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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
5a9sNAPPutative dehydrogenase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
5a9sNAPPutative dehydrogenase/1.000
5fwnNAPPutative dehydrogenase/0.638
2cy0NAPShikimate dehydrogenase (NADP(+))/0.504
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.501
4g7gVFVLanosterol 14-alpha-demethylase/0.497
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.495
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.492
1nvtNAPShikimate dehydrogenase (NADP(+))/0.489
4q71FADBifunctional protein PutA/0.489
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.489
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.488
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.487
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.486
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.484
2vn0TDZCytochrome P450 2C8/0.484
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.483
2znq401Peroxisome proliferator-activated receptor delta/0.482
1bwsNDPGDP-L-fucose synthase/0.481
3lqfNADGalactitol dehydrogenase/0.478
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.477
2rh9IGPTryptophan synthase alpha chain/0.477
1kkq471Peroxisome proliferator-activated receptor alpha/0.476
2uxoTACHTH-type transcriptional regulator TtgR/0.475
5c41ACPRibokinase/0.473
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.472
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.472
4uymVOR14-alpha sterol demethylase Cyp51B/0.472
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.471
1beuIPLTryptophan synthase alpha chain/0.469
1u54ACPActivated CDC42 kinase 1/0.469
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.469
4gavFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.468
4l4eCAMCamphor 5-monooxygenase1.14.15.10.468
1kfbIGPTryptophan synthase alpha chain/0.467
3h3t16HCollagen type IV alpha-3-binding protein/0.467
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.466
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.465
2ev9NAPShikimate dehydrogenase (NADP(+))/0.465
1o9bNAIQuinate/shikimate dehydrogenase/0.464
3ukuC69Actin-related protein 3/0.464
2ohvNHLGlutamate racemase/0.463
3nl6TPSUncharacterized protein/0.463
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.462
1nzdUPGDNA beta-glucosyltransferase/0.461
1xe55FEPlasmepsin-23.4.23.390.461
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
2fy4COACholine O-acetyltransferase2.3.1.60.460
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.460
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.459
1t85CAMCamphor 5-monooxygenase1.14.15.10.459
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.459
2znpK55Peroxisome proliferator-activated receptor delta/0.459
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.458
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.458
3atzFMNProstaglandin F2a synthase/0.458
3fwgCAMCamphor 5-monooxygenase1.14.15.10.458
3kb1ADPIron-sulfur cluster carrier protein/0.458
3oewNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
4g74FADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.458
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.457
3qt62P0Mevalonate diphosphate decarboxylase/0.457
4tuvCPZCytochrome P450 1191.140.457
5hwsNAP2-dehydropantoate 2-reductase/0.457
1ha3MAUElongation factor Tu-A/0.456
1xelUPGUDP-glucose 4-epimerase5.1.3.20.456
2abbFMNPentaerythritol tetranitrate reductase/0.456
2feuCAMCamphor 5-monooxygenase1.14.15.10.456
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.456
3a3gDLZLumazine protein/0.456
3l9hEMQKinesin-like protein KIF11/0.456
4q72FADBifunctional protein PutA/0.456
4v2gITCTetracycline repressor protein class D/0.456
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.456
1k8y13PTryptophan synthase alpha chain/0.455
3h18PMSEsterase/lipase/0.455
3p62FMNPentaerythritol tetranitrate reductase/0.455
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.454
2ejvNADL-threonine 3-dehydrogenase/0.454
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
3gwfNAPCyclohexanone monooxygenase/0.454
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.454
3r6sCMPCRP-like cAMP-activated global transcriptional regulator/0.454
3r9uFADThioredoxin reductase/0.454
3s1dZIRCytokinin dehydrogenase 11.5.99.120.454
4tmbFMNOld yellow enzyme/0.454
1e3eNAIAlcohol dehydrogenase 41.1.1.10.453
2gjlFMNNitronate monooxygenase1.13.12.160.453
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.453
3u9eCOALmo1369 protein/0.453
3wrjCAMCamphor 5-monooxygenase1.14.15.10.453
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.453
4a6bQG8Gag-Pol polyprotein3.4.23.160.453
4g6gFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.453
4zowCLMMultidrug transporter MdfA/0.453
1phePIYCamphor 5-monooxygenase1.14.15.10.452
1xe65FPPlasmepsin-23.4.23.390.452
2ath3EAPeroxisome proliferator-activated receptor gamma/0.452
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
3fwiCAMCamphor 5-monooxygenase1.14.15.10.452
3t4eNADQuinate/shikimate dehydrogenase/0.452
4dfrMTXDihydrofolate reductase1.5.1.30.452
4du82P0Mevalonate diphosphate decarboxylase/0.452
4er6AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.452
1ipeNDPTropinone reductase 21.1.1.2360.451
1jioDEB6-deoxyerythronolide B hydroxylase/0.451
1o76CAMCamphor 5-monooxygenase1.14.15.10.451
1pjcNADAlanine dehydrogenase/0.451
1rfuADPPyridoxal kinase2.7.1.350.451
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
3b895GP16S rRNA methylase/0.451
3fwjCAMCamphor 5-monooxygenase1.14.15.10.451
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.451
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.451
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.451
1t86CAMCamphor 5-monooxygenase1.14.15.10.450
1w6hTITPlasmepsin-23.4.23.390.450
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.450
2he5NDPAldo-keto reductase family 1 member C211.1.10.450
2m56CAMCamphor 5-monooxygenase1.14.15.10.450
2xfsJ01Uncharacterized protein/0.450
2zbaZBATrichothecene 3-O-acetyltransferase/0.450
3t3c017Gag-Pol polyprotein3.4.23.160.450
3wrmCAMCamphor 5-monooxygenase1.14.15.10.450
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.449
1nytNAPShikimate dehydrogenase (NADP(+))/0.449
1yrcCAMCamphor 5-monooxygenase1.14.15.10.449
2iko7IGRenin3.4.23.150.449
2rhgIGPTryptophan synthase alpha chain/0.449
3gwfFADCyclohexanone monooxygenase/0.449
3h3r14HCollagen type IV alpha-3-binding protein/0.449
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.449
3uylTYDProbable NDP-rhamnosyltransferase/0.449
1dirNADDihydropteridine reductase1.5.1.340.448
1m13HYFNuclear receptor subfamily 1 group I member 2/0.448
1rx8NAPDihydrofolate reductase1.5.1.30.448
2d8aNADL-threonine 3-dehydrogenase/0.448
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.448
3a1nNADNDP-sugar epimerase/0.448
3tjzGNPADP-ribosylation factor 1/0.448
4p8rNADGlyceraldehyde-3-phosphate dehydrogenase/0.448
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
6cp4CAMCamphor 5-monooxygenase1.14.15.10.448
1dnpFADDeoxyribodipyrimidine photo-lyase4.1.99.30.447
1gadNADGlyceraldehyde-3-phosphate dehydrogenase A/0.447
1gqtACPRibokinase/0.447
1icpFMN12-oxophytodienoate reductase 11.3.1.420.447
1tqf32PBeta-secretase 13.4.23.460.447
1x8lOXRRetinol dehydratase/0.447
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.447
3fwfCAMCamphor 5-monooxygenase1.14.15.10.447
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.447
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.447
4m9aFDAAcyl-CoA dehydrogenase/0.447
3nglNAPBifunctional protein FolD/0.446
3phiNDPShikimate dehydrogenase (NADP(+))/0.446
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.446
5ftfADPTPR domain protein/0.446
1jolFFODihydrofolate reductase1.5.1.30.445
1nooCAHCamphor 5-monooxygenase1.14.15.10.445
1yrdCAMCamphor 5-monooxygenase1.14.15.10.445
2a1nCAMCamphor 5-monooxygenase1.14.15.10.445
2dftADPShikimate kinase2.7.1.710.445
2dfvNADL-threonine 3-dehydrogenase/0.445
2f1kNAPPrephenate dehydrogenase/0.445
2werRDCATP-dependent molecular chaperone HSP82/0.445
3f03FMNPentaerythritol tetranitrate reductase/0.445
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.445
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.445
4ktl1CQCytochrome P450/0.445
4nbwNADShort-chain dehydrogenase/reductase SDR/0.445
1bsvNDPGDP-L-fucose synthase/0.444
1eupASD6-deoxyerythronolide B hydroxylase/0.444
1h50FMNPentaerythritol tetranitrate reductase/0.444
1k7l544Peroxisome proliferator-activated receptor alpha/0.444
1msmJE2Gag-Pol polyprotein3.4.23.160.444
1t87CAMCamphor 5-monooxygenase1.14.15.10.444
1vi2NADQuinate/shikimate dehydrogenase/0.444
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.444
3b6zCO7Enoyl reductase LovC10.444
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.444
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.444
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.444
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.444
4a83DXCMajor pollen allergen Bet v 1-A/0.444
4r21STRCytochrome P450 family 17 polypeptide 2/0.444
1ddrMTXDihydrofolate reductase1.5.1.30.443
2po7CHDFerrochelatase, mitochondrial4.99.1.10.443
3gobHXXDdmC/0.443
3hwrNDP2-dehydropantoate 2-reductase/0.443
3tz3B36Acetyl-CoA carboxylase/0.443
4g3rCAMCamphor 5-monooxygenase1.14.15.10.443
5cp4CAMCamphor 5-monooxygenase1.14.15.10.443
1dyhDZFDihydrofolate reductase1.5.1.30.442
1e3lNADAlcohol dehydrogenase 41.1.1.10.442
1ep1FMNDihydroorotate dehydrogenase B (NAD(+)), catalytic subunit1.3.1.140.442
1udbUFGUDP-glucose 4-epimerase5.1.3.20.442
3icrFADCoenzyme A disulfide reductase/0.442
3pgqGY3Acetyl-CoA carboxylase/0.442
3r374CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.442
3sx2NADUncharacterized protein/0.442
4ek1CAMCamphor 5-monooxygenase1.14.15.10.442
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.442
4hnc0UTMandelate racemase/0.442
4jqlVJ6Heat shock protein HSP 90-alpha/0.442
4l4fCAMCamphor 5-monooxygenase1.14.15.10.442
4q73FADBifunctional protein PutA/0.442
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.442
1ddsMTXDihydrofolate reductase1.5.1.30.441
1kfcIPLTryptophan synthase alpha chain/0.441
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.441
1tezFADDeoxyribodipyrimidine photo-lyase4.1.99.30.441
1udaUFGUDP-glucose 4-epimerase5.1.3.20.441
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2xa4AZ5Tyrosine-protein kinase JAK2/0.441
3d4pNADL-lactate dehydrogenase 11.1.1.270.441
3il1B5DGlutamate receptor 2/0.441
3tnlNADShikimate dehydrogenase (NADP(+))/0.441
4ejmNAPPutative zinc-binding dehydrogenase/0.441
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.441
1fmlRTLRetinol dehydratase/0.440
1xddAAYIntegrin alpha-L/0.440
1zeoC01Peroxisome proliferator-activated receptor gamma/0.440
2zuiCAMCamphor 5-monooxygenase1.14.15.10.440
3mtwM3RXaa-Pro dipeptidase, putative/0.440
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
3u33FADPutative acyl-CoA dehydrogenase AidB1.3.990.440
3w6hAZMCarbonic anhydrase 14.2.1.10.440
3wrlCAMCamphor 5-monooxygenase1.14.15.10.440
4a99FADTetX family tetracycline inactivation enzyme/0.440
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4jicFMNGTN Reductase/0.440