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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3w3lRX8Toll-like receptor 8

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3w3lRX8Toll-like receptor 8/1.000
3w3nRX8Toll-like receptor 8/0.647
3w3kL07Toll-like receptor 8/0.527
4r09URIToll-like receptor 8/0.518
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.498
4r08URIToll-like receptor 8/0.496
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.491
3gwfNAPCyclohexanone monooxygenase/0.489
4r07URIToll-like receptor 8/0.489
2g1s4IGRenin3.4.23.150.488
2qimZEAClass 10 plant pathogenesis-related protein/0.487
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.487
2r0cFADPutative FAD-monooxygenase/0.486
2g1y5IGRenin3.4.23.150.484
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.483
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.483
2g1o2IGRenin3.4.23.150.482
3owaFADAcyl-CoA dehydrogenase/0.482
2g247IGRenin3.4.23.150.481
4bb3KKAIsopenicillin N synthase1.21.3.10.479
7stdCRPScytalone dehydratase4.2.1.940.479
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
3u5ySCGRaucaffricine-O-beta-D-glucosidase3.2.1.1250.476
2gyuHI6Acetylcholinesterase3.1.1.70.475
4ey6GNTAcetylcholinesterase3.1.1.70.474
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.473
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.472
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.471
1pfyMSPMethionine--tRNA ligase6.1.1.100.470
2ejzSAHDiphthine synthase/0.470
2vrbNAPTriphenylmethane reductase/0.470
4a83DXCMajor pollen allergen Bet v 1-A/0.470
1u65CP0Acetylcholinesterase3.1.1.70.469
3g72A6TRenin3.4.23.150.468
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.467
2iko7IGRenin3.4.23.150.467
2xukTZ5Acetylcholinesterase3.1.1.70.467
2ct8MSPMethionine--tRNA ligase6.1.1.100.466
4ycpFMNtRNA-dihydrouridine(16) synthase/0.466
1bil0IURenin3.4.23.150.464
1h60STRPentaerythritol tetranitrate reductase/0.464
2webPP4Penicillopepsin-13.4.23.200.464
4a802ANMajor pollen allergen Bet v 1-A/0.464
4a862ANMajor pollen allergen Bet v 1-A/0.464
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.464
2xvfFADPutative flavin-containing monooxygenase/0.463
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3psyRB9Endothiapepsin3.4.23.220.463
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.463
1zgbA1EAcetylcholinesterase3.1.1.70.462
2hejNDPAldo-keto reductase family 1 member C211.1.10.462
2j3qTFLAcetylcholinesterase3.1.1.70.462
3qj0QI3Botulinum neurotoxin type A3.4.24.690.461
1c7oPPGHemolysin/0.460
5stdUNNScytalone dehydratase4.2.1.940.460
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
3p0fBAUUridine phosphorylase 22.4.2.30.459
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.458
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.458
2a3bCFFEndochitinase B13.2.1.140.458
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.458
1gaxVAAValine--tRNA ligase6.1.1.90.457
2oz57XYUncharacterized protein/0.457
2v58LZJBiotin carboxylase6.3.4.140.457
2wecPP5Penicillopepsin-13.4.23.200.457
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.457
4m0f1YKAcetylcholinesterase3.1.1.70.457
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.457
4x81MVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.457
1dliUDXUDP-glucose 6-dehydrogenase/0.456
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.456
2xuiTZ5Acetylcholinesterase3.1.1.70.456
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.456
3g70A5TRenin3.4.23.150.456
4a81DXCMajor pollen allergen Bet v 1-A/0.456
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.456
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.455
1ppl1Z7Penicillopepsin-13.4.23.200.455
2abaSTRPentaerythritol tetranitrate reductase/0.455
2cekN8TAcetylcholinesterase3.1.1.70.455
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3rvhHQ2Lysine-specific demethylase 4A1.14.110.455
5c1mCLRMu-type opioid receptor/0.455
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.454
1obnASVIsopenicillin N synthase1.21.3.10.454
1q84TZ4Acetylcholinesterase3.1.1.70.454
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3h3qH13Collagen type IV alpha-3-binding protein/0.454
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.454
3zv7NHGAcetylcholinesterase3.1.1.70.454
5f8eSAHPossible transcriptional regulatory protein/0.454
1dx6GNTAcetylcholinesterase3.1.1.70.453
2whqHI6Acetylcholinesterase3.1.1.70.453
3k1wBFXRenin3.4.23.150.453
3pqbVGPPutative oxidoreductase/0.453
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.453
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.452
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.452
2il2LIXRenin3.4.23.150.452
2jl1NAPTriphenylmethane reductase/0.452
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.452
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4bfxZVXPantothenate kinase2.7.1.330.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1x1dSAHC-20 methyltransferase/0.451
2cftPLPPyridoxal phosphate phosphatase/0.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
2vbpVB1Isopenicillin N synthase1.21.3.10.451
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.451
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.451
4x7vMIVMycinamicin III 3''-O-methyltransferase2.1.1.2370.451
1qrpHH0Pepsin A-43.4.23.10.450
1zgaHMKIsoflavone 4'-O-methyltransferase/0.450
2a4xBLMMitomycin-binding protein/0.450
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2c12FADNitroalkane oxidase1.7.3.10.450
2xupTZ5Acetylcholinesterase3.1.1.70.450
3mj4URMUDP-galactopyranose mutase/0.450
3q7fED2Uncharacterized protein/0.450
3vyfVYFRenin3.4.23.150.450
1fkbRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.449
1psa0ZLPepsin A3.4.23.10.449
2dvlFADAcyl-CoA dehydrogenase/0.449
2zhe13UProthrombin3.4.21.50.449
3c1kT15Prothrombin3.4.21.50.449
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3t6iNC8Endothiapepsin3.4.23.220.449
4awsFMNNADH:flavin oxidoreductase Sye1/0.449
4mlp2CXCryptochrome-2/0.449
4xr9NADCalS8/0.449
1odcA8BAcetylcholinesterase3.1.1.70.448
1u1gBBBUridine phosphorylase2.4.2.30.448
2uxoTACHTH-type transcriptional regulator TtgR/0.448
2wedPP6Penicillopepsin-13.4.23.200.448
3h3t16HCollagen type IV alpha-3-binding protein/0.448
3zncBZ1Carbonic anhydrase 44.2.1.10.448
4q0kGA3Phytohormone-binding protein/0.448
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.447
1s63778Protein farnesyltransferase subunit beta2.5.1.580.447
2xujTZ5Acetylcholinesterase3.1.1.70.447
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.447
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.447
3p8iFMNPentaerythritol tetranitrate reductase/0.447
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.447
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.447
4bfvZVVPantothenate kinase2.7.1.330.447
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4fxy0W2Neurolysin, mitochondrial3.4.24.160.447
4j4nD44Peptidylprolyl isomerase/0.447
4nv1TYDFormyl transferase/0.447
1mxfMTXPutative pteridine reductase 2/0.446
2gv8NDPThiol-specific monooxygenase1.14.130.446
2gvdFKPAdenylate cyclase type 2/0.446
2gvdFKPAdenylate cyclase type 5/0.446
2iviACWIsopenicillin N synthase1.21.3.10.446
2vbdV10Isopenicillin N synthase1.21.3.10.446
3h3r14HCollagen type IV alpha-3-binding protein/0.446
3mknDNBPyrimidine-specific ribonucleoside hydrolase RihB/0.446
3qeoLLTDeoxycytidine kinase2.7.1.740.446
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.446
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.446
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.445
2rlcCHDCholoylglycine hydrolase3.5.1.240.445
3tdaPN0Cytochrome P450 2D6/0.445
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.445
1dljUGAUDP-glucose 6-dehydrogenase/0.444
1el4CTZObelin/0.444
1oq5CELCarbonic anhydrase 24.2.1.10.444
1r5gAO1Methionine aminopeptidase 2/0.444
1t7o152Carnitine O-acetyltransferase2.3.1.70.444
1xh5R68cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1xh6R94cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2ea2F77Methionine aminopeptidase 2/0.444
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3igpDT7Carbonic anhydrase 24.2.1.10.444
3mauPLRPutative sphingosine-1-phosphate lyase/0.444
3qiyQI1Botulinum neurotoxin type A3.4.24.690.444
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.444
4esoNAPPutative oxidoreductase/0.444
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4mk828QGenome polyprotein2.7.7.480.444
4uy6SAHHistidine N-alpha-methyltransferase/0.444
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.444
1eveE20Acetylcholinesterase3.1.1.70.443
1fm4DXCMajor pollen allergen Bet v 1-L/0.443
1mu6CDAProthrombin3.4.21.50.443
1n77ATPGlutamate--tRNA ligase6.1.1.170.443
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
2xugTZ4Acetylcholinesterase3.1.1.70.443
2y60M8FIsopenicillin N synthase1.21.3.10.443
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.443
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.443
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.443
1egeFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.442
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.442
1pqc444Oxysterols receptor LXR-beta/0.442
1zsbAZMCarbonic anhydrase 24.2.1.10.442
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.442
3zoiM2WIsopenicillin N synthase1.21.3.10.442
4bfuZVUPantothenate kinase2.7.1.330.442
4dvi2IWTankyrase-12.4.2.300.442
4fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.442
4fapARDSerine/threonine-protein kinase mTOR2.7.11.10.442
4hcy0YNTransketolase/0.442
4m83ERYOleandomycin glycosyltransferase2.4.10.442
4rp8ASCAscorbate-specific PTS system EIIC component/0.442
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
1ay0TPPTransketolase 12.2.1.10.441
1bk0ACVIsopenicillin N synthase1.21.3.10.441
1ydaAZMCarbonic anhydrase 24.2.1.10.441
2bktRPFRenin3.4.23.150.441
2fhjH4ZFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.441
2g1n1IGRenin3.4.23.150.441
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.441
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.441
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.441
3f8sPF2Dipeptidyl peptidase 4/0.441
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.441
3qizQI2Botulinum neurotoxin type A3.4.24.690.441
3vswR31Renin3.4.23.150.441
4a87NARMajor pollen allergen Bet v 1-A/0.441
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.441
4ilx1EZCarbonic anhydrase 24.2.1.10.441
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
1pq944BOxysterols receptor LXR-beta/0.440
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1qtiGNTAcetylcholinesterase3.1.1.70.440
1waj5GPDNA-directed DNA polymerase/0.440
2dg4RAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.440
2dzbHH2Dihydropteroate synthase/0.440
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.440
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.440
2xlrFADPutative flavin-containing monooxygenase/0.440
3prsRITEndothiapepsin3.4.23.220.440
3q9bB3NAcetylpolyamine amidohydrolase/0.440
4b63NAPL-ornithine N(5)-monooxygenase/0.440
4bfzZVZPantothenate kinase2.7.1.330.440
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.440