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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
3pd2A3SThreonine--tRNA ligase6.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3pd2A3SThreonine--tRNA ligase6.1.1.31.000
3pd3A3TThreonine--tRNA ligase6.1.1.30.620
4rrrA3TThreonine--tRNA ligase6.1.1.30.613
3pd4A3GThreonine--tRNA ligase6.1.1.30.585
2hl1A3SThreonine--tRNA ligase6.1.1.30.581
3pd5TSBThreonine--tRNA ligase6.1.1.30.574
4rrqA3SThreonine--tRNA ligase6.1.1.30.569
2hl2SSAThreonine--tRNA ligase6.1.1.30.564
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.563
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.560
2hl0A3SThreonine--tRNA ligase6.1.1.30.558
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.555
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.549
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.543
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.539
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.525
4rrgA3TThreonine--tRNA ligase6.1.1.30.524
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.521
4rrfA3SThreonine--tRNA ligase6.1.1.30.504
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.503
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.493
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.485
4b8wNAPGDP-L-fucose synthase1.1.1.2710.484
4b8zNAPGDP-L-fucose synthase1.1.1.2710.484
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.483
1bwsNDPGDP-L-fucose synthase/0.482
3q43D66M1 family aminopeptidase3.4.110.482
2znq401Peroxisome proliferator-activated receptor delta/0.481
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.479
3ns2PYVAbscisic acid receptor PYL2/0.477
3t7x4SHEndothiapepsin3.4.23.220.477
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.477
3pbzF02Endothiapepsin3.4.23.220.475
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.475
5eccNAPDehydrofolate reductase type I/0.475
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.472
1u54ACPActivated CDC42 kinase 1/0.471
2yxuATPPyridoxal kinase2.7.1.350.470
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.470
2qo9ANPEphrin type-A receptor 32.7.10.10.469
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.469
4rrcA3TProbable threonine--tRNA ligase 26.1.1.30.469
2hckQUETyrosine-protein kinase HCK2.7.10.20.468
3a4pDFQHepatocyte growth factor receptor2.7.10.10.468
3nr4PYVAbscisic acid receptor PYL2/0.468
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.468
4qmySTUSerine/threonine-protein kinase 242.7.11.10.468
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.467
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.467
3nj0PYVAbscisic acid receptor PYL2/0.467
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.467
1zrzBI1Protein kinase C iota type2.7.11.130.466
3a60STURibosomal protein S6 kinase beta-12.7.11.10.465
1ai9NDPDihydrofolate reductase1.5.1.30.464
1bxoPP7Penicillopepsin-13.4.23.200.464
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.464
3a783EVVitamin D3 receptor/0.464
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
1s19MC9Vitamin D3 receptor/0.462
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.462
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.462
4c02TAKActivin receptor type-12.7.11.300.462
1jvsNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.461
3bbrBHYGlutamate receptor 2/0.461
3qf9NM8Serine/threonine-protein kinase pim-12.7.11.10.461
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.461
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.460
3q9wEMOCasein kinase II subunit alpha2.7.11.10.460
3qt62P0Mevalonate diphosphate decarboxylase/0.460
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.459
1y0s331Peroxisome proliferator-activated receptor delta/0.459
4l445FIRibosomal protein S6 kinase beta-12.7.11.10.459
5e8wSTUTGF-beta receptor type-12.7.11.300.459
1rfvADPPyridoxal kinase2.7.1.350.458
3u9n09HSerine/threonine-protein kinase Chk12.7.11.10.458
3w0yDS4Vitamin D3 receptor/0.458
1hquHBYGag-Pol polyprotein2.7.7.490.457
1kquBR4Phospholipase A2, membrane associated/0.457
2w9hTOPDihydrofolate reductase1.5.1.30.457
2zbaZBATrichothecene 3-O-acetyltransferase/0.457
3we45FIRibosomal protein S6 kinase beta-12.7.11.10.457
4bieIE6Mitogen-activated protein kinase kinase kinase 52.7.11.250.457
4gu610NFocal adhesion kinase 12.7.10.20.457
4ivd15TTyrosine-protein kinase JAK1/0.457
3a4vNADNDP-sugar epimerase/0.456
3mtfA3FActivin receptor type-12.7.11.300.456
3pi0F91Endothiapepsin3.4.23.220.456
4fob0USALK tyrosine kinase receptor2.7.10.10.456
1ci7UMPThymidylate synthase2.1.1.450.455
2p5uNADUDP-glucose 4-epimerase/0.455
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
4la7A1OAbscisic acid receptor PYL2/0.455
1rfuADPPyridoxal kinase2.7.1.350.454
2ojg19AMitogen-activated protein kinase 12.7.11.240.454
3gqvNAPEnoyl reductase LovC10.454
3gwfFADCyclohexanone monooxygenase/0.454
3rfxNADUronate dehydrogenase/0.454
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4fod0UVALK tyrosine kinase receptor2.7.10.10.454
4gk3L87Ephrin type-A receptor 32.7.10.10.454
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1xddAAYIntegrin alpha-L/0.453
1yw2PGJMitogen-activated protein kinase 14/0.453
2balPQAMitogen-activated protein kinase 14/0.453
2hamC33Vitamin D3 receptor/0.453
2wxvWXVCyclin-dependent kinase 22.7.11.220.453
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.453
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.453
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.453
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.453
4gk2L66Ephrin type-A receptor 32.7.10.10.453
5e8xSTUTGF-beta receptor type-12.7.11.300.453
1ay0TPPTransketolase 12.2.1.10.452
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.452
1yi4ADNSerine/threonine-protein kinase pim-12.7.11.10.452
2an9GDPGuanylate kinase2.7.4.80.452
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.452
4u0mGTPCyclic GMP-AMP synthase/0.452
5dp2NAPCurF/0.452
4xnw2IDP2Y purinoceptor 1/0.452
1eh4IC1Casein kinase I homolog 12.7.11.10.451
2y99NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.451
3h3r14HCollagen type IV alpha-3-binding protein/0.451
3hztJ60Calmodulin-like domain protein kinase isoform 3/0.451
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.451
4ewqMWLMitogen-activated protein kinase 14/0.451
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
2xj2985Serine/threonine-protein kinase pim-12.7.11.10.450
3cy2MB9Serine/threonine-protein kinase pim-12.7.11.10.450
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.450
1bsvNDPGDP-L-fucose synthase/0.449
1me6IVSPlasmepsin-23.4.23.390.449
1o9bNAIQuinate/shikimate dehydrogenase/0.449
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.449
2a94AP0L-lactate dehydrogenase1.1.1.270.449
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.449
2o65MYFSerine/threonine-protein kinase pim-12.7.11.10.449
2qblCAMCamphor 5-monooxygenase1.14.15.10.449
2wgjVGHHepatocyte growth factor receptor2.7.10.10.449
3hllI45Mitogen-activated protein kinase 14/0.449
3ibqATPPyridoxal kinase/0.449
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.449
4gg70J8Hepatocyte growth factor receptor2.7.10.10.449
4gllNADUDP-glucuronic acid decarboxylase 14.1.1.350.449
4rqkATP3-phosphoinositide-dependent protein kinase 12.7.11.10.449
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.449
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.448
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.448
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.448
2ituITQEpidermal growth factor receptor2.7.10.10.448
2ojj82AMitogen-activated protein kinase 12.7.11.240.448
2x8eX8ESerine/threonine-protein kinase Chk12.7.11.10.448
3h3sH15Collagen type IV alpha-3-binding protein/0.448
3vw6IM6Mitogen-activated protein kinase kinase kinase 52.7.11.250.448
3zlx5EZDual specificity mitogen-activated protein kinase kinase 12.7.12.20.448
4gmy0X5Tyrosine-protein kinase JAK2/0.448
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.448
1bim0QBRenin3.4.23.150.447
3ggfGVDSerine/threonine-protein kinase 26/0.447
3lqfNADGalactitol dehydrogenase/0.447
4anwO92Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4f650S9Fibroblast growth factor receptor 1/0.447
4iteTEYVitamin D3 receptor/0.447
4nmcFADBifunctional protein PutA/0.447
4y3zF41Endothiapepsin3.4.23.220.447
1fwkADPHomoserine kinase2.7.1.390.446
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1sreHABStreptavidin/0.446
1vyw292Cyclin-dependent kinase 22.7.11.220.446
2drcMTXDihydrofolate reductase1.5.1.30.446
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.446
2iebZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
2itqITQEpidermal growth factor receptor2.7.10.10.446
3bhtMFRCyclin-dependent kinase 22.7.11.220.446
3eyhIZATyrosine-protein kinase JAK1/0.446
3vt7VDXVitamin D3 receptor/0.446
4bgg844Activin receptor type-12.7.11.300.446
4dfrMTXDihydrofolate reductase1.5.1.30.446
4hgs15GCasein kinase I isoform gamma-32.7.11.10.446
4ng2OHNTranscriptional activator protein LasR/0.446
4zlaBESCytosol aminopeptidase3.4.11.10.446
5im3DTPRibonucleoside-diphosphate reductase/0.446
3sn6P0GBeta-2 adrenergic receptor/0.446
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.445
2rg6287Mitogen-activated protein kinase 14/0.445
2wmqZYQSerine/threonine-protein kinase Chk12.7.11.10.445
3drcMTXDihydrofolate reductase1.5.1.30.445
3rdqDTBStreptavidin/0.445
4c36ZO9cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
4m4821BSodium-dependent dopamine transporter/0.445
4mwhATPCasein kinase II subunit alpha2.7.11.10.445
4n702HXSerine/threonine-protein kinase pim-12.7.11.10.445
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.444
1gvv0GMEndothiapepsin3.4.23.220.444
2b7aIZATyrosine-protein kinase JAK2/0.444
2brhDFWSerine/threonine-protein kinase Chk12.7.11.10.444
2cy0NAPShikimate dehydrogenase (NADP(+))/0.444
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.444
2ieaTDPPyruvate dehydrogenase E1 component1.2.4.10.444
2znpK55Peroxisome proliferator-activated receptor delta/0.444
3i81EBIInsulin-like growth factor 1 receptor2.7.10.10.444
3r2b05BMAP kinase-activated protein kinase 22.7.11.10.444
4blcNDPCatalase1.11.1.60.444
4hjoAQ4Epidermal growth factor receptor2.7.10.10.444
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.444
1dirNADDihydropteridine reductase1.5.1.340.443
1g1aNADdTDP-glucose 4,6-dehydratase/0.443
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.443
1jmhUMPThymidylate synthase/0.443
1ppjANYCytochrome b/0.443
1u4dDBQActivated CDC42 kinase 1/0.443
1udaUFGUDP-glucose 4-epimerase5.1.3.20.443
2abi1CAMineralocorticoid receptor/0.443
2om9AJAPeroxisome proliferator-activated receptor gamma/0.443
2vttLZDCyclin-dependent kinase 22.7.11.220.443
3hrcATP3-phosphoinositide-dependent protein kinase 12.7.11.10.443
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3s1dZIRCytokinin dehydrogenase 11.5.99.120.443
4enhFVXCholesterol 24-hydroxylase/0.443
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4zeaIMIEndothiapepsin3.4.23.220.443
5c8d5ADProbable transcriptional regulator/0.443
4zj8SUVOrexin receptor type 1/0.443
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1hvyD16Thymidylate synthase2.1.1.450.442
1nzfUPGDNA beta-glucosyltransferase/0.442
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
2brmDFZSerine/threonine-protein kinase Chk12.7.11.10.442
2cgx3D3Serine/threonine-protein kinase Chk12.7.11.10.442
2ejvNADL-threonine 3-dehydrogenase/0.442
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.442
2he5NDPAldo-keto reductase family 1 member C211.1.10.442
2op18PCEnoyl-ACP reductase/0.442
3qj5022Alcohol dehydrogenase class-31.1.1.10.442
3sp9IL2Peroxisome proliferator-activated receptor delta/0.442
4bfuZVUPantothenate kinase2.7.1.330.442
4bfvZVVPantothenate kinase2.7.1.330.442
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.442
4oztP1AEcdysone receptor, putative/0.442
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.442
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1fxsNAPGDP-L-fucose synthase/0.441
1t2cNAIL-lactate dehydrogenase1.1.1.270.441
2c3iIYZSerine/threonine-protein kinase pim-12.7.11.10.441
2jjj0QSEndothiapepsin3.4.23.220.441
2ohvNHLGlutamate racemase/0.441
2xikJ60Serine/threonine-protein kinase 252.7.11.10.441
3cgdCOACoenzyme A disulfide reductase/0.441
3p62FMNPentaerythritol tetranitrate reductase/0.441
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3vt9YI4Vitamin D3 receptor/0.441
4a9hTVPBromodomain-containing protein 2/0.441
4dymIYZActivin receptor type-12.7.11.300.441
4fi1ATPCasein kinase II subunit alpha2.7.11.10.441
1cbfSAHCobalt-precorrin-4 C(11)-methyltransferase2.1.1.2710.440
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.440
1n3rGTPGTP cyclohydrolase 13.5.4.160.440
1pjkANPCasein kinase II subunit alpha2.7.11.10.440
1rx1NAPDihydrofolate reductase1.5.1.30.440
1u4oNDDL-lactate dehydrogenase1.1.1.270.440
1y4sADPChaperone protein HtpG/0.440
2gjnFMNNitronate monooxygenase1.13.12.160.440
2j2iLY4Serine/threonine-protein kinase pim-12.7.11.10.440
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.440
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.440
2xuuADPDeath-associated protein kinase 12.7.11.10.440
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.440
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.440
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3qlsNDPDihydrofolate reductase1.5.1.30.440
3vs7KS1Tyrosine-protein kinase HCK2.7.10.20.440
3wqmB29Diterpene synthase3.1.7.80.440
3zewSTUEphrin type-B receptor 42.7.10.10.440
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
4cdmFO1Deoxyribodipyrimidine photolyase/0.440
4gii0X6Non-receptor tyrosine-protein kinase TYK22.7.10.20.440
4kne1CYDihydrofolate reductase1.5.1.30.440
4ockANPN-acetylhexosamine 1-kinase2.7.1.1620.440
4ure1PSCyclohexanol dehydrogenase/0.440
5a3cNADSIR2 family protein/0.440
5adhAPRAlcohol dehydrogenase E chain1.1.1.10.440