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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
1swnBTNStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1swnBTNStreptavidin/1.000
1n9mBTNStreptavidin/0.655
1swpBTNStreptavidin/0.635
1sweBTNStreptavidin/0.622
1swpBTQStreptavidin/0.622
2zscBTNTamavidin2/0.621
1nc9IMIStreptavidin/0.608
4yvbBTNStreptavidin/0.603
1mepBTNStreptavidin/0.594
1sriDMBStreptavidin/0.587
1stpBTNStreptavidin/0.586
1swdBTNStreptavidin/0.581
4bx7B4FStreptavidin/0.577
1srgMHBStreptavidin/0.574
1ndjBTNStreptavidin/0.567
4gd9BTNStreptavidin/0.566
1swtBTNStreptavidin/0.562
3wypBSOStreptavidin/0.560
1swrBTNStreptavidin/0.559
2rtoIMIStreptavidin/0.556
4bj8BTNAvidin/0.556
2fhnBNIAvidin-related protein 4/5/0.555
2izhBTNStreptavidin/0.554
2rtfBTNStreptavidin/0.552
1srfMTBStreptavidin/0.550
3vgwNVZAvidin/0.547
2izfBTNStreptavidin/0.546
2rtrIMIStreptavidin/0.541
1rxhBNIStreptavidin/0.539
1sreHABStreptavidin/0.539
2rtqIMIStreptavidin/0.539
3ry2BTNStreptavidin/0.539
1n43BTNStreptavidin/0.536
1luqBTNStreptavidin/0.535
3wznBTNStreptavidin/0.535
1lcwSHMStreptavidin/0.534
2aviBTNAvidin/0.533
2y3fBTNStreptavidin/0.533
2rtdBTNStreptavidin/0.532
2rteBTNStreptavidin/0.532
4dneDTBStreptavidin/0.532
1df8BTNStreptavidin/0.528
3vhmNPKAvidin/0.527
4gdaBTNStreptavidin/0.525
1srjNABStreptavidin/0.524
2izlIMIStreptavidin/0.523
1nqmBTNStreptavidin/0.520
2rtnIMIStreptavidin/0.518
1i9hBNIStreptavidin/0.517
2izgBTNStreptavidin/0.517
2c4iBTNAvidin/0.513
1avdBTNAvidin/0.512
2rtgBTNStreptavidin/0.507
1mk5BTNStreptavidin/0.505
2rtpIMIStreptavidin/0.504
3vhiVHIAvidin/0.503
4ggzBTNBll1558 protein/0.503
3wyqBTNStreptavidin/0.502
1srhMOBStreptavidin/0.501
2rtmIMIStreptavidin/0.501
2uz2BTNAvd protein/0.501
3vhhVHHAvidin/0.500
4jq4IMNAldo-keto reductase family 1 member C2/0.491
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.489
4z28BTNHoefavidin/0.484
1pqc444Oxysterols receptor LXR-beta/0.483
3rdqDTBStreptavidin/0.483
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.481
2uywBTNAvd protein/0.478
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.476
3n0hTOPDihydrofolate reductase1.5.1.30.476
1obnASVIsopenicillin N synthase1.21.3.10.475
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.475
4bb3KKAIsopenicillin N synthase1.21.3.10.475
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.474
2fhlBNIAvidin-related protein 4/5/0.474
3h3sH15Collagen type IV alpha-3-binding protein/0.473
2jgsBTNAvidin/0.472
1pq944BOxysterols receptor LXR-beta/0.471
2jb4A14Isopenicillin N synthase1.21.3.10.471
2vbdV10Isopenicillin N synthase1.21.3.10.470
3zkyWT4Isopenicillin N synthase1.21.3.10.470
1fvpFMANon-fluorescent flavoprotein/0.468
2iziBTNStreptavidin/0.468
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.468
2y6fM9FIsopenicillin N synthase1.21.3.10.468
3zkuHCVIsopenicillin N synthase1.21.3.10.468
4phlPILPhosphodiesterase/0.468
1y52BTNAvidin-related protein 4/5/0.467
4ambDUDPutative glycosyl transferase/0.467
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.467
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.466
4kxjP34Nucleoprotein/0.466
1yhjR6CPyridoxal kinase2.7.1.350.465
1ygkRRCPyridoxal kinase2.7.1.350.464
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.464
2xlrFADPutative flavin-containing monooxygenase/0.464
3s5wFADL-ornithine N(5)-monooxygenase/0.464
1rkwPNTHTH-type transcriptional regulator QacR/0.462
3gwfFADCyclohexanone monooxygenase/0.462
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.462
8catNDPCatalase1.11.1.60.462
4mqt2CUMuscarinic acetylcholine receptor M2/0.462
3bg7FADPyranose 2-oxidase/0.461
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.461
4j7hTRHPCZA361.3/0.461
1g8jMGDArsenite oxidase subunit AioA1.20.9.10.460
1qvtPRLHTH-type transcriptional regulator QacR/0.460
3bgxMEFThymidylate synthase/0.460
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.459
1hb3SCVIsopenicillin N synthase1.21.3.10.459
1qjfACSIsopenicillin N synthase1.21.3.10.459
2xveFADPutative flavin-containing monooxygenase/0.459
4jlj1NMDeoxycytidine kinase2.7.1.740.459
4pnmNU1Tankyrase-22.4.2.300.459
1ry0PG2Aldo-keto reductase family 1 member C3/0.458
2vcmM11Isopenicillin N synthase1.21.3.10.458
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.458
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.458
4bcsBTNAvidin-related protein 4/5/0.458
4buiW2ETankyrase-22.4.2.300.458
4l091URTankyrase-22.4.2.300.458
4psbGA3Cytokinin-specific binding protein/0.458
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.457
4b68NAPL-ornithine N(5)-monooxygenase/0.457
4xd1T3QQdtf/0.457
1hfqMOTDihydrofolate reductase1.5.1.30.456
4jlm1NNDeoxycytidine kinase2.7.1.740.456
1j9zFADNADPH--cytochrome P450 reductase/0.455
2vkeTACTetracycline repressor protein class D/0.455
7catNDPCatalase1.11.1.60.455
4s0vSUVOrexin receptor type 2/0.455
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.454
1hb1OCVIsopenicillin N synthase1.21.3.10.454
1lczBH7Streptavidin/0.454
1lf3EH5Plasmepsin-23.4.23.390.454
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
2vbpVB1Isopenicillin N synthase1.21.3.10.454
4q0kGA3Phytohormone-binding protein/0.454
1e2nRCAThymidine kinase/0.453
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1oc1ASVIsopenicillin N synthase1.21.3.10.453
2bjsACVIsopenicillin N synthase1.21.3.10.453
2zjwREFCasein kinase II subunit alpha2.7.11.10.453
4fam0SZAldo-keto reductase family 1 member C3/0.453
1mp0NADAlcohol dehydrogenase class-31.1.1.10.452
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.452
1ye4NADNAD(P)H-dependent D-xylose reductase1.1.1.3070.452
2xlsFADPutative flavin-containing monooxygenase/0.452
3f3y4OABile salt sulfotransferase2.8.2.140.452
3oqkS52Renin3.4.23.150.452
4b63NAPL-ornithine N(5)-monooxygenase/0.452
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.452
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.452
2xvfFADPutative flavin-containing monooxygenase/0.451
3br3ETHTH-type transcriptional regulator QacR/0.451
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.451
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.450
1synF89Thymidylate synthase/0.450
2iviACWIsopenicillin N synthase1.21.3.10.450
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.450
3sf6FDAGlutaryl-CoA dehydrogenase/0.450
3zoiM2WIsopenicillin N synthase1.21.3.10.450
4g5dNDPProstaglandin F synthase1.1.1.1880.450
4kwhNAPReductase homolog/0.450
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.450
5d1bTSNHistone deacetylase 83.5.1.980.450
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.449
1qiqACCIsopenicillin N synthase1.21.3.10.449
2rm2W43Genome polyprotein/0.449
3t2wBTNAvidin/streptavidin/0.449
4dc0NDPPutative ketoacyl reductase1.3.10.449
1pj6FOLDimethylglycine oxidase1.5.3.100.448
2iko7IGRenin3.4.23.150.448
2xlpFADPutative flavin-containing monooxygenase/0.448
3f0aACOSpermidine N(1)-acetyltransferase/0.448
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.448
4iarERM5-hydroxytryptamine receptor 1B/0.448
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.447
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.447
3d5qT30Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
3gwdNAPCyclohexanone monooxygenase/0.447
4bquCLRJapanin/0.447
4j6cSTRCytochrome P450 monooxygenase/0.447
4l5b1UXDeoxycytidine kinase2.7.1.740.447
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.447
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.446
1fwmCB3Thymidylate synthase/0.446
1o6qR17Squalene--hopene cyclase4.2.1.1290.446
1q23FUAChloramphenicol acetyltransferase2.3.1.280.446
2g1s4IGRenin3.4.23.150.446
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4a2aATPCell division protein FtsA/0.446
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.446
4n4wSNTSmoothened homolog/0.446
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.445
1mczRMNBenzoylformate decarboxylase4.1.1.70.445
1umcTDP2-oxoisovalerate dehydrogenase subunit alpha1.2.4.40.445
1umcTDP2-oxoisovalerate dehydrogenase subunit beta1.2.4.40.445
2bktRPFRenin3.4.23.150.445
2qtrNXXProbable nicotinate-nucleotide adenylyltransferase/0.445
2wmdZZ0NmrA-like family domain-containing protein 1/0.445
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3o6o94MHeat shock protein 83/0.445
3oagLPQRenin3.4.23.150.445
3pefNAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase/0.445
4e2zJHZMethyltransferase/0.445
4jlk1NODeoxycytidine kinase2.7.1.740.445
5ch7MD1DMSO reductase family type II enzyme, molybdopterin subunit/0.445
1s7nCOAAcetyl transferase/0.444
1vzaUMPThymidylate synthase/0.444
1x8lOXRRetinol dehydratase/0.444
2w6oOA3Biotin carboxylase6.3.4.140.444
2wwjY28Lysine-specific demethylase 4A/0.444
2z1qFADAcyl-CoA dehydrogenase/0.444
2z3uCRRCytochrome P450/0.444
3aosJH2Hemolymph juvenile hormone binding protein/0.444
3uthFDAUDP-galactopyranose mutase/0.444
4pmjNAPPutative oxidoreductase/0.444
1h35R01Squalene--hopene cyclase4.2.1.1290.443
1h36R88Squalene--hopene cyclase4.2.1.1290.443
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
1wsvTHHAminomethyltransferase, mitochondrial/0.443
2g263LGRenin3.4.23.150.443
2i4qUA4Renin3.4.23.150.443
2xtbKRMAdenosine kinase, putative/0.443
2y60M8FIsopenicillin N synthase1.21.3.10.443
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.443
3d4bDZDNAD-dependent protein deacetylase/0.443
4dbs0HVAldo-keto reductase family 1 member C3/0.443
4hlg20BTankyrase-22.4.2.300.443
4rtsSAMDNA adenine methylase2.1.1.720.443
3sn6P0GBeta-2 adrenergic receptor/0.443
1o1t2NHProtein farnesyltransferase subunit beta2.5.1.580.442
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2fznFADBifunctional protein PutA1.5.5.20.442
2w6qOA5Biotin carboxylase6.3.4.140.442
3bw4FMNPutative 2-nitropropane dioxygenase/0.442
3r96ACOMccE protein/0.442
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.442
4q72FADBifunctional protein PutA/0.442
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.442
1jf0CZHObelin/0.441
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.441
1s7lCOAAcetyl transferase/0.441
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.441
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.441
4l4xNDPAmphI/0.441
4xczT3QQdtf/0.441
1bsvNDPGDP-L-fucose synthase/0.440
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.440
3c3xNAPEugenol synthase 11.1.1.3180.440
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4m9aFDAAcyl-CoA dehydrogenase/0.440
4r81FMNPredicted NADH dehydrogenase/0.440
4ybnFADFlavin-nucleotide-binding protein/0.440