P450/0.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4kwhNAPReductase homolog/0.440
4l8u9AZSerum albumin/0.440
4njoNADD-3-phosphoglycerate dehydrogenase, putative/0.440
4xymCOAAcyl-CoA synthetase (NDP forming)/0.440