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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
1swrBTNStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1swrBTNStreptavidin/1.000
2izhBTNStreptavidin/0.600
4bx7B4FStreptavidin/0.593
1swnBTNStreptavidin/0.585
1nqmBTNStreptavidin/0.575
1swpBTNStreptavidin/0.574
2rtqIMIStreptavidin/0.572
2rteBTNStreptavidin/0.570
2aviBTNAvidin/0.568
2fhnBNIAvidin-related protein 4/5/0.565
1sriDMBStreptavidin/0.564
2rtfBTNStreptavidin/0.560
2rtdBTNStreptavidin/0.557
1srfMTBStreptavidin/0.556
1stpBTNStreptavidin/0.556
2izlIMIStreptavidin/0.556
2rtpIMIStreptavidin/0.556
2izgBTNStreptavidin/0.551
1avdBTNAvidin/0.549
2zscBTNTamavidin2/0.546
1mk5BTNStreptavidin/0.545
2rtgBTNStreptavidin/0.545
2y3fBTNStreptavidin/0.545
4yvbBTNStreptavidin/0.544
1srgMHBStreptavidin/0.542
1n9mBTNStreptavidin/0.538
1swdBTNStreptavidin/0.538
4bj8BTNAvidin/0.538
1sreHABStreptavidin/0.536
1swpBTQStreptavidin/0.536
1nc9IMIStreptavidin/0.535
2fhlBNIAvidin-related protein 4/5/0.535
4dneDTBStreptavidin/0.535
1lcwSHMStreptavidin/0.534
2rtoIMIStreptavidin/0.532
2rtrIMIStreptavidin/0.532
1sweBTNStreptavidin/0.531
3ry2BTNStreptavidin/0.530
1luqBTNStreptavidin/0.528
2uz2BTNAvd protein/0.527
3wznBTNStreptavidin/0.527
2c4iBTNAvidin/0.525
1i9hBNIStreptavidin/0.523
2rtmIMIStreptavidin/0.523
1mepBTNStreptavidin/0.520
4gd9BTNStreptavidin/0.520
2izfBTNStreptavidin/0.518
1rxhBNIStreptavidin/0.516
1n43BTNStreptavidin/0.515
4gdaBTNStreptavidin/0.515
1df8BTNStreptavidin/0.513
1ndjBTNStreptavidin/0.512
1swtBTNStreptavidin/0.511
3wyqBTNStreptavidin/0.509
1y52BTNAvidin-related protein 4/5/0.506
4z28BTNHoefavidin/0.505
3rdqDTBStreptavidin/0.504
2rtnIMIStreptavidin/0.502
4bcsBTNAvidin-related protein 4/5/0.499
1srjNABStreptavidin/0.496
4a2aATPCell division protein FtsA/0.493
1srhMOBStreptavidin/0.491
1d3pBT3Prothrombin3.4.21.50.490
3arvSAUChitinase A/0.490
3vhiVHIAvidin/0.487
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.486
3vgwNVZAvidin/0.485
1pq944BOxysterols receptor LXR-beta/0.483
3w8wFADPutative FAD-dependent oxygenase EncM/0.482
3wypBSOStreptavidin/0.477
3zkyWT4Isopenicillin N synthase1.21.3.10.475
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.475
1fvpFMANon-fluorescent flavoprotein/0.474
2uywBTNAvd protein/0.474
3mzhCMPCRP-like cAMP-activated global transcriptional regulator/0.474
2y6fM9FIsopenicillin N synthase1.21.3.10.473
3bi6396Wee1-like protein kinase2.7.10.20.473
4pd6URINucleoside permease/0.471
5irnADPNucleotide binding oligomerization domain containing 2/0.471
2y60M8FIsopenicillin N synthase1.21.3.10.469
2iviACWIsopenicillin N synthase1.21.3.10.468
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.468
4l5b1UXDeoxycytidine kinase2.7.1.740.468
3v76FDAUncharacterized protein/0.467
4n4wSNTSmoothened homolog/0.467
1bk0ACVIsopenicillin N synthase1.21.3.10.466
2xrlDXTTetracycline repressor protein class D/0.466
3vhhVHHAvidin/0.466
2iziBTNStreptavidin/0.465
1z7yAA5Cysteine synthase 12.5.1.470.464
2x86ADPADP-L-glycero-D-manno-heptose-6-epimerase/0.464
1ypeUIPProthrombin3.4.21.50.463
4j3mAJ8Tankyrase-22.4.2.300.463
2izjBTNStreptavidin/0.462
4ntcFADThioredoxin reductase gliT/0.462
1k4hAPQQueuine tRNA-ribosyltransferase2.4.2.290.461
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.460
2gqfFADUncharacterized protein HI_0933/0.460
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.459
2vbdV10Isopenicillin N synthase1.21.3.10.459
3vf60H6Glucokinase2.7.1.20.459
1lczBH7Streptavidin/0.458
3mg3ECHOrange carotenoid-binding protein/0.458
3vhmNPKAvidin/0.458
5fuwTHMThymidine kinase, putative/0.458
5iqdGNPBifunctional AAC/APH2.3.10.458
2xtbKRMAdenosine kinase, putative/0.457
2xveFADPutative flavin-containing monooxygenase/0.457
3biy01KHistone acetyltransferase p300/0.457
3t2wBTNAvidin/streptavidin/0.457
5dwqSFGHistone-arginine methyltransferase CARM1/0.457
7catNDPCatalase1.11.1.60.457
2gsdNADFormate dehydrogenase/0.456
3mjhGTPRas-related protein Rab-5A/0.456
2wo7ASVIsopenicillin N synthase1.21.3.10.455
3bg7FADPyranose 2-oxidase/0.455
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.455
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.454
2cahNDPCatalase1.11.1.60.454
2culFADGidA-related protein/0.454
2trtTACTetracycline repressor protein class D/0.454
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.454
4d7mTDCTetracycline repressor protein class D/0.454
3frkTQPQdtB/0.453
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.453
3pg3DG7Mitogen-activated protein kinase 14/0.453
1zdwFLVPrenyltransferase/0.452
3tp0FO5HTH-type transcriptional regulator EthR/0.452
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
3ha5SFGHydroxymycolate synthase MmaA42.1.10.451
4c1fX8ZMetallo-beta-lactamase type 2/0.451
4n3cUD1UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.451
2pncCLUPrimary amine oxidase, liver isozyme/0.450
2rtiGLLStreptavidin/0.450
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.450
3mteSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.450
4an4DUDPutative glycosyl transferase/0.450
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.450
4bfuZVUPantothenate kinase2.7.1.330.450
4j6cSTRCytochrome P450 monooxygenase/0.450
4kf1HT5Aryldialkylphosphatase3.1.8.10.450
1oytFSNProthrombin3.4.21.50.449
4i1c1BEBeta-secretase 13.4.23.460.449
1efvFADElectron transfer flavoprotein subunit alpha, mitochondrial/0.448
1f0xFADD-lactate dehydrogenase1.1.1.280.448
1gheACOAcetyltransferase2.3.10.448
1kt3RTLRetinol-binding protein 4/0.448
2anmCDOProthrombin3.4.21.50.448
2p2qPRXAcetyl-coenzyme A synthetase/0.448
2vbpVB1Isopenicillin N synthase1.21.3.10.448
2xlsFADPutative flavin-containing monooxygenase/0.448
3h3t16HCollagen type IV alpha-3-binding protein/0.448
4dpwAGSMevalonate diphosphate decarboxylase/0.448
4eajATP5'-AMP-activated protein kinase subunit gamma-1/0.448
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.448
1nzq162Prothrombin3.4.21.50.447
2jgsBTNAvidin/0.447
2vkeTACTetracycline repressor protein class D/0.447
2zjwREFCasein kinase II subunit alpha2.7.11.10.447
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.447
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3q44D50M1 family aminopeptidase3.4.110.447
3v0o4GWHisto-blood group ABO system transferase/0.447
4bftZVTPantothenate kinase2.7.1.330.447
4dvi2IWTankyrase-12.4.2.300.447
5eccNAPDehydrofolate reductase type I/0.447
2ehuNAD1-pyrroline-5-carboxylate dehydrogenase/0.446
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.446
3gkiCLRNiemann-Pick C1 protein/0.446
3pe13NGCasein kinase II subunit alpha2.7.11.10.446
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.446
4rh10TTSpore photoproduct lyase/0.446
5er0FADUncharacterized NAD(FAD)-dependent dehydrogenase/0.446
1hb1OCVIsopenicillin N synthase1.21.3.10.445
1jjeBYSBeta-lactamase/0.445
1zgbA1EAcetylcholinesterase3.1.1.70.445
2hq9FADMll6688 protein/0.445
2z3uCRRCytochrome P450/0.445
3gkjHC3Niemann-Pick C1 protein/0.445
3jv7NADSecondary alcohol dehydrogenase/0.445
3v9v21LPeroxisome proliferator-activated receptor gamma/0.445
4a6eASEAcetylserotonin O-methyltransferase2.1.1.40.445
4phlPILPhosphodiesterase/0.445
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.444
1hb3SCVIsopenicillin N synthase1.21.3.10.444
1oj4CDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.444
2xlrFADPutative flavin-containing monooxygenase/0.444
3biu10UProthrombin3.4.21.50.444
3bw2FMNPutative 2-nitropropane dioxygenase/0.444
4bb3KKAIsopenicillin N synthase1.21.3.10.444
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.444
1e7aPFLSerum albumin/0.443
1x31FMNSubunit alpha of sarocosine oxidase/0.443
1x31FMNSubunit beta of sarcosine oxidase/0.443
1ypjUIBProthrombin3.4.21.50.443
2igoFADPyranose 2-oxidase/0.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
2x7hPFNProstaglandin reductase 310.443
2zhw12UProthrombin3.4.21.50.443
3zeiAWHO-acetylserine sulfhydrylase/0.443
4b3aTACTetracycline repressor protein class D/0.443
4buiW2ETankyrase-22.4.2.300.443
4fxy0W2Neurolysin, mitochondrial3.4.24.160.443
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.443
4z24FADPutative GMC-type oxidoreductase R13510.443
5l3rGCPCell division protein FtsY homolog, chloroplastic/0.443
1cjtFOKAdenylate cyclase type 2/0.442
1cjtFOKAdenylate cyclase type 5/0.442
1h36R88Squalene--hopene cyclase4.2.1.1290.442
1me6IVSPlasmepsin-23.4.23.390.442
1mo9FAD2-oxopropyl-CoM reductase, carboxylating1.8.1.50.442
1ojtFADDihydrolipoyl dehydrogenase/0.442
1p8dCO1Oxysterols receptor LXR-beta/0.442
1vzqSHYProthrombin3.4.21.50.442
1x1cSAHC-20 methyltransferase/0.442
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.442
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.442
3bw4FMNPutative 2-nitropropane dioxygenase/0.442
4cdmFO1Deoxyribodipyrimidine photolyase/0.442
4nieNBHNuclear receptor ROR-gamma/0.442
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.442
5dxjSFGHistone-arginine methyltransferase CARM1/0.442
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.442
1ycgFMNNitric oxide reductase10.441
1z6tADPApoptotic protease-activating factor 1/0.441
2wdzNADGalactitol dehydrogenase/0.441
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
2ym1FADPhenylacetone monooxygenase1.14.13.920.441
2zevB71Geranylgeranyl pyrophosphate synthase/0.441
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3eq6BCOAcyl-coenzyme A synthetase ACSM2A, mitochondrial6.2.1.20.441
3jpuTY4Transcriptional activator protein LasR/0.441
4aosFADSteroid monooxygenase/0.441
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.441
4jlm1NNDeoxycytidine kinase2.7.1.740.441
1d3dBZTProthrombin3.4.21.50.440
1qf5RPLAdenylosuccinate synthetase/0.440
1ty8ADPProbable ADP-ribose 1''-phosphate phosphatase YML087W3.1.3.840.440
2ignFADPyranose 2-oxidase/0.440
2o7oDXTTetracycline repressor protein class D/0.440
2r2mI50Prothrombin3.4.21.50.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2wmdZZ0NmrA-like family domain-containing protein 1/0.440
2yg3FADPutrescine oxidase/0.440
3b3fSAHHistone-arginine methyltransferase CARM1/0.440
3fznD7KBenzoylformate decarboxylase4.1.1.70.440
3p2kSAM16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.440
3pe2E1BCasein kinase II subunit alpha2.7.11.10.440
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.440
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.440
5e7oMGDDMSO reductase family type II enzyme, molybdopterin subunit/0.440