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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
1yrxFMNAppA protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1yrxFMNAppA protein/1.000
2iygFMNAppA, antirepressor of ppsR, sensor of blue light/0.639
2iyiFMNAppA, antirepressor of ppsR, sensor of blue light/0.608
4hh0FMNAppA protein/0.596
1x0pFADTll0078 protein/0.541
3gfxFMNUncharacterized protein/0.529
2bycFMNBlue-light receptor of the BLUF-family/0.526
3gg0FMNUncharacterized protein/0.522
4yusFMNFamily 3 adenylate cyclase/0.521
3gg1FMNUncharacterized protein/0.494
4yutFMNFamily 3 adenylate cyclase/0.492
1dirNADDihydropteridine reductase1.5.1.340.488
3gfzFMNUncharacterized protein/0.487
3gfyFMNUncharacterized protein/0.485
4a83DXCMajor pollen allergen Bet v 1-A/0.479
3raiX85Cyclin-dependent kinase 22.7.11.220.478
2gfsPQBMitogen-activated protein kinase 14/0.475
1ruoCMPcAMP-activated global transcriptional regulator CRP/0.474
4mv8ACPBiotin carboxylase6.3.4.140.474
1nzdUPGDNA beta-glucosyltransferase/0.469
3ed1GA3Gibberellin receptor GID1/0.469
5c8wPCGcGMP-dependent protein kinase 22.7.11.120.469
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
4r20AERCytochrome P450 family 17 polypeptide 2/0.467
3b9lAZZSerum albumin/0.466
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.466
2hfnFMNActivator of photopigment and puc expression/0.464
4hyh1AMSerine/threonine-protein kinase Chk12.7.11.10.464
4c34STUcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.463
5iu4ZMAAdenosine receptor A2a/0.462
2pmnK51Protein kinase 7/0.461
5k2cZMAAdenosine receptor A2a/0.461
3fp0FP015-O-acetyltransferase/0.460
4k771Q4Tyrosine-protein kinase JAK1/0.459
2woeAR6ADP-ribosyl-[dinitrogen reductase] glycohydrolase3.2.2.240.458
4bfuZVUPantothenate kinase2.7.1.330.458
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.456
5k2bZMAAdenosine receptor A2a/0.456
1w7h3IPMitogen-activated protein kinase 14/0.455
1x2hLPALipoate-protein ligase A6.3.1.200.455
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.455
3zkbANPDNA gyrase subunit B/0.454
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4s0vSUVOrexin receptor type 2/0.454
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.453
4a99FADTetX family tetracycline inactivation enzyme/0.453
4ej4EJ4Delta-type opioid receptor/0.453
1nzfUPGDNA beta-glucosyltransferase/0.452
2abbFMNPentaerythritol tetranitrate reductase/0.452
2v59LZKBiotin carboxylase6.3.4.140.452
3bkbSTUTyrosine-protein kinase Fes/Fps2.7.10.20.452
4bzo676Serine/threonine-protein kinase pim-12.7.11.10.452
4n6hEJ4Delta-type opioid receptor/0.452
3r8vZ62Cyclin-dependent kinase 22.7.11.220.451
1phhFADp-hydroxybenzoate hydroxylase/0.450
2qbmCAMCamphor 5-monooxygenase1.14.15.10.450
3akm11DFatty acid-binding protein, intestinal/0.450
3uylTYDProbable NDP-rhamnosyltransferase/0.450
5fm6ADPRuvB-like helicase/0.450
1kqnNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.449
3eblGA4Gibberellin receptor GID1/0.449
3vt45YIVitamin D3 receptor/0.449
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.449
5k2aZMAAdenosine receptor A2a/0.449
1mbtFADUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.448
1zeoC01Peroxisome proliferator-activated receptor gamma/0.448
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.448
2p83MR0Beta-secretase 13.4.23.460.448
2pv7NADT-protein1.3.1.120.448
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.448
2rqfJH3Hemolymph juvenile hormone binding protein/0.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4bb3KKAIsopenicillin N synthase1.21.3.10.448
4g8bHL6Alpha/beta hydrolase fold protein/0.448
1e800GQEndothiapepsin3.4.23.220.447
1ezvUQ6Cytochrome b/0.447
2gr2APRFerredoxin reductase/0.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3uawADNPurine nucleoside phosphorylase DeoD-type/0.447
4y9lFADAcyl-CoA dehydrogenase family member 11/0.447
1pdhFASp-hydroxybenzoate hydroxylase/0.446
1yp4ADQGlucose-1-phosphate adenylyltransferase small subunit, chloroplastic/amyloplastic2.7.7.270.446
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3eyhIZATyrosine-protein kinase JAK1/0.446
3fjqATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.446
3itzP66Mitogen-activated protein kinase 14/0.446
4eiyZMAAdenosine receptor A2a/0.446
2v58LZJBiotin carboxylase6.3.4.140.445
3arvSAUChitinase A/0.445
3nmpPYVAbscisic acid receptor PYL2/0.445
3orzBI43-phosphoinositide-dependent protein kinase 12.7.11.10.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4kq2U5PGlycogen [starch] synthase isoform 22.4.1.110.445
4l4eCAMCamphor 5-monooxygenase1.14.15.10.445
4z5wILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.445
5ackATP3-phosphoinositide-dependent protein kinase 12.7.11.10.445
3sn6P0GBeta-2 adrenergic receptor/0.445
2p9eNAID-3-phosphoglycerate dehydrogenase1.1.1.950.444
2ym44YMSerine/threonine-protein kinase Chk12.7.11.10.444
3fwjCAMCamphor 5-monooxygenase1.14.15.10.444
4iarERM5-hydroxytryptamine receptor 1B/0.444
4jq8KJ8Epidermal growth factor receptor2.7.10.10.444
1x14NADNAD(P) transhydrogenase subunit alpha1.6.1.20.443
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.443
2v5aLZLBiotin carboxylase6.3.4.140.443
2x8iX8ISerine/threonine-protein kinase Chk12.7.11.10.443
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3in6FMNUncharacterized protein/0.443
3nj8NJ8Enoyl-acyl carrier reductase/0.443
3ntaCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.443
3zh8C58Protein kinase C iota type2.7.11.130.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4a81DXCMajor pollen allergen Bet v 1-A/0.443
4jq7KJQEpidermal growth factor receptor2.7.10.10.443
4o8aFADBifunctional protein PutA1.2.1.880.443
2cy0NAPShikimate dehydrogenase (NADP(+))/0.442
3pj8404Cyclin-dependent kinase 22.7.11.220.442
3r83Z14Cyclin-dependent kinase 22.7.11.220.442
3s1dZIRCytokinin dehydrogenase 11.5.99.120.442
4dpy2P0Mevalonate diphosphate decarboxylase/0.442
4jc51K5Stimulator of interferon genes protein/0.442
4kgmATPUncharacterized protein/0.442
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.442
1tj0FADBifunctional protein PutA1.5.5.20.441
2b53D23Cyclin-dependent kinase 22.7.11.220.441
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2jb4A14Isopenicillin N synthase1.21.3.10.441
2o7oDXTTetracycline repressor protein class D/0.441
2pxaSAHGenome polyprotein2.7.7.480.441
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.441
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.441
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.441
3mtfA3FActivin receptor type-12.7.11.300.441
4dh5ADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
4m10ICDProstaglandin G/H synthase 21.14.99.10.441
4zu44TGWxcM-like protein/0.441
1dliUDXUDP-glucose 6-dehydrogenase/0.440
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.440
2vd5BI8Myotonin-protein kinase2.7.11.10.440
2w6qOA5Biotin carboxylase6.3.4.140.440
2y9qANPMitogen-activated protein kinase 12.7.11.240.440
3ds6A17Mitogen-activated protein kinase 14/0.440
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.440
3qqhX0ACyclin-dependent kinase 22.7.11.220.440
4a8v2ANMajor pollen allergen Bet v 1-J/0.440
4iafADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
5iua6DXAdenosine receptor A2a/0.440
4zj8SUVOrexin receptor type 1/0.440