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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
1mepBTNStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1mepBTNStreptavidin/1.000
1sweBTNStreptavidin/0.640
1ndjBTNStreptavidin/0.586
2zscBTNTamavidin2/0.583
1swnBTNStreptavidin/0.577
1n43BTNStreptavidin/0.575
1swdBTNStreptavidin/0.570
1swpBTQStreptavidin/0.561
1n9mBTNStreptavidin/0.558
2fhnBNIAvidin-related protein 4/5/0.553
1swpBTNStreptavidin/0.552
1sriDMBStreptavidin/0.550
1nc9IMIStreptavidin/0.540
3wypBSOStreptavidin/0.538
1srgMHBStreptavidin/0.537
2rtrIMIStreptavidin/0.536
1swtBTNStreptavidin/0.535
2aviBTNAvidin/0.528
3wznBTNStreptavidin/0.528
3vhiVHIAvidin/0.524
1stpBTNStreptavidin/0.520
1sreHABStreptavidin/0.516
1nqmBTNStreptavidin/0.513
2izfBTNStreptavidin/0.513
3vgwNVZAvidin/0.513
4bx7B4FStreptavidin/0.512
4dneDTBStreptavidin/0.510
4yvbBTNStreptavidin/0.510
2rtqIMIStreptavidin/0.509
1mk5BTNStreptavidin/0.507
1df8BTNStreptavidin/0.506
1avdBTNAvidin/0.505
4bj8BTNAvidin/0.504
2rtfBTNStreptavidin/0.502
1srfMTBStreptavidin/0.501
3vhhVHHAvidin/0.498
2y3fBTNStreptavidin/0.497
3ry2BTNStreptavidin/0.496
2izhBTNStreptavidin/0.495
2rtoIMIStreptavidin/0.495
2uz2BTNAvd protein/0.492
2izlIMIStreptavidin/0.489
2rtdBTNStreptavidin/0.488
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.488
2rtgBTNStreptavidin/0.487
2rtmIMIStreptavidin/0.487
3zkyWT4Isopenicillin N synthase1.21.3.10.487
2izgBTNStreptavidin/0.485
4gd9BTNStreptavidin/0.485
3bg7FADPyranose 2-oxidase/0.484
4ggzBTNBll1558 protein/0.484
1bk0ACVIsopenicillin N synthase1.21.3.10.482
1gqtACPRibokinase/0.481
1srjNABStreptavidin/0.481
2iviACWIsopenicillin N synthase1.21.3.10.481
3gwfFADCyclohexanone monooxygenase/0.480
1swrBTNStreptavidin/0.479
2jb4A14Isopenicillin N synthase1.21.3.10.479
1hb1OCVIsopenicillin N synthase1.21.3.10.478
4bb3KKAIsopenicillin N synthase1.21.3.10.478
3zoiM2WIsopenicillin N synthase1.21.3.10.477
4dvi2IWTankyrase-12.4.2.300.477
1lcwSHMStreptavidin/0.476
2rtpIMIStreptavidin/0.475
2rtnIMIStreptavidin/0.474
3zkuHCVIsopenicillin N synthase1.21.3.10.474
4phlPILPhosphodiesterase/0.474
1rxhBNIStreptavidin/0.473
1hb3SCVIsopenicillin N synthase1.21.3.10.472
2xveFADPutative flavin-containing monooxygenase/0.472
4gdaBTNStreptavidin/0.472
1luqBTNStreptavidin/0.471
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.471
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.471
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.470
5dcyNAPIridoid synthase1.3.1.990.470
1y52BTNAvidin-related protein 4/5/0.469
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.468
2y6fM9FIsopenicillin N synthase1.21.3.10.468
1blzACVIsopenicillin N synthase1.21.3.10.467
2xlrFADPutative flavin-containing monooxygenase/0.467
1sdwIYTPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.466
1yqdNAPSinapyl alcohol dehydrogenase/0.466
2rteBTNStreptavidin/0.466
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.466
2bfrADP[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.465
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.465
1w06W05Isopenicillin N synthase1.21.3.10.464
2trtTACTetracycline repressor protein class D/0.464
3nx4NAPPutative oxidoreductase/0.464
5dp2NAPCurF/0.464
5g53NECAdenosine receptor A2a/0.464
1pqc444Oxysterols receptor LXR-beta/0.462
2c12FADNitroalkane oxidase1.7.3.10.462
2rs1W84Genome polyprotein/0.462
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.462
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.462
1qjfACSIsopenicillin N synthase1.21.3.10.461
1qorNDPQuinone oxidoreductase 1/0.461
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.461
2givACOHistone acetyltransferase KAT8/0.460
2hq9FADMll6688 protein/0.460
2x9dITCTetracycline repressor protein class D/0.460
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.460
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.460
3mzhCMPCRP-like cAMP-activated global transcriptional regulator/0.460
4q0kGA3Phytohormone-binding protein/0.460
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.459
1qiqACCIsopenicillin N synthase1.21.3.10.459
3ukoNADAlcohol dehydrogenase class-3/0.459
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.459
2y60M8FIsopenicillin N synthase1.21.3.10.458
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.458
3mj4FADUDP-galactopyranose mutase/0.458
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.458
2jgsBTNAvidin/0.457
5ch7MD1DMSO reductase family type II enzyme, molybdopterin subunit/0.457
1obnASVIsopenicillin N synthase1.21.3.10.456
1srhMOBStreptavidin/0.456
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.456
2fj1CTCTetracycline repressor protein class D/0.456
2xpuTDCTetracycline repressor protein class D/0.456
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.456
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.456
2eixFADNADH-cytochrome b5 reductase/0.455
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.454
3bi6396Wee1-like protein kinase2.7.10.20.454
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
5dbfNDPIridoid synthase1.3.1.990.454
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.454
2c0cNAPProstaglandin reductase 310.453
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.453
4bxk1IUAngiotensin-converting enzyme3.2.10.453
4xybNDPFormate dehydrogenase/0.453
1g8jMGDArsenite oxidase subunit AioA1.20.9.10.452
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.452
2vbpVB1Isopenicillin N synthase1.21.3.10.452
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.452
3ohh3HHBeta-secretase 13.4.23.460.452
4b1rITCTetracycline repressor protein class D/0.452
4xulGTPUncharacterized protein mg662/0.452
1pq944BOxysterols receptor LXR-beta/0.451
2po7CHDFerrochelatase, mitochondrial4.99.1.10.451
2uywBTNAvd protein/0.451
2vkeTACTetracycline repressor protein class D/0.451
2wo7ASVIsopenicillin N synthase1.21.3.10.451
3cid318Beta-secretase 13.4.23.460.451
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.451
3ndjJHZMethyltransferase/0.451
4kxjP34Nucleoprotein/0.451
4mihFADPyranose 2-oxidase1.1.3.100.451
4zu44TGWxcM-like protein/0.451
7catNDPCatalase1.11.1.60.451
1fvpFMANon-fluorescent flavoprotein/0.450
1tysDHFThymidylate synthase/0.450
2i0zFADNAD(FAD)-utilizing dehydrogenases/0.450
2vczVC3Hematopoietic prostaglandin D synthase/0.450
3pqbVGPPutative oxidoreductase/0.450
4k8s1QTBeta-secretase 13.4.23.460.450
4lsaBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.450
4z28BTNHoefavidin/0.450
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.449
2xvfFADPutative flavin-containing monooxygenase/0.449
3q9bB3NAcetylpolyamine amidohydrolase/0.449
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.449
1o97FADElectron transfer flavoprotein subunit alpha/0.448
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.448
3adaNADSubunit alpha of sarocosine oxidase/0.448
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3mjhGTPRas-related protein Rab-5A/0.448
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.448
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.448
4dpf0LGBeta-secretase 13.4.23.460.448
4e2yJHZMethyltransferase/0.448
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.448
1mjbACOHistone acetyltransferase ESA1/0.447
1xgjHTCBeta-lactamase3.5.2.60.447
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.447
2igyA2TPlasmepsin 2/0.447
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.447
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.447
2r2mI50Prothrombin3.4.21.50.447
2vcmM11Isopenicillin N synthase1.21.3.10.447
2ym2NAPPhenylacetone monooxygenase1.14.13.920.447
4aosFADSteroid monooxygenase/0.447
4e2zJHZMethyltransferase/0.447
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4wx1FDAUDP-galactopyranose mutase/0.447
1eveE20Acetylcholinesterase3.1.1.70.446
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.446
2anmCDOProthrombin3.4.21.50.446
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.446
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.446
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.446
3bgxMEFThymidylate synthase/0.446
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.446
3jynNDPQuinone oxidoreductase/0.446
3to6LYS_CMCHistone acetyltransferase ESA1/0.446
3up0D7SaceDAF-12/0.446
4gh5NADShort-chain dehydrogenase/reductase SDR/0.446
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.446
1i9hBNIStreptavidin/0.445
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.445
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.445
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.445
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
3k5c0BIBeta-secretase 13.4.23.460.445
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
3wyqBTNStreptavidin/0.445
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.445
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.445
4dpi0N1Beta-secretase 13.4.23.460.445
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4i0h1BLBeta-secretase 13.4.23.460.445
4jqh1MFAlr2278 protein/0.445
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.445
1wp4NDP3-hydroxyisobutyrate dehydrogenase/0.444
2gcgNDPGlyoxylate reductase/hydroxypyruvate reductase1.1.1.790.444
2vprTDCTetracycline repressor protein class H/0.444
2xlsFADPutative flavin-containing monooxygenase/0.444
2xrlDXTTetracycline repressor protein class D/0.444
3n0hTOPDihydrofolate reductase1.5.1.30.444
3qlrNDPDihydrofolate reductase1.5.1.30.444
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.444
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.444
4tm1FDAKtzI/0.444
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.444
5dbgNADIridoid synthase1.3.1.990.444
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.443
1nahNADUDP-glucose 4-epimerase5.1.3.20.443
1nuqNXXNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.443
1wnbNAIGamma-aminobutyraldehyde dehydrogenase1.2.1.190.443
2ftoCB3Thymidylate synthase/0.443
2rm2W43Genome polyprotein/0.443
2ylzFADPhenylacetone monooxygenase1.14.13.920.443
3a783EVVitamin D3 receptor/0.443
3dmeFADPutative conserved exported protein/0.443
4e32DWNMethyltransferase/0.443
4pnmNU1Tankyrase-22.4.2.300.443
4rupH97Vitamin D3 receptor A/0.443
5idwNAPShort-chain dehydrogenase/reductase SDR/0.443
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
1mvtDTMDihydrofolate reductase1.5.1.30.442
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.442
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.442
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.442
1t4v14AProthrombin3.4.21.50.442
1txiTX5Vitamin D3 receptor/0.442
2bjsACVIsopenicillin N synthase1.21.3.10.442
2hamC33Vitamin D3 receptor/0.442
2ok7FADFerredoxin--NADP reductase, apicoplast/0.442
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.442
2xpwOTCTetracycline repressor protein class D/0.442
3f63GTXGlutathione transferase GST1-4/0.442
3qwbNDPProbable quinone oxidoreductase1.6.5.50.442
4ambDUDPutative glycosyl transferase/0.442
4exg916Beta-secretase 13.4.23.460.442
4h3j10WBeta-secretase 13.4.23.460.442
4q71FADBifunctional protein PutA/0.442
4uugPXGBranched-chain amino acid aminotransferase, putative/0.442
5ig2NADShort-chain dehydrogenase/reductase SDR/0.442
5jscFADPutative acyl-CoA dehydrogenase/0.442
1ryiFADGlycine oxidase1.4.3.190.441
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.441
1uydPU8Heat shock protein HSP 90-alpha/0.441
1wn3HXCPhenylacetic acid degradation protein PaaI/0.441
1z7yAA5Cysteine synthase 12.5.1.470.441
2bjhFERFeruloyl esterase A3.1.1.730.441
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.441
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.441
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.441
4dh60KNBeta-secretase 13.4.23.460.441
4idgNADPutative UDP-glucose 4-epimerase/0.441
4jlj1NMDeoxycytidine kinase2.7.1.740.441
4rvgTYDD-mycarose 3-C-methyltransferase/0.441
1n5dNDPCarbonyl reductase [NADPH] 1/0.440
1xkqNDPUncharacterized protein/0.440
2bdyUNBProthrombin3.4.21.50.440
2fzwNADAlcohol dehydrogenase class-31.1.1.10.440
2r0pK2CPutative FAD-monooxygenase/0.440
2wu4HBPAcetylcholinesterase3.1.1.70.440
2xb5I7TTetracycline repressor protein class D/0.440
2xviFADPutative flavin-containing monooxygenase/0.440
2ykiYKIHeat shock protein HSP 90-alpha/0.440
3lpjZ75Beta-secretase 13.4.23.460.440
4bcsBTNAvidin-related protein 4/5/0.440
4dc0NDPPutative ketoacyl reductase1.3.10.440
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4jq3NAPAldo-keto reductase family 1 member C2/0.440
4k9h1QUBeta-secretase 13.4.23.460.440
4kwhNAPReductase homolog/0.440
4l9q9TPSerum albumin/0.440
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.440
8catNDPCatalase1.11.1.60.440
5uviZMAAdenosine receptor A2a/0.440