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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
2hl0A3SThreonine--tRNA ligase6.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2hl0A3SThreonine--tRNA ligase6.1.1.31.000
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.589
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.569
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.550
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.550
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.549
3pd2A3SThreonine--tRNA ligase6.1.1.30.548
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.548
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.547
4rrqA3SThreonine--tRNA ligase6.1.1.30.546
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.545
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.542
2hl1A3SThreonine--tRNA ligase6.1.1.30.535
3pd3A3TThreonine--tRNA ligase6.1.1.30.532
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.529
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.524
4rrcA3TProbable threonine--tRNA ligase 26.1.1.30.519
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.512
4rrrA3TThreonine--tRNA ligase6.1.1.30.504
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.495
4i6gFADCryptochrome-2/0.490
3pd4A3GThreonine--tRNA ligase6.1.1.30.489
3vt8YI3Vitamin D3 receptor/0.485
4rrgA3TThreonine--tRNA ligase6.1.1.30.485
4g1z0VPVitamin D3 receptor A/0.484
2hl2SSAThreonine--tRNA ligase6.1.1.30.480
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.480
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.480
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.480
4iteTEYVitamin D3 receptor/0.479
1fmjRTLRetinol dehydratase/0.476
2o4rVD5Vitamin D3 receptor/0.473
2g1n1IGRenin3.4.23.150.472
2g1s4IGRenin3.4.23.150.472
3vt5YI2Vitamin D3 receptor/0.472
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.471
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.471
3a783EVVitamin D3 receptor/0.470
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.469
3vt45YIVitamin D3 receptor/0.469
3p62FMNPentaerythritol tetranitrate reductase/0.467
3pd5TSBThreonine--tRNA ligase6.1.1.30.467
3vrvYSDVitamin D3 receptor/0.467
3w0hW12Vitamin D3 receptor/0.467
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.466
3jpuTY4Transcriptional activator protein LasR/0.465
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.465
3rbqGLY_ALA_GLY_ALA_DAOProtein unc-119 homolog A/0.465
4jbsP52Endoplasmic reticulum aminopeptidase 23.4.110.465
3w0jT08Vitamin D3 receptor/0.464
1vyrFMNPentaerythritol tetranitrate reductase/0.463
2zl9VDAVitamin D3 receptor/0.463
3gfbNADL-threonine 3-dehydrogenase/0.463
4fhi0S4Vitamin D3 receptor A/0.463
1txiTX5Vitamin D3 receptor/0.462
1ykdCMPAdenylate cyclase/0.462
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.462
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.462
4qzuRTLRetinol-binding protein 2/0.462
1s19MC9Vitamin D3 receptor/0.461
3ey9TDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.461
4ead0NPThymidine phosphorylase2.4.2.40.461
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.461
5kgpACOPredicted acetyltransferase/0.461
1crbRTLRetinol-binding protein 1/0.460
1ppjANYCytochrome b/0.460
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.460
3f03FMNPentaerythritol tetranitrate reductase/0.460
3kpzZNEVitamin D3 receptor/0.460
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
1xddAAYIntegrin alpha-L/0.459
2uxoTACHTH-type transcriptional regulator TtgR/0.459
4enhFVXCholesterol 24-hydroxylase/0.459
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.459
1h50FMNPentaerythritol tetranitrate reductase/0.458
1h63FMNPentaerythritol tetranitrate reductase/0.458
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.458
2po7CHDFerrochelatase, mitochondrial4.99.1.10.458
4ia7BIVVitamin D3 receptor A/0.458
1ie9VDXVitamin D3 receptor/0.457
1kqwRTLCellular retinol-binding protein type II/0.457
3ha5SFGHydroxymycolate synthase MmaA42.1.10.457
3w0gW07Vitamin D3 receptor/0.457
4g090VDHistidinol dehydrogenase/0.457
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.457
1g6kNADGlucose 1-dehydrogenase1.1.1.470.456
2mm3CHOGastrotropin/0.456
2wd9IBPAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.456
3fhxPLPPyridoxal kinase2.7.1.350.456
3mdvCL6Cholesterol 24-hydroxylase/0.456
4fki09KCyclin-dependent kinase 22.7.11.220.456
1bwsNDPGDP-L-fucose synthase/0.455
1fmlRTLRetinol dehydratase/0.455
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.455
2gv8NDPThiol-specific monooxygenase1.14.130.455
3dr1C5DVitamin D3 receptor A/0.455
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.455
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.455
1rkhVD2Vitamin D3 receptor/0.454
3dufR1TPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.454
3dufR1TPyruvate dehydrogenase E1 component subunit beta1.2.4.10.454
3hl0NADMaleylacetate reductase/0.454
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4xymCOAAcyl-CoA synthetase (NDP forming)/0.454
5ajqDB8Serine/threonine-protein kinase 102.7.11.10.454
1bwkFMNNADPH dehydrogenase 11.6.99.10.453
1osvCHCBile acid receptor/0.453
2lbaCHOFatty acid binding protein 6/0.453
3gy9COAGCN5-related N-acetyltransferase/0.453
4fhh0U3Vitamin D3 receptor A/0.453
4ia3BIVVitamin D3 receptor A/0.453
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1owpFADDeoxyribodipyrimidine photo-lyase4.1.99.30.452
2hcdBIVVitamin D3 receptor A/0.452
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
3vrwYS5Vitamin D3 receptor/0.452
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.452
3w0yDS4Vitamin D3 receptor/0.452
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
1s5kCOAAminoglycoside N(6')-acetyltransferase type 1/0.451
1x1bSAHC-20 methyltransferase/0.451
2fpcSCGStrictosidine synthase4.3.3.20.451
2hc4VDXVitamin D3 receptor A/0.451
2q9fC3SCholesterol 24-hydroxylase/0.451
2xh9J01Uncharacterized protein/0.451
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3vswR31Renin3.4.23.150.451
3w5tLHPVitamin D3 receptor/0.451
4q0kGA3Phytohormone-binding protein/0.451
4r81FMNPredicted NADH dehydrogenase/0.451
4y8wSTRSteroid 21-hydroxylase/0.451
5a0112VO-glycosyltransferase/0.451
1s0zEB1Vitamin D3 receptor/0.450
2bd0NAPSepiapterin reductase/0.450
2zlcVDXVitamin D3 receptor/0.450
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
4ho8THMGlucose-1-phosphate thymidylyltransferase/0.450
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.450
1pkfEPDEpothilone C/D epoxidase1.140.449
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2zlaVDBVitamin D3 receptor/0.449
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.449
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.449
3hy310F5-formyltetrahydrofolate cyclo-ligase6.3.3.20.449
4g210VPVitamin D3 receptor A/0.449
1cjtFOKAdenylate cyclase type 2/0.448
1cjtFOKAdenylate cyclase type 5/0.448
1xxjUNCUricase1.7.3.30.448
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
2cdaNAPGlucose 1-dehydrogenase/0.448
2fk8SAMHydroxymycolate synthase MmaA42.1.10.448
2hl3GLU_GLU_TYRDynactin subunit 1/0.448
3junAKDPhenazine biosynthesis protein A/B/0.448
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
3w0aDS5Vitamin D3 receptor/0.448
4a2aATPCell division protein FtsA/0.448
4j7xSASSepiapterin reductase1.1.1.1530.448
4q71FADBifunctional protein PutA/0.448
3sn6P0GBeta-2 adrenergic receptor/0.448
3akn11DFatty acid-binding protein, intestinal/0.447
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3p4tFAOPutative acyl-CoA dehydrogenase/0.447
3r7vZ02Cyclin-dependent kinase 22.7.11.220.447
3vyfVYFRenin3.4.23.150.447
4bfvZVVPantothenate kinase2.7.1.330.447
4jlj1NMDeoxycytidine kinase2.7.1.740.447
4olfHFGProline--tRNA ligase6.1.1.150.447
4q0a4OAVitamin D3 receptor A/0.447
5cvhADPCasein kinase II subunit alpha2.7.11.10.447
1bwlFMNNADPH dehydrogenase 11.6.99.10.446
1e7qNAPGDP-L-fucose synthase/0.446
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.446
1g3mPCQEstrogen sulfotransferase2.8.2.40.446
1gky5GPGuanylate kinase2.7.4.80.446
1nhz486Glucocorticoid receptor/0.446
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2g1r3IGRenin3.4.23.150.446
2hamC33Vitamin D3 receptor/0.446
2w71L23Biotin carboxylase6.3.4.140.446
3h3t16HCollagen type IV alpha-3-binding protein/0.446
1ay0TPPTransketolase 12.2.1.10.445
1dkfBMSRetinoic acid receptor alpha/0.445
1f5fDHTSex hormone-binding globulin/0.445
1rdtL79Retinoic acid receptor RXR-alpha/0.445
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.445
1zdwFLVPrenyltransferase/0.445
2qmzLDPRibosyldihydronicotinamide dehydrogenase [quinone]/0.445
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.445
3nhwZXZRibosyldihydronicotinamide dehydrogenase [quinone]/0.445
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3vtbTKAVitamin D3 receptor/0.445
5fliQUEQuercetinase QueD/0.445
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.444
1y4lSVRBasic phospholipase A2 homolog 2/0.444
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.444
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.444
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3owuEQUSteroid Delta-isomerase5.3.3.10.444
3th8TH9Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.444
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.444
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.444
4u7wNDPMxaA/0.444
1al8DHPPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.443
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
2e0nSAHPrecorrin-2 C20-methyltransferase/0.443
3c4hDRLPoly [ADP-ribose] polymerase 32.4.2.300.443
3f1kNAPUncharacterized oxidoreductase YciK10.443
3gwfFADCyclohexanone monooxygenase/0.443
3mdmFJZCholesterol 24-hydroxylase/0.443
3mg3ECHOrange carotenoid-binding protein/0.443
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.443
3roy22ZCyclin-dependent kinase 22.7.11.220.443
3vgnFNNSteroid Delta-isomerase5.3.3.10.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4eqrFADCoenzyme A disulfide reductase/0.443
5h8tRTLRetinol-binding protein 1/0.443
1uh5TCLEnoyl-ACP reductase/0.442
2j3qTFLAcetylcholinesterase3.1.1.70.442
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.442
3mtfA3FActivin receptor type-12.7.11.300.442
3vf9477Tyrosine-protein kinase SYK2.7.10.20.442
3vsxR32Renin3.4.23.150.442
3vtcTK3Vitamin D3 receptor/0.442
3w0c6DSVitamin D3 receptor/0.442
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.442
4c02TAKActivin receptor type-12.7.11.300.442
4ez30S0Cyclin-dependent kinase 22.7.11.220.442
4in44IDKelch-like ECH-associated protein 1/0.442
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.442
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
5eccNAPDehydrofolate reductase type I/0.442
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.441
1rd4L08Integrin alpha-L/0.441
2aqkNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
2wo7ASVIsopenicillin N synthase1.21.3.10.441
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.441
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3elbC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.441
3junAJDPhenazine biosynthesis protein A/B/0.441
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3rm618ZCyclin-dependent kinase 22.7.11.220.441
3vt7VDXVitamin D3 receptor/0.441
4bchT7ZCyclin-dependent kinase 92.7.11.220.441
5a9sNAPPutative dehydrogenase/0.441
1ddtAPUDiphtheria toxin/0.440
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1mvtDTMDihydrofolate reductase1.5.1.30.440
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.440
1zq9SAMProbable dimethyladenosine transferase/0.440
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.440
2z52H23Geranylgeranyl pyrophosphate synthase/0.440
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3f63GTXGlutathione transferase GST1-4/0.440
3r7eX88Cyclin-dependent kinase 22.7.11.220.440
3vt65YIVitamin D3 receptor/0.440
3zk5Z18Cytochrome P450 monooxygenase PikC/0.440
4bfxZVXPantothenate kinase2.7.1.330.440
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.440
4o701QKBromodomain-containing protein 4/0.440