Logo scPDB

sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

Logo CNRS Logo Unistra
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
1swdBTNStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1swdBTNStreptavidin/1.000
1swpBTQStreptavidin/0.605
1swnBTNStreptavidin/0.594
1mepBTNStreptavidin/0.580
1sweBTNStreptavidin/0.580
1n9mBTNStreptavidin/0.570
1swpBTNStreptavidin/0.569
1ndjBTNStreptavidin/0.555
1nc9IMIStreptavidin/0.554
2zscBTNTamavidin2/0.546
4yvbBTNStreptavidin/0.546
2izhBTNStreptavidin/0.539
3wypBSOStreptavidin/0.534
1stpBTNStreptavidin/0.531
2rtfBTNStreptavidin/0.531
4bj8BTNAvidin/0.526
1sreHABStreptavidin/0.524
1sriDMBStreptavidin/0.524
2rtgBTNStreptavidin/0.524
2izfBTNStreptavidin/0.517
1srgMHBStreptavidin/0.513
1rxhBNIStreptavidin/0.511
2fhnBNIAvidin-related protein 4/5/0.511
4bx7B4FStreptavidin/0.511
4ggzBTNBll1558 protein/0.511
1mk5BTNStreptavidin/0.502
3rdqDTBStreptavidin/0.502
1srfMTBStreptavidin/0.500
2rtoIMIStreptavidin/0.498
1n43BTNStreptavidin/0.496
3ry2BTNStreptavidin/0.493
2y3fBTNStreptavidin/0.491
4gd9BTNStreptavidin/0.490
2vczVC3Hematopoietic prostaglandin D synthase/0.488
2aviBTNAvidin/0.486
1df8BTNStreptavidin/0.485
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.485
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.484
4ambDUDPutative glycosyl transferase/0.482
1luqBTNStreptavidin/0.481
3s5wFADL-ornithine N(5)-monooxygenase/0.481
4gdaBTNStreptavidin/0.481
1swrBTNStreptavidin/0.480
1lcwSHMStreptavidin/0.478
2rtmIMIStreptavidin/0.478
3i0pNADMalate dehydrogenase, putative/0.478
3vgwNVZAvidin/0.473
2fj1CTCTetracycline repressor protein class D/0.471
1obnASVIsopenicillin N synthase1.21.3.10.470
3vhhVHHAvidin/0.470
1nqmBTNStreptavidin/0.469
2gpjFADSiderophore-interacting protein/0.469
2izlIMIStreptavidin/0.469
3zkyWT4Isopenicillin N synthase1.21.3.10.469
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.468
3vhiVHIAvidin/0.467
1avdBTNAvidin/0.466
3d4bDZDNAD-dependent protein deacetylase/0.465
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.464
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.464
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.463
5dp2NAPCurF/0.463
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.461
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.461
4bkqNAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.461
1w4zNAPPutative ketoacyl reductase1.3.10.459
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.459
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.459
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.459
1yhjR6CPyridoxal kinase2.7.1.350.458
4dbzNDPPutative ketoacyl reductase1.3.10.458
4z28BTNHoefavidin/0.458
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.457
2uywBTNAvd protein/0.457
2x9dITCTetracycline repressor protein class D/0.457
5cb3APRO-acetyl-ADP-ribose deacetylase/0.457
1blzACVIsopenicillin N synthase1.21.3.10.456
1z7yAA5Cysteine synthase 12.5.1.470.456
2rtrIMIStreptavidin/0.456
4d0lGSPRas-related protein Rab-11A/0.456
5fm7ADPRuvB-like helicase/0.456
3pm1ETHTH-type transcriptional regulator QacR/0.455
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.455
2hdjNDPAldo-keto reductase family 1 member C2/0.454
2vkeTACTetracycline repressor protein class D/0.454
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.454
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.454
3mjhGTPRas-related protein Rab-5A/0.454
4bfvZVVPantothenate kinase2.7.1.330.454
2i0zFADNAD(FAD)-utilizing dehydrogenases/0.453
2rtnIMIStreptavidin/0.453
3go4SAHUncharacterized protein/0.453
3o4rNAPDehydrogenase/reductase SDR family member 41.1.1.1840.453
3toxNAPPutative oxidoreductase/0.453
4bb3KKAIsopenicillin N synthase1.21.3.10.453
4xybNDPFormate dehydrogenase/0.453
1ygkRRCPyridoxal kinase2.7.1.350.452
3kxoKXOHematopoietic prostaglandin D synthase/0.452
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.452
4dvi2IWTankyrase-12.4.2.300.452
1ay0TPPTransketolase 12.2.1.10.451
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.451
2rtqIMIStreptavidin/0.451
2xlrFADPutative flavin-containing monooxygenase/0.451
1hvyD16Thymidylate synthase2.1.1.450.450
1pr9NAPL-xylulose reductase1.1.1.100.450
2xviFADPutative flavin-containing monooxygenase/0.450
1ot7CHCBile acid receptor/0.449
1yqzCOACoenzyme A disulfide reductase/0.449
2g8yNADHydroxycarboxylate dehydrogenase B/0.449
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.449
2vcqD25Hematopoietic prostaglandin D synthase/0.449
3bi6396Wee1-like protein kinase2.7.10.20.449
3br3ETHTH-type transcriptional regulator QacR/0.449
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.449
2rgoFADAlpha-Glycerophosphate Oxidase/0.448
2wu4HBPAcetylcholinesterase3.1.1.70.448
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.448
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.448
4q71FADBifunctional protein PutA/0.448
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.448
2ol4JPNEnoyl-ACP reductase/0.447
2zjwREFCasein kinase II subunit alpha2.7.11.10.447
3w8fNAD3-hydroxybutyrate dehydrogenase/0.447
3emlZMAAdenosine receptor A2a/0.447
1sqi8694-hydroxyphenylpyruvate dioxygenase/0.446
2r6jNDPEugenol synthase 11.1.1.3180.446
2ym1NAPPhenylacetone monooxygenase1.14.13.920.446
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.446
4c77N01Phenylacetone monooxygenase1.14.13.920.446
4uugPXGBranched-chain amino acid aminotransferase, putative/0.446
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.445
2mm3CHOGastrotropin/0.445
2x7hPFNProstaglandin reductase 310.445
3h3sH15Collagen type IV alpha-3-binding protein/0.445
4d86ADPPoly [ADP-ribose] polymerase 142.4.2.300.445
1bxkNADdTDP-glucose 4,6-dehydratase 2/0.444
2xlpFADPutative flavin-containing monooxygenase/0.444
3slkNDPPolyketide synthase extender module 2/0.444
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
5ifyUMPGlucose-1-phosphate thymidylyltransferase/0.444
1p4mADPRiboflavin kinase2.7.1.260.443
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.443
2vcwZZAHematopoietic prostaglandin D synthase/0.443
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.443
3lqfNADGalactitol dehydrogenase/0.443
4dc0NDPPutative ketoacyl reductase1.3.10.443
4h6pFMNChromate reductase/0.443
4rrgA3TThreonine--tRNA ligase6.1.1.30.443
1fvpFMANon-fluorescent flavoprotein/0.442
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.442
2ntvP1HEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
2y6fM9FIsopenicillin N synthase1.21.3.10.442
3d7zGK5Mitogen-activated protein kinase 14/0.442
3q43D66M1 family aminopeptidase3.4.110.442
4bfsZVSPantothenate kinase2.7.1.330.442
4edz0O5Hematopoietic prostaglandin D synthase/0.442
5jtbZMAAdenosine receptor A2a/0.442
1hb1OCVIsopenicillin N synthase1.21.3.10.441
2hu2NADC-terminal binding protein 1/0.441
2p2mPRXAcetyl-coenzyme A synthetase/0.441
2uz2BTNAvd protein/0.441
2z3uCRRCytochrome P450/0.441
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.441
3ekuCY9Actin-5C/0.441
3mzhCMPCRP-like cAMP-activated global transcriptional regulator/0.441
4ieiADPGene 2 protein/0.441
4l1xNAPAldo-keto reductase family 1 member C2/0.441
1c7oPPGHemolysin/0.440
1d3pBT3Prothrombin3.4.21.50.440
1h60STRPentaerythritol tetranitrate reductase/0.440
1ma0NADAlcohol dehydrogenase class-31.1.1.10.440
1tezFADDeoxyribodipyrimidine photo-lyase4.1.99.30.440
3w2fNADNADH-cytochrome b5 reductase 31.6.2.20.440
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.440