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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
3il6B833-oxoacyl-[acyl-carrier-protein] synthase 3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3il6B833-oxoacyl-[acyl-carrier-protein] synthase 3/1.000
3il5B823-oxoacyl-[acyl-carrier-protein] synthase 3/0.508
3b9lAZZSerum albumin/0.486
1hnhCOA3-oxoacyl-[acyl-carrier-protein] synthase 3/0.484
3f46I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.483
1t88CAMCamphor 5-monooxygenase1.14.15.10.482
4cd2FOLDihydrofolate reductase1.5.1.30.482
4ejmNAPPutative zinc-binding dehydrogenase/0.479
3csdEMOPutative ketoacyl reductase1.3.10.477
2ylxFADPhenylacetone monooxygenase1.14.13.920.475
3h65I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.473
3ixp834Ecdysone receptor/0.473
1eioGCHGastrotropin/0.472
3dafFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.472
3v1nHPK2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase3.7.1.80.470
3q9zTXQCasein kinase II subunit alpha2.7.11.10.468
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.467
2rqfJH3Hemolymph juvenile hormone binding protein/0.467
5k2dZMAAdenosine receptor A2a/0.467
5kp2COA3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2/0.466
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.465
2idkC2FGlycine N-methyltransferase2.1.1.200.465
5hs1VORLanosterol 14-alpha demethylase/0.465
1cqp803Integrin alpha-L/0.464
1dr5NAPDihydrofolate reductase1.5.1.30.464
1ia1NDPDihydrofolate reductase1.5.1.30.464
2rhrEMOPutative ketoacyl reductase1.3.10.464
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.464
3unj0BXCyclin-dependent kinase 22.7.11.220.464
1pq944BOxysterols receptor LXR-beta/0.463
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.463
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.463
3eksCY9Actin-5C/0.462
2rehFADNitroalkane oxidase1.7.3.10.460
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
3iaeD7KBenzaldehyde lyase/0.460
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
4c717RD3-oxoacyl-ACP synthase/0.460
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.459
2bxmIMNSerum albumin/0.459
2kceD16Thymidylate synthase/0.459
3a9wNADNDP-sugar epimerase/0.459
3ijdC2FMethylenetetrahydrofolate reductase/0.459
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.459
4g1y0VOVitamin D3 receptor A/0.459
4lxhC1EAlpha/beta hydrolase fold/0.459
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.459
4z34ON7Lysophosphatidic acid receptor 1/0.459
1dd6MCIMetallo-beta-lactamase type 2/0.458
1kceCB3Thymidylate synthase/0.458
1phePIYCamphor 5-monooxygenase1.14.15.10.458
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.458
3gy9COAGCN5-related N-acetyltransferase/0.458
3w5hFADNADH-cytochrome b5 reductase 31.6.2.20.458
5jtbZMAAdenosine receptor A2a/0.458
1mvsDTMDihydrofolate reductase1.5.1.30.457
1w4zNAPPutative ketoacyl reductase1.3.10.457
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.457
2zb45OPProstaglandin reductase 21.3.1.480.457
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.457
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.457
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.456
1dr2TAPDihydrofolate reductase1.5.1.30.456
2q9fC3SCholesterol 24-hydroxylase/0.456
2zbaZBATrichothecene 3-O-acetyltransferase/0.456
3gagFMNPutative NADH dehydrogenase NAD(P)H nitroreductase/0.456
3p2oNADBifunctional protein FolD/0.456
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.456
1fvt106Cyclin-dependent kinase 22.7.11.220.455
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.455
3fwgCAMCamphor 5-monooxygenase1.14.15.10.455
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.455
4z9g1Q5Corticotropin-releasing factor receptor 1/0.455
1nooCAHCamphor 5-monooxygenase1.14.15.10.454
2qo9ANPEphrin type-A receptor 32.7.10.10.454
2w1fL0FAurora kinase A2.7.11.10.454
4ruoBIVVitamin D3 receptor A/0.454
1dz6CAMCamphor 5-monooxygenase1.14.15.10.453
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
3gwfFADCyclohexanone monooxygenase/0.453
3pghFLPProstaglandin G/H synthase 21.14.99.10.453
4awo99BHeat shock protein HSP 90-alpha/0.453
4l4xNDPAmphI/0.453
4nmdFDABifunctional protein PutA/0.453
4tvbNADHomospermidine synthase2.5.1.440.453
5dhgDGVNociceptin receptor/0.453
1f123HCHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
1hndCOA3-oxoacyl-[acyl-carrier-protein] synthase 3/0.452
2xviFADPutative flavin-containing monooxygenase/0.452
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.452
3ha5SFGHydroxymycolate synthase MmaA42.1.10.452
3emlZMAAdenosine receptor A2a/0.452
1dkfBMSRetinoic acid receptor alpha/0.451
1n83CLRNuclear receptor ROR-alpha/0.451
1p0hACOMycothiol acetyltransferase2.3.1.1890.451
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
2o4rVD5Vitamin D3 receptor/0.451
3d84NDPDihydrofolate reductase1.5.1.30.451
3dagFEG5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.451
4c58824Cyclin-G-associated kinase2.7.11.10.451
4ktkKTKCytochrome P450/0.451
4xiwAZMCarbonic anhydrase, alpha type/0.451
1ay0TPPTransketolase 12.2.1.10.450
1fmjRTLRetinol dehydratase/0.450
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.450
1x8lOXRRetinol dehydratase/0.450
2imfTOM2-hydroxychromene-2-carboxylate isomerase5.99.1.40.450
2oc9IMHPurine nucleoside phosphorylase2.4.2.10.450
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.450
3nglNAPBifunctional protein FolD/0.450
4enhFVXCholesterol 24-hydroxylase/0.450
4l8u9AZSerum albumin/0.450
4mihFADPyranose 2-oxidase1.1.3.100.450
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.450
1dirNADDihydropteridine reductase1.5.1.340.449
1eblCOA3-oxoacyl-[acyl-carrier-protein] synthase 3/0.449
1tduDURThymidylate synthase/0.449
2ay84TBAromatic-amino-acid aminotransferase2.6.1.570.449
2hcdBIVVitamin D3 receptor A/0.449
2i1vADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.449
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.449
3d4pNADL-lactate dehydrogenase 11.1.1.270.449
3oqkS52Renin3.4.23.150.449
3s1dZIRCytokinin dehydrogenase 11.5.99.120.449
4du82P0Mevalonate diphosphate decarboxylase/0.449
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.449
1kzjCB3Thymidylate synthase/0.448
1osvCHCBile acid receptor/0.448
3orfNADDihydropteridine reductase1.5.1.340.448
3pqbVGPPutative oxidoreductase/0.448
3u9eCOALmo1369 protein/0.448
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.448
4a8v2ANMajor pollen allergen Bet v 1-J/0.448
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.448
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.448
4jqh1MFAlr2278 protein/0.448
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.448
4nb6444Nuclear receptor ROR-gamma/0.448
4tuvCPZCytochrome P450 1191.140.448
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.448
5a3cNADSIR2 family protein/0.448
1hvyD16Thymidylate synthase2.1.1.450.447
2qblCAMCamphor 5-monooxygenase1.14.15.10.447
3of2NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3p62FMNPentaerythritol tetranitrate reductase/0.447
3vruYS3Vitamin D3 receptor/0.447
4acg6LQGlycogen synthase kinase-3 beta2.7.11.260.447
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.447
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.447
3fwjCAMCamphor 5-monooxygenase1.14.15.10.446
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.446
3s79ASDAromatase1.14.14.140.446
4a6bQG8Gag-Pol polyprotein3.4.23.160.446
4er6AW2Histone-lysine N-methyltransferase, H3 lysine-79 specific2.1.1.430.446
1ai9NDPDihydrofolate reductase1.5.1.30.445
1dr3TAPDihydrofolate reductase1.5.1.30.445
1dz8CAMCamphor 5-monooxygenase1.14.15.10.445
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1jq5NADGlycerol dehydrogenase1.1.1.60.445
1ohkCOPDihydrofolate reductase1.5.1.30.445
1xddAAYIntegrin alpha-L/0.445
2xvq9DSSerum albumin/0.445
3drcMTXDihydrofolate reductase1.5.1.30.445
3f47I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.445
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.445
3oeyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3up0D7SaceDAF-12/0.445
4ez8DHFThymidylate synthase2.1.1.450.445
4i6gFADCryptochrome-2/0.445
4iah1DXAlr2278 protein/0.445
5k2bZMAAdenosine receptor A2a/0.445
4k5y1Q5Corticotropin-releasing factor receptor 1/0.445
1dhrNADDihydropteridine reductase1.5.1.340.444
1q4l679Glycogen synthase kinase-3 beta2.7.11.260.444
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2ejvNADL-threonine 3-dehydrogenase/0.444
3lqfNADGalactitol dehydrogenase/0.444
3s7a684Dihydrofolate reductase1.5.1.30.444
4c6zTLE3-oxoacyl-ACP synthase/0.444
4g47TZFMycocyclosin synthase1.14.21.90.444
4ia3BIVVitamin D3 receptor A/0.444
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.444
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.444
5bsgNAPPyrroline-5-carboxylate reductase/0.444
3pwhZMAAdenosine receptor A2a/0.444
1ndzFR5Adenosine deaminase3.5.4.40.443
1pd9CO4Dihydrofolate reductase1.5.1.30.443
2ij7TPFMycocyclosin synthase1.14.21.90.443
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.443
2j14GNIPeroxisome proliferator-activated receptor delta/0.443
3ac1KZITyrosine-protein kinase Lck2.7.10.20.443
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.443
3r354CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.443
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.443
4g48PZBMycocyclosin synthase1.14.21.90.443
4h4yNAPBiphenyl dioxygenase ferredoxin reductase subunit/0.443
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.443
4xwtU5PRibonuclease J/0.443
4xnw2IDP2Y purinoceptor 1/0.443
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.442
1ie9VDXVitamin D3 receptor/0.442
1jpaANPEphrin type-B receptor 22.7.10.10.442
1x2hLPALipoate-protein ligase A6.3.1.200.442
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.442
2hasC3OVitamin D3 receptor/0.442
2ituITQEpidermal growth factor receptor2.7.10.10.442
2z3uCRRCytochrome P450/0.442
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.442
3r7cFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.442
4dtiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4g7gVFVLanosterol 14-alpha-demethylase/0.442
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.442
1f4fTP3Thymidylate synthase/0.441
1o76CAMCamphor 5-monooxygenase1.14.15.10.441
1rd4L08Integrin alpha-L/0.441
1yrdCAMCamphor 5-monooxygenase1.14.15.10.441
2g97DGBNicotinamide phosphoribosyltransferase2.4.2.120.441
2iw84SPCyclin-dependent kinase 22.7.11.220.441
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
2qboCAMCamphor 5-monooxygenase1.14.15.10.441
2z6jTUI2-nitropropane dioxygenase/0.441
3d80Q22Dihydrofolate reductase1.5.1.30.441
3eai328Nitric oxide synthase, inducible1.14.13.390.441
3sdkP3NProteasome subunit beta type-53.4.25.10.441
3sdkP3NProteasome subunit beta type-63.4.25.10.441
4b4oNDPEpimerase family protein SDR39U1/0.441
4n5nNAPAcetoacetyl-CoA reductase1.1.1.360.441
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1ci7UMPThymidylate synthase2.1.1.450.440
1drhNAPDihydrofolate reductase1.5.1.30.440
1nzfUPGDNA beta-glucosyltransferase/0.440
1pq6965Oxysterols receptor LXR-beta/0.440
1rx1NAPDihydrofolate reductase1.5.1.30.440
2abbFMNPentaerythritol tetranitrate reductase/0.440
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.440
2ylrFADPhenylacetone monooxygenase1.14.13.920.440
2ylzFADPhenylacetone monooxygenase1.14.13.920.440
2znpK55Peroxisome proliferator-activated receptor delta/0.440
3ibqATPPyridoxal kinase/0.440
3kjm245Cytokinin dehydrogenase 11.5.99.120.440
3oom507Activin receptor type-12.7.11.300.440
3r3b4CO4-hydroxybenzoyl-CoA thioesterase3.1.2.230.440
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
5cvhADPCasein kinase II subunit alpha2.7.11.10.440