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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
4rrrA3TThreonine--tRNA ligase6.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4rrrA3TThreonine--tRNA ligase6.1.1.31.000
3pd2A3SThreonine--tRNA ligase6.1.1.30.555
3pd4A3GThreonine--tRNA ligase6.1.1.30.534
3pd3A3TThreonine--tRNA ligase6.1.1.30.532
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.509
4rrgA3TThreonine--tRNA ligase6.1.1.30.502
3s1dZIRCytokinin dehydrogenase 11.5.99.120.501
2hl1A3SThreonine--tRNA ligase6.1.1.30.496
3pd5TSBThreonine--tRNA ligase6.1.1.30.493
4rrqA3SThreonine--tRNA ligase6.1.1.30.492
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.488
1dhrNADDihydropteridine reductase1.5.1.340.485
2cnsACORibosomal-protein-alanine acetyltransferase/0.483
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.483
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.482
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.481
3bbrBHYGlutamate receptor 2/0.480
4fpy0V8Sialidase B3.2.1.180.477
3ha5SFGHydroxymycolate synthase MmaA42.1.10.476
4a86H35Major pollen allergen Bet v 1-A/0.476
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.474
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.474
1xddAAYIntegrin alpha-L/0.472
3q43D66M1 family aminopeptidase3.4.110.472
4a862ANMajor pollen allergen Bet v 1-A/0.472
1vyrFMNPentaerythritol tetranitrate reductase/0.471
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.471
3v2uATPProtein GAL3/0.471
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.470
2xfsJ01Uncharacterized protein/0.469
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.469
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.468
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.468
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.468
1rj6AZMCarbonic anhydrase 144.2.1.10.468
2zbaZBATrichothecene 3-O-acetyltransferase/0.468
3atyFMNProstaglandin F2a synthase/0.468
3oqkS52Renin3.4.23.150.468
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.468
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.468
1a59COA2-methylcitrate synthase/0.467
1dirNADDihydropteridine reductase1.5.1.340.467
4i6gFADCryptochrome-2/0.467
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.466
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.466
3fktSIIBeta-secretase 13.4.23.460.465
3h3t16HCollagen type IV alpha-3-binding protein/0.465
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.465
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.465
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.464
2ejvNADL-threonine 3-dehydrogenase/0.464
2hl0A3SThreonine--tRNA ligase6.1.1.30.464
2hl2SSAThreonine--tRNA ligase6.1.1.30.464
3imgBZ2Pantothenate synthetase6.3.2.10.464
4klaCHDFerrochelatase, mitochondrial4.99.1.10.464
1bwsNDPGDP-L-fucose synthase/0.463
3g70A5TRenin3.4.23.150.463
2g8yNADHydroxycarboxylate dehydrogenase B/0.462
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.462
2uxoTACHTH-type transcriptional regulator TtgR/0.462
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.462
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.462
4a8v2ANMajor pollen allergen Bet v 1-J/0.462
4m9aFDAAcyl-CoA dehydrogenase/0.462
1h50FMNPentaerythritol tetranitrate reductase/0.461
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.461
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.461
4ejh0QACytochrome P450 2A131.14.14.10.461
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.460
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
1fmlRTLRetinol dehydratase/0.460
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.459
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.459
3i0pNADMalate dehydrogenase, putative/0.459
3lqfNADGalactitol dehydrogenase/0.459
3tqxPLP2-amino-3-ketobutyrate coenzyme A ligase/0.459
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.459
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.459
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
4rrfA3SThreonine--tRNA ligase6.1.1.30.459
2cgx3D3Serine/threonine-protein kinase Chk12.7.11.10.458
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3h3r14HCollagen type IV alpha-3-binding protein/0.458
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.458
4enhFVXCholesterol 24-hydroxylase/0.458
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.458
1w6hTITPlasmepsin-23.4.23.390.457
1bxoPP7Penicillopepsin-13.4.23.200.456
1qoqIGPTryptophan synthase alpha chain/0.456
2om9AJAPeroxisome proliferator-activated receptor gamma/0.456
2znq401Peroxisome proliferator-activated receptor delta/0.456
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3f63GTXGlutathione transferase GST1-4/0.456
3hllI45Mitogen-activated protein kinase 14/0.456
3qt62P0Mevalonate diphosphate decarboxylase/0.456
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.456
1bwlFMNNADPH dehydrogenase 11.6.99.10.455
1i59ANPChemotaxis protein CheA2.7.13.30.455
1lf3EH5Plasmepsin-23.4.23.390.455
3gggNADPrephenate dehydrogenase/0.455
3iodA6DPantothenate synthetase6.3.2.10.455
3pl8FADPyranose 2-oxidase/0.455
3pqbVGPPutative oxidoreductase/0.455
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.455
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.455
1c9wNAPAldose reductase-related protein 2/0.454
1x1aSAMC-20 methyltransferase/0.454
2dvlFADAcyl-CoA dehydrogenase/0.454
3qlsNDPDihydrofolate reductase1.5.1.30.454
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.454
4r81FMNPredicted NADH dehydrogenase/0.454
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.453
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.453
4eji0QACytochrome P450 2A131.14.14.10.453
4yryFADGlutamate synthase, beta subunit/0.453
5irnADPNucleotide binding oligomerization domain containing 2/0.453
1v35NAIEnoyl-ACP reductase/0.452
2gv8NDPThiol-specific monooxygenase1.14.130.452
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3gfbNADL-threonine 3-dehydrogenase/0.452
3lzxNAPFerredoxin--NADP reductase 21.18.1.20.452
3nxxNDPDihydrofolate reductase1.5.1.30.452
3qlrNDPDihydrofolate reductase1.5.1.30.452
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.452
4a83DXCMajor pollen allergen Bet v 1-A/0.452
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.452
4r1lADPPhenylacetate-coenzyme A ligase/0.452
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.451
1q23FUAChloramphenicol acetyltransferase2.3.1.280.451
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.451
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.451
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.451
2yxuATPPyridoxal kinase2.7.1.350.451
4g95OAGDihydrofolate reductase1.5.1.30.451
1e3eNAIAlcohol dehydrogenase 41.1.1.10.450
1jd0AZMCarbonic anhydrase 124.2.1.10.450
1k7l544Peroxisome proliferator-activated receptor alpha/0.450
1m78NDPDihydrofolate reductase1.5.1.30.450
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.450
1nzdUPGDNA beta-glucosyltransferase/0.450
1rfuADPPyridoxal kinase2.7.1.350.450
1rszDIHPurine nucleoside phosphorylase2.4.2.10.450
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.450
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.450
2xviFADPutative flavin-containing monooxygenase/0.450
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.450
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.450
3eigMTXDihydrofolate reductase1.5.1.30.450
3kb1ADPIron-sulfur cluster carrier protein/0.450
3lzwNAPFerredoxin--NADP reductase 21.18.1.20.450
3own3OWRenin3.4.23.150.450
3tneRITCandidapepsin-13.4.23.240.450
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
5dp2NAPCurF/0.450
1h51FMNPentaerythritol tetranitrate reductase/0.449
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1lbcCYZGlutamate receptor 2/0.449
2bbwGP5Adenylate kinase 4, mitochondrial/0.449
2nniMTKCytochrome P450 2C8/0.449
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.449
2rqfJH3Hemolymph juvenile hormone binding protein/0.449
3t3q9PLCytochrome P450 2A61.14.130.449
4a28ADPKinesin-like protein KIF11/0.449
4bfuZVUPantothenate kinase2.7.1.330.449
4f7iNAD3-isopropylmalate dehydrogenase1.1.1.850.449
4jtqNAPAldo-keto reductase family 1 member C2/0.449
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.449
4yafFADNADPH--cytochrome P450 reductase/0.449
1lp4ANPCasein kinase II subunit alpha2.7.11.10.448
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.448
1o9bNAIQuinate/shikimate dehydrogenase/0.448
1qrpHH0Pepsin A-43.4.23.10.448
2g1s4IGRenin3.4.23.150.448
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3own3OXRenin3.4.23.150.448
3r7kFDAProbable acyl CoA dehydrogenase/0.448
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.448
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.448
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.447
1ia1NDPDihydrofolate reductase1.5.1.30.447
1iidNHMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.447
1vbiNADMalate/L-lactate dehydrogenase family protein/0.447
2d29FADAcyl-CoA dehydrogenase/0.447
3d84NDPDihydrofolate reductase1.5.1.30.447
3oadLPORenin3.4.23.150.447
3oqfS51Renin3.4.23.150.447
4lfiGNPCasein kinase II subunit alpha2.7.11.10.447
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.447
4ure1PSCyclohexanol dehydrogenase/0.447
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.446
1jumBERHTH-type transcriptional regulator QacR/0.446
1jvsNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.446
1ra3MTXDihydrofolate reductase1.5.1.30.446
1wuuANPGalactokinase2.7.1.60.446
2g5w8PG12-oxophytodienoate reductase 31.3.1.420.446
3pm1ETHTH-type transcriptional regulator QacR/0.446
3sp9IL2Peroxisome proliferator-activated receptor delta/0.446
4e2dFMNDehydrogenase/0.446
4f97VDOPutative glycosyltransferase/0.446
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.446
4x5gFOLDihydrofolate reductase1.5.1.30.446
1ndzFR5Adenosine deaminase3.5.4.40.445
1nvtNAPShikimate dehydrogenase (NADP(+))/0.445
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.445
1x1dSAHC-20 methyltransferase/0.445
1y0s331Peroxisome proliferator-activated receptor delta/0.445
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.445
2wjoQUDBeta-secretase 13.4.23.460.445
3nz4TCAPhenylalanine aminomutase (L-beta-phenylalanine forming)/0.445
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.445
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.445
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.445
1gthFADDihydropyrimidine dehydrogenase [NADP(+)]1.3.1.20.444
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.444
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.444
2vr1ATFBiotin carboxylase6.3.4.140.444
2vttLZDCyclin-dependent kinase 22.7.11.220.444
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.444
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3imgBZ3Pantothenate synthetase6.3.2.10.444
3oafOAGDihydrofolate reductase1.5.1.30.444
3orfNADDihydropteridine reductase1.5.1.340.444
3otwCOAPhosphopantetheine adenylyltransferase/0.444
3w8eNAD3-hydroxybutyrate dehydrogenase/0.444
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.444
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.444
5ebuFMNLactate oxidase/0.444
5itzLOCTubulin beta-2B chain/0.444
1beuIPLTryptophan synthase alpha chain/0.443
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.443
1j49NADD-lactate dehydrogenase1.1.1.280.443
1jpaANPEphrin type-B receptor 22.7.10.10.443
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2ev9NAPShikimate dehydrogenase (NADP(+))/0.443
2fk8SAMHydroxymycolate synthase MmaA42.1.10.443
2g226IGRenin3.4.23.150.443
2gjlFMNNitronate monooxygenase1.13.12.160.443
2ikuLIYRenin3.4.23.150.443
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.443
3h6vNS6Glutamate receptor 2/0.443
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.443
3nl6TPSUncharacterized protein/0.443
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.443
4a32MYAGlycylpeptide N-tetradecanoyltransferase/0.443
4y7cFADNADPH--cytochrome P450 reductase/0.443
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
1ai9NDPDihydrofolate reductase1.5.1.30.442
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.442
1o76CAMCamphor 5-monooxygenase1.14.15.10.442
1pdhFASp-hydroxybenzoate hydroxylase/0.442
2b7aIZATyrosine-protein kinase JAK2/0.442
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.442
2trtTACTetracycline repressor protein class D/0.442
2v9jATP5'-AMP-activated protein kinase subunit gamma-1/0.442
2xhd7T9Glutamate receptor 2/0.442
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.442
3bw4FMNPutative 2-nitropropane dioxygenase/0.442
3il1B5DGlutamate receptor 2/0.442
3iqhTYR_ASP_ILECysteine synthase2.5.1.470.442
3ivcFG4Pantothenate synthetase6.3.2.10.442
3ziuLSSLeucyl-tRNA synthetase/0.442
3zuyTCHTransporter/0.442
4dgnLU2Casein kinase II subunit alpha2.7.11.10.442
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.442
4qi9MTXDihydrofolate reductase/0.442
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.442
1f0xFADD-lactate dehydrogenase1.1.1.280.441
1h62ANBPentaerythritol tetranitrate reductase/0.441
2wedPP6Penicillopepsin-13.4.23.200.441
3ov7ATPCCA-adding enzyme2.7.7.720.441
3tjzGNPADP-ribosylation factor 1/0.441
3v0p4GWHisto-blood group ABO system transferase/0.441
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.441
4lxhC1EAlpha/beta hydrolase fold/0.441
4q71FADBifunctional protein PutA/0.441
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.441
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
5eccNAPDehydrofolate reductase type I/0.441
1bw9NADPhenylalanine dehydrogenase/0.440
1bxqPP8Penicillopepsin-13.4.23.200.440
1h73ANPHomoserine kinase2.7.1.390.440
2g1r3IGRenin3.4.23.150.440
2j2pSC2Ficolin-2/0.440
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.440
3ie3N11Glutathione S-transferase P2.5.1.180.440
3lnbCOAN-acetyltransferase family protein/0.440
3ooiSAMHistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific2.1.1.430.440
3rvhHQ2Lysine-specific demethylase 4A1.14.110.440
3t3r9PLCytochrome P450 2A61.14.130.440
3x2vATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.440
4b68NAPL-ornithine N(5)-monooxygenase/0.440
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440