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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
4rrcA3TProbable threonine--tRNA ligase 26.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4rrcA3TProbable threonine--tRNA ligase 26.1.1.31.000
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.636
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.627
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.627
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.621
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.619
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.619
4rr9A3SProbable threonine--tRNA ligase 26.1.1.30.617
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.615
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.611
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.610
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.603
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.592
2hl0A3SThreonine--tRNA ligase6.1.1.30.578
4rrfA3SThreonine--tRNA ligase6.1.1.30.548
4rrqA3SThreonine--tRNA ligase6.1.1.30.542
3pd4A3GThreonine--tRNA ligase6.1.1.30.537
2hl2SSAThreonine--tRNA ligase6.1.1.30.533
3pd2A3SThreonine--tRNA ligase6.1.1.30.532
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.527
3pd3A3TThreonine--tRNA ligase6.1.1.30.522
2hl1A3SThreonine--tRNA ligase6.1.1.30.518
4rrrA3TThreonine--tRNA ligase6.1.1.30.516
4rrgA3TThreonine--tRNA ligase6.1.1.30.515
1fmjRTLRetinol dehydratase/0.508
3emlZMAAdenosine receptor A2a/0.503
4xymCOAAcyl-CoA synthetase (NDP forming)/0.499
2ea4F79Methionine aminopeptidase 2/0.495
2oazI96Methionine aminopeptidase 2/0.492
3w0yDS4Vitamin D3 receptor/0.492
4qzuRTLRetinol-binding protein 2/0.492
3vt7VDXVitamin D3 receptor/0.491
2xvw9NRSerum albumin/0.489
4xz3COAAcyl-CoA synthetase (NDP forming)/0.486
2rh1CAUBeta-2 adrenergic receptor/0.485
1nhz486Glucocorticoid receptor/0.483
2fpcSCGStrictosidine synthase4.3.3.20.483
1tl7ONMAdenylate cyclase type 2/0.482
1tl7ONMAdenylate cyclase type 5/0.482
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.482
5c4cUPGHisto-blood group ABO system transferase/0.481
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.478
1r58AO5Methionine aminopeptidase 2/0.477
2po7CHDFerrochelatase, mitochondrial4.99.1.10.476
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.475
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.475
4j6cSTRCytochrome P450 monooxygenase/0.475
2xvv9DNSerum albumin/0.474
3ew2BTNHypothetical conserved protein/0.474
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.473
3v0p4GWHisto-blood group ABO system transferase/0.473
4pnmNU1Tankyrase-22.4.2.300.473
1kqwRTLCellular retinol-binding protein type II/0.472
3q9bB3NAcetylpolyamine amidohydrolase/0.472
4bfzZVZPantothenate kinase2.7.1.330.472
4ead0NPThymidine phosphorylase2.4.2.40.472
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.472
2ociTYCValacyclovir hydrolase3.10.471
3tk3CPZCytochrome P450 2B41.14.14.10.471
1x8lOXRRetinol dehydratase/0.469
1yw7A41Methionine aminopeptidase 2/0.469
3pd5TSBThreonine--tRNA ligase6.1.1.30.469
3vswR31Renin3.4.23.150.469
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
4lsjLSJGlucocorticoid receptor/0.469
2oaxSNLMineralocorticoid receptor/0.468
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3jpuTY4Transcriptional activator protein LasR/0.467
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3pqbVGPPutative oxidoreductase/0.467
4klaCHDFerrochelatase, mitochondrial4.99.1.10.467
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.467
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.466
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.466
3vf9477Tyrosine-protein kinase SYK2.7.10.20.466
1yw9A84Methionine aminopeptidase 2/0.465
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.465
1o6qR17Squalene--hopene cyclase4.2.1.1290.464
2a4nCOAAac(6')-Ii protein/0.464
2vteIK4UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.464
3akn11DFatty acid-binding protein, intestinal/0.464
3junAKDPhenazine biosynthesis protein A/B/0.464
4aoxFADSteroid monooxygenase/0.464
2bxqIMNSerum albumin/0.463
2op18PCEnoyl-ACP reductase/0.463
2xpc051UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.463
3lqfNADGalactitol dehydrogenase/0.463
3ox1695Ribosyldihydronicotinamide dehydrogenase [quinone]/0.463
4i6gFADCryptochrome-2/0.463
4kxjP34Nucleoprotein/0.463
4zu44TGWxcM-like protein/0.463
3b9lAZZSerum albumin/0.462
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.462
2pvkP45Casein kinase II subunit alpha2.7.11.10.461
3caqNDP3-oxo-5-beta-steroid 4-dehydrogenase/0.461
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
3iogSDFMetallo-beta-lactamase type 2/0.461
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.461
1ppjANYCytochrome b/0.460
2zulSAMProbable ribosomal RNA small subunit methyltransferase/0.460
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.460
3pahXDEPhenylalanine-4-hydroxylase1.14.16.10.460
1crbRTLRetinol-binding protein 1/0.459
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
2imfTOM2-hydroxychromene-2-carboxylate isomerase5.99.1.40.458
2uuoLK3UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.458
3fsjD7KBenzoylformate decarboxylase4.1.1.70.458
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.458
4uhrNGIAdenosine receptor A2a/0.458
2bl9CP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.457
2g1n1IGRenin3.4.23.150.457
2vr1ATFBiotin carboxylase6.3.4.140.457
3adaNADSubunit alpha of sarocosine oxidase/0.457
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.457
3fpjSAMUncharacterized protein/0.457
3v0o4GWHisto-blood group ABO system transferase/0.457
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.457
4jlj1NMDeoxycytidine kinase2.7.1.740.457
2ea2F77Methionine aminopeptidase 2/0.456
3a783EVVitamin D3 receptor/0.456
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.456
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.456
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
4jq3NAPAldo-keto reductase family 1 member C2/0.456
4mbsMRVC-C chemokine receptor type 5/0.456
4y1bNAPAntE/0.456
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.456
3pwhZMAAdenosine receptor A2a/0.456
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.455
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.455
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
3gwfFADCyclohexanone monooxygenase/0.455
4iteTEYVitamin D3 receptor/0.455
1ddtAPUDiphtheria toxin/0.454
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1opbRETRetinol-binding protein 2/0.454
1swtBTNStreptavidin/0.454
3nhyA7BRibosyldihydronicotinamide dehydrogenase [quinone]/0.454
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
2cekN8TAcetylcholinesterase3.1.1.70.453
2hamC33Vitamin D3 receptor/0.453
2jfz003Glutamate racemase/0.453
3l9lL9LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.453
3d4sTIMBeta-2 adrenergic receptor/0.453
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.452
1kquBR4Phospholipase A2, membrane associated/0.452
1obnASVIsopenicillin N synthase1.21.3.10.452
1osvCHCBile acid receptor/0.452
1qorNDPQuinone oxidoreductase 1/0.452
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.452
2g1r3IGRenin3.4.23.150.452
2zwvSAHProbable ribosomal RNA small subunit methyltransferase/0.452
3pm1ETHTH-type transcriptional regulator QacR/0.452
3up3XCAaceDAF-12/0.452
3vt9YI4Vitamin D3 receptor/0.452
3zkyWT4Isopenicillin N synthase1.21.3.10.452
4amjCVDBeta-1 adrenergic receptor/0.452
4b2gV1NUncharacterized protein/0.452
4dpeNGHStromelysin-13.4.24.170.452
4jtqNAPAldo-keto reductase family 1 member C2/0.452
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
1mrqSTRAldo-keto reductase family 1 member C1/0.451
1s0xC3SNuclear receptor ROR-alpha/0.451
1t7o152Carnitine O-acetyltransferase2.3.1.70.451
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.451
3dmhSAMProbable ribosomal RNA small subunit methyltransferase/0.451
3h3t16HCollagen type IV alpha-3-binding protein/0.451
3hy310F5-formyltetrahydrofolate cyclo-ligase6.3.3.20.451
3n6uTSUHTH-type transcriptional regulator TsaR/0.451
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.451
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.451
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.450
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.450
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.450
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.450
3p8iFMNPentaerythritol tetranitrate reductase/0.450
3v1s0LHStrictosidine synthase4.3.3.20.450
4bz8J38Histone deacetylase/0.450
4dvi2IWTankyrase-12.4.2.300.450
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4j6dTESCytochrome P450 monooxygenase/0.450
5k2cZMAAdenosine receptor A2a/0.450
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.449
1q20PLOSulfotransferase family cytosolic 2B member 12.8.2.20.449
1s36CEIObelin/0.449
2hcdBIVVitamin D3 receptor A/0.449
2p1u4TNRetinoic acid receptor RXR-alpha/0.449
2y01Y00Beta-1 adrenergic receptor/0.449
3dtcVINMitogen-activated protein kinase kinase kinase 92.7.11.250.449
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.449
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.449
3w0hW12Vitamin D3 receptor/0.449
3zsvZSVIntegrase/0.449
4cebZSVIntegrase/0.449
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4twnB96Ephrin type-A receptor 32.7.10.10.449
1fmlRTLRetinol dehydratase/0.448
2bp1NDPAflatoxin B1 aldehyde reductase member 2/0.448
2gbyBRNHTH-type transcriptional regulator QacR/0.448
3af1GDPPantothenate kinase2.7.1.330.448
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3q7fED2Uncharacterized protein/0.448
3qzhX69Cyclin-dependent kinase 22.7.11.220.448
3vtdTKDVitamin D3 receptor/0.448
3w0aDS5Vitamin D3 receptor/0.448
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.448
4mm729JNa(+):neurotransmitter symporter (Snf family)/0.448
4xwtU5PRibonuclease J/0.448
1f4gTP4Thymidylate synthase/0.447
2bxmIMNSerum albumin/0.447
2ovhAS0Progesterone receptor/0.447
2zevB71Geranylgeranyl pyrophosphate synthase/0.447
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3elm24FCollagenase 33.4.240.447
3gfbNADL-threonine 3-dehydrogenase/0.447
3hdyGDUUDP-galactopyranose mutase/0.447
3s79ASDAromatase1.14.14.140.447
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.447
4iwv1J9Glucokinase2.7.1.20.447
4kvzSAHPtnL protein/0.447
4yekTHMThymidine phosphorylase/0.447
5difGNPGTP-binding nuclear protein Ran/0.447
5d5bCAUBeta-2 adrenergic receptor/0.447
3sn6P0GBeta-2 adrenergic receptor/0.447
1q23FUAChloramphenicol acetyltransferase2.3.1.280.446
2wd9IBPAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.446
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3gwfNAPCyclohexanone monooxygenase/0.446
3sfy3FYUncharacterized protein/0.446
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.446
3uxhUXHRibosyldihydronicotinamide dehydrogenase [quinone]/0.446
4bfpSWYTankyrase-22.4.2.300.446
4fxy0W2Neurolysin, mitochondrial3.4.24.160.446
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.446
5iubCLRAdenosine receptor A2a/0.446
5k2bZMAAdenosine receptor A2a/0.446
5k2dZMAAdenosine receptor A2a/0.446
1nw5SAMModification methylase RsrI2.1.1.720.445
1t85CAMCamphor 5-monooxygenase1.14.15.10.445
2v59LZKBiotin carboxylase6.3.4.140.445
2wo7ASVIsopenicillin N synthase1.21.3.10.445
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.445
2z9dFMNFMN-dependent NADH-azoreductase/0.445
3a1l2CCCytochrome P450/0.445
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3inrGDUUDP-galactopyranose mutase5.4.99.90.445
3nhuM42Ribosyldihydronicotinamide dehydrogenase [quinone]/0.445
3nhwZXZRibosyldihydronicotinamide dehydrogenase [quinone]/0.445
5d5aCAUBeta-2 adrenergic receptor/0.445
1akcPPEAspartate aminotransferase, mitochondrial2.6.1.10.444
1dirNADDihydropteridine reductase1.5.1.340.444
1itzTPPTransketolase, chloroplastic2.2.1.10.444
1mmkH4BPhenylalanine-4-hydroxylase1.14.16.10.444
1rk3VDXVitamin D3 receptor/0.444
1zdwFLVPrenyltransferase/0.444
2fhnBNIAvidin-related protein 4/5/0.444
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.444
3gy9COAGCN5-related N-acetyltransferase/0.444
3uic09TEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
3zr7OR8Progesterone receptor/0.444
3zs7ATPPyridoxine/pyridoxal/pyridoxamine kinase/0.444
4zm6ACON-acetyl-beta-D glucosaminidase/0.444
5c4fUPGHisto-blood group ABO system transferase/0.444
5fsxADPUncharacterized protein/0.444
4amiG90Beta-1 adrenergic receptor/0.444
1h36R88Squalene--hopene cyclase4.2.1.1290.443
1nw6SFGModification methylase RsrI2.1.1.720.443
1z8962PAldose reductase1.1.1.210.443
2r4uADPGlycogen synthase2.4.1.210.443
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.443
2zawCAMCamphor 5-monooxygenase1.14.15.10.443
3b9oFMNAlkane monoxygenase/0.443
3btjDEQHTH-type transcriptional regulator QacR/0.443
3i2834NBifunctional epoxide hydrolase 23.3.2.100.443
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3pg3DG7Mitogen-activated protein kinase 14/0.443
3qizQI2Botulinum neurotoxin type A3.4.24.690.443
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.443
3w0gW07Vitamin D3 receptor/0.443
5cb3APRO-acetyl-ADP-ribose deacetylase/0.443
5i2hAGIO-methyltransferase family 2/0.443
2ycxP32Beta-1 adrenergic receptor/0.443
5iu86DZAdenosine receptor A2a/0.443
3uzaT4GAdenosine receptor A2a/0.443
1lp4ANPCasein kinase II subunit alpha2.7.11.10.442
1r5hAO2Methionine aminopeptidase 2/0.442
2ovmAS0Progesterone receptor/0.442
2p7zOHTEstrogen-related receptor gamma/0.442
2q16ITTdITP/XTP pyrophosphatase/0.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
2y99NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.442
3bejMUFBile acid receptor/0.442
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3fhxPLPPyridoxal kinase2.7.1.350.442
3ipuO40Oxysterols receptor LXR-alpha/0.442
3p74FMNPentaerythritol tetranitrate reductase/0.442
3qfxCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.442
4jq4IMNAldo-keto reductase family 1 member C2/0.442
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.442
1gt5BZQOdorant-binding protein/0.441
1tllFADNitric oxide synthase, brain1.14.13.390.441
1ve3SAMUncharacterized protein/0.441
1xseNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
1zg32HIIsoflavone 4'-O-methyltransferase/0.441
2ol4JPNEnoyl-ACP reductase/0.441
2vqbFADPutative flavin-containing monooxygenase/0.441
2ywvADPPhosphoribosylaminoimidazole-succinocarboxamide synthase/0.441
3c14FOKAdenylate cyclase type 2/0.441
3c14FOKAdenylate cyclase type 5/0.441
3c3xNAPEugenol synthase 11.1.1.3180.441
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3nmhPYVAbscisic acid receptor PYL2/0.441
3p9tTCLRepressor/0.441
3pxyJWSCyclin-dependent kinase 22.7.11.220.441
3vspEK8Peroxisome proliferator-activated receptor gamma/0.441
3vsxR32Renin3.4.23.150.441
4bchT7ZCyclin-dependent kinase 92.7.11.220.441
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.441
4g2h0VQVitamin D3 receptor A/0.441
4hxs1A3Bromodomain-containing protein 4/0.441
4l4eCAMCamphor 5-monooxygenase1.14.15.10.441
4l4fCAMCamphor 5-monooxygenase1.14.15.10.441
4pahLNRPhenylalanine-4-hydroxylase1.14.16.10.441
4u7wNDPMxaA/0.441
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1wc0APCAdenylate cyclase/0.440
2xlsFADPutative flavin-containing monooxygenase/0.440
2z3uCRRCytochrome P450/0.440
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.440
5uviZMAAdenosine receptor A2a/0.440