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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
3w3kL07Toll-like receptor 8

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3w3kL07Toll-like receptor 8/1.000
3w3lRX8Toll-like receptor 8/0.595
3w3nRX8Toll-like receptor 8/0.586
4r09URIToll-like receptor 8/0.546
4r08URIToll-like receptor 8/0.537
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.528
4r07URIToll-like receptor 8/0.527
5c1mCLRMu-type opioid receptor/0.516
1jdzFMBPurine nucleoside phosphorylase/0.496
2j0sANPEukaryotic initiation factor 4A-III3.6.4.130.494
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.492
4iyg1HUStrictosidine synthase4.3.3.20.478
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.477
1jdvADNPurine nucleoside phosphorylase/0.476
1qvuPRLHTH-type transcriptional regulator QacR/0.473
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.472
3bt9DEQHTH-type transcriptional regulator QacR/0.471
4b78KGGBeta-secretase 13.4.23.460.470
1qvtPRLHTH-type transcriptional regulator QacR/0.468
3mauPLRPutative sphingosine-1-phosphate lyase/0.467
1hfqMOTDihydrofolate reductase1.5.1.30.465
1k9sFM1Purine nucleoside phosphorylase DeoD-type/0.465
3py4TYLLactoperoxidase1.11.1.70.465
4y6nUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.464
1pr5TBNPurine nucleoside phosphorylase DeoD-type/0.462
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.462
4fr10V2Queuine tRNA-ribosyltransferase2.4.2.290.462
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.461
4ej4EJ4Delta-type opioid receptor/0.461
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.460
4h1e10JBeta-secretase 13.4.23.460.460
3nmhPYVAbscisic acid receptor PYL2/0.459
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.458
2oa1FADFlavin-dependent tryptophan halogenase RebH1.14.19.90.458
4mk828QGenome polyprotein2.7.7.480.458
3ge7AFQQueuine tRNA-ribosyltransferase2.4.2.290.457
2bn4FMNNADPH--cytochrome P450 reductase/0.456
3vv8B02Beta-secretase 13.4.23.460.456
4frkDWDBeta-secretase 13.4.23.460.456
4x7uZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.456
2b35TCLEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.455
3wd3A1LChitinase B3.2.1.140.455
1jdtMTAPurine nucleoside phosphorylase/0.454
3ou2SAHSAM-dependent methyltransferase/0.454
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.454
1n77ATPGlutamate--tRNA ligase6.1.1.170.453
2flhZEACytokinin-specific binding protein/0.453
2y02WHJBeta-1 adrenergic receptor/0.453
3ebf332Nitric oxide synthase, inducible1.14.13.390.453
4e0u0MVCyclic dipeptide N-prenyltransferase/0.453
2ojf4PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.452
3aw9GDUNAD-dependent epimerase/dehydratase/0.452
3dqrJI2Nitric oxide synthase, brain1.14.13.390.452
3rmeRMEAcidic mammalian chitinase3.2.1.140.452
1gvv0GMEndothiapepsin3.4.23.220.451
2dxiATPGlutamate--tRNA ligase6.1.1.170.451
2zu8GDDMannosyl-3-phosphoglycerate synthase2.4.1.2170.451
3uxvGUNNADPH-dependent 7-cyano-7-deazaguanine reductase/0.451
4b722FBBeta-secretase 13.4.23.460.450
4jq8KJ8Epidermal growth factor receptor2.7.10.10.450
4lwaQ13Nitric oxide synthase oxygenase1.14.13.1650.450
1qtqQSIGlutamine--tRNA ligase6.1.1.180.449
3nnz59WNitric oxide synthase, brain1.14.13.390.449
2vbpVB1Isopenicillin N synthase1.21.3.10.448
3isjA8DPantothenate synthetase6.3.2.10.448
3wb40B3Beta-secretase 13.4.23.460.448
4jxxATPGlutamine--tRNA ligase6.1.1.180.448
2wvmGDDMannosyl-3-phosphogylcerate synthase/0.447
4dju0KKBeta-secretase 13.4.23.460.447
3pblETQD(3) dopamine receptor/0.447
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.446
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.446
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.446
4imfSI3N-acetylneuraminate lyase/0.446
4h3i10VBeta-secretase 13.4.23.460.445
4iarERM5-hydroxytryptamine receptor 1B/0.445
4u7wNDPMxaA/0.445
5dhhDGWNociceptin receptor/0.445
2xveFADPutative flavin-containing monooxygenase/0.444
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.444
3fr5I4AFatty acid-binding protein, adipocyte/0.444
3udq09EBeta-secretase 13.4.23.460.444
1gaxVAAValine--tRNA ligase6.1.1.90.443
1n2iPAJPantothenate synthetase6.3.2.10.443
1tllFMNNitric oxide synthase, brain1.14.13.390.443
3cow52HPantothenate synthetase6.3.2.10.443
3v1s0LHStrictosidine synthase4.3.3.20.443
2re8GSUGlutamine--tRNA ligase6.1.1.180.442
3k1wBFXRenin3.4.23.150.442
4djx0KQBeta-secretase 13.4.23.460.442
4rawZZ7Metallo-beta-lactamase type 2/0.442
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.442
1je1GMPPurine nucleoside phosphorylase/0.441
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.441
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.441
1w7h3IPMitogen-activated protein kinase 14/0.440
3e7tB14Nitric oxide synthase, inducible1.14.13.390.440
4djw0KPBeta-secretase 13.4.23.460.440
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.440