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
1srjNABStreptavidin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1srjNABStreptavidin/1.000
1sriDMBStreptavidin/0.662
1srhMOBStreptavidin/0.637
1srfMTBStreptavidin/0.625
1sreHABStreptavidin/0.624
1srgMHBStreptavidin/0.619
2rtrIMIStreptavidin/0.603
1i9hBNIStreptavidin/0.599
4bx7B4FStreptavidin/0.597
2rtoIMIStreptavidin/0.592
1lczBH7Streptavidin/0.589
1swtBTNStreptavidin/0.588
2rtdBTNStreptavidin/0.577
2rteBTNStreptavidin/0.572
2izlIMIStreptavidin/0.569
3wznBTNStreptavidin/0.569
1stpBTNStreptavidin/0.567
2rtpIMIStreptavidin/0.567
2rtgBTNStreptavidin/0.564
4gdaBTNStreptavidin/0.564
3ry2BTNStreptavidin/0.558
3rdqDTBStreptavidin/0.557
2rtfBTNStreptavidin/0.553
2izhBTNStreptavidin/0.550
2rtqIMIStreptavidin/0.549
1rxhBNIStreptavidin/0.543
4dneDTBStreptavidin/0.541
2izgBTNStreptavidin/0.540
1lcwSHMStreptavidin/0.534
2y3fBTNStreptavidin/0.533
1nqmBTNStreptavidin/0.525
2rtnIMIStreptavidin/0.525
1mk5BTNStreptavidin/0.524
2izfBTNStreptavidin/0.524
1luqBTNStreptavidin/0.522
1swnBTNStreptavidin/0.522
2iziBTNStreptavidin/0.522
4z28BTNHoefavidin/0.522
1y52BTNAvidin-related protein 4/5/0.521
2rtmIMIStreptavidin/0.516
1df8BTNStreptavidin/0.515
2fhnBNIAvidin-related protein 4/5/0.515
4gd9BTNStreptavidin/0.514
3wyqBTNStreptavidin/0.511
2uywBTNAvd protein/0.507
2fhlBNIAvidin-related protein 4/5/0.498
1sweBTNStreptavidin/0.497
2uz2BTNAvd protein/0.497
1swpBTNStreptavidin/0.496
1avdBTNAvidin/0.495
1fmlRTLRetinol dehydratase/0.493
2c4iBTNAvidin/0.492
2rtiGLLStreptavidin/0.492
2zscBTNTamavidin2/0.492
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.491
1swrBTNStreptavidin/0.487
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.487
4ez8DHFThymidylate synthase2.1.1.450.487
1iiuRTLRetinol-binding protein 4/0.485
2aviBTNAvidin/0.485
4bcsBTNAvidin-related protein 4/5/0.483
2x9dITCTetracycline repressor protein class D/0.481
1swpBTQStreptavidin/0.480
2zjwREFCasein kinase II subunit alpha2.7.11.10.480
4bb3KKAIsopenicillin N synthase1.21.3.10.480
1m78NDPDihydrofolate reductase1.5.1.30.479
2jgsBTNAvidin/0.478
1mepBTNStreptavidin/0.477
1r8qAFBCytohesin-2/0.477
1r8qAFBADP-ribosylation factor 1/0.477
1y0s331Peroxisome proliferator-activated receptor delta/0.476
2a5c8DAAvidin/0.476
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.474
1ia4TQ6Dihydrofolate reductase1.5.1.30.473
1trgCB3Thymidylate synthase/0.473
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.472
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
3zkuHCVIsopenicillin N synthase1.21.3.10.471
2izjBTNStreptavidin/0.470
5fd8A5APutative carboxypeptidase yocD/0.470
1n43BTNStreptavidin/0.469
3arvSAUChitinase A/0.469
3fhxPXLPyridoxal kinase2.7.1.350.469
1jtuLYBThymidylate synthase/0.468
3qlrNDPDihydrofolate reductase1.5.1.30.468
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.468
3fhxPLPPyridoxal kinase2.7.1.350.467
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3d5qT30Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.465
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.465
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.464
1n9mBTNStreptavidin/0.464
3bhrTHGThymidylate synthase/0.464
1blzACVIsopenicillin N synthase1.21.3.10.463
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.463
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.463
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.463
4bfuZVUPantothenate kinase2.7.1.330.463
4twnB96Ephrin type-A receptor 32.7.10.10.463
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.462
2rtkGLLStreptavidin/0.462
3h4vDVPPteridine reductase 11.5.1.330.462
4qzuRTLRetinol-binding protein 2/0.462
1ay0TPPTransketolase 12.2.1.10.461
1e7qNAPGDP-L-fucose synthase/0.461
1hb1OCVIsopenicillin N synthase1.21.3.10.461
3c3xNAPEugenol synthase 11.1.1.3180.461
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3ew2BTNHypothetical conserved protein/0.461
3nxyD2HDihydrofolate reductase1.5.1.30.461
4y9lFADAcyl-CoA dehydrogenase family member 11/0.461
1ne6SP1cAMP-dependent protein kinase type I-alpha regulatory subunit/0.460
1pq944BOxysterols receptor LXR-beta/0.460
1tkaN3TTransketolase 12.2.1.10.460
2zhw12UProthrombin3.4.21.50.460
4iarERM5-hydroxytryptamine receptor 1B/0.460
1kquBR4Phospholipase A2, membrane associated/0.459
1tysDHFThymidylate synthase/0.459
1x8lOXRRetinol dehydratase/0.459
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.459
1hdoNAPFlavin reductase (NADPH)/0.458
1hndCOA3-oxoacyl-[acyl-carrier-protein] synthase 3/0.458
1opbRETRetinol-binding protein 2/0.458
2z3uCRRCytochrome P450/0.458
4dbs0HVAldo-keto reductase family 1 member C3/0.458
4knzCB3Thymidylate synthase/0.458
4s1iPLPPyridoxal kinase, putative/0.458
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
4fgrADPPhosphoribosylaminoimidazole-succinocarboxamide synthase6.3.2.60.457
4uugPXGBranched-chain amino acid aminotransferase, putative/0.457
1nm6L86Prothrombin3.4.21.50.456
2c42TPPPyruvate synthase/0.456
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.456
2dvlFADAcyl-CoA dehydrogenase/0.456
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3hbbNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.456
3t2wBTNAvidin/streptavidin/0.456
4a2aATPCell division protein FtsA/0.456
1zg32HIIsoflavone 4'-O-methyltransferase/0.455
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.455
3bgxMEFThymidylate synthase/0.455
3vgwNVZAvidin/0.455
4pkl1GHUncharacterized protein/0.455
4rupH97Vitamin D3 receptor A/0.455
1e2nRCAThymidine kinase/0.454
1p8dCO1Oxysterols receptor LXR-beta/0.454
1r2jFADFkbI/0.454
2a9z26AAdenosine kinase2.7.1.200.454
2izkGLLStreptavidin/0.454
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.454
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
4g1z0VPVitamin D3 receptor A/0.454
5iu86DZAdenosine receptor A2a/0.454
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3q44D50M1 family aminopeptidase3.4.110.453
4at0FADPossible succinate dehydrogenase/0.453
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1ygkRRCPyridoxal kinase2.7.1.350.452
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.452
2g2hP16Tyrosine-protein kinase ABL12.7.10.20.452
2tohHBITyrosine 3-monooxygenase1.14.16.20.452
2xtbKRMAdenosine kinase, putative/0.452
2y6o1N1Ephrin type-A receptor 42.7.10.10.452
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.452
4b4vL34Bifunctional protein FolD/0.452
4ocpADPN-acetylhexosamine 1-kinase2.7.1.1620.452
4rquNADAlcohol dehydrogenase class-P/0.452
1kt3RTLRetinol-binding protein 4/0.451
1ndjBTNStreptavidin/0.451
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.451
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
2pksG44Prothrombin3.4.21.50.451
2qmzLDPRibosyldihydronicotinamide dehydrogenase [quinone]/0.451
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.451
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.451
3h3r14HCollagen type IV alpha-3-binding protein/0.451
4hdrDMDNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase/0.451
4hdrDMDArsB/0.451
4m6p20RNicotinamide phosphoribosyltransferase2.4.2.120.451
1dr2TAPDihydrofolate reductase1.5.1.30.450
1jnzFADAdenylylsulfate reductase, subunit A (AprA)/0.450
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.450
1xp8AGSProtein RecA/0.450
2zbaZBATrichothecene 3-O-acetyltransferase/0.450
3af0GDPPantothenate kinase2.7.1.330.450
3ixp834Ecdysone receptor/0.450
3q43D66M1 family aminopeptidase3.4.110.450
3up3XCAaceDAF-12/0.450
4bj8BTNAvidin/0.450
4eilCB3Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.450
4l5b1UXDeoxycytidine kinase2.7.1.740.450
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.450
1cgzSTLChalcone synthase 22.3.1.740.449
1l8qADPChromosomal replication initiator protein DnaA/0.449
1nc9IMIStreptavidin/0.449
1pqc444Oxysterols receptor LXR-beta/0.449
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.449
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
1jtqLY3Thymidylate synthase/0.448
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
2bn4FADNADPH--cytochrome P450 reductase/0.448
2jfhLK1UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.448
2jh5895Prothrombin3.4.21.50.448
2v3hI25Prothrombin3.4.21.50.448
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3p9tTCLRepressor/0.448
4dc0NDPPutative ketoacyl reductase1.3.10.448
4dliIRGMitogen-activated protein kinase 14/0.448
4o71CPBBromodomain-containing protein 4/0.448
4ocvANPAminoglycoside phosphotransferase/0.448
4qa2SHHHistone deacetylase 83.5.1.980.448
1crbRTLRetinol-binding protein 1/0.447
1gqyACPUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.447
1h36R88Squalene--hopene cyclase4.2.1.1290.447
1jpaANPEphrin type-B receptor 22.7.10.10.447
1kqoDNDNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.447
1kt6RTLRetinol-binding protein 4/0.447
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.447
2f0y3MNProtein farnesyltransferase subunit beta2.5.1.580.447
2j9gADPBiotin carboxylase6.3.4.140.447
2q3oFMN12-oxophytodienoate reductase 31.3.1.420.447
2xlrFADPutative flavin-containing monooxygenase/0.447
2z2w770Wee1-like protein kinase2.7.10.20.447
3i2834NBifunctional epoxide hydrolase 23.3.2.100.447
3lz6A0DCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.447
4b1iA8PPoly(ADP-ribose) glycohydrolase3.2.1.1430.447
4fm80UQBeta-secretase 13.4.23.460.447
4fqsLYAThymidylate synthase ThyA/0.447
4ku5DCC3-oxoacyl-[ACP] synthase III/0.447
4qa0SHHHistone deacetylase 83.5.1.980.447
5iubCLRAdenosine receptor A2a/0.447
1dnaCB3Thymidylate synthase/0.446
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
1nceCB3Thymidylate synthase/0.446
1nw6SFGModification methylase RsrI2.1.1.720.446
1pj6FOLDimethylglycine oxidase1.5.3.100.446
1skgVAL_ALA_PHE_ARG_SERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.446
2ftoCB3Thymidylate synthase/0.446
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.446
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.446
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.446
3fznD7KBenzoylformate decarboxylase4.1.1.70.446
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
3pd4A3GThreonine--tRNA ligase6.1.1.30.446
4c1fX8ZMetallo-beta-lactamase type 2/0.446
4pnmNU1Tankyrase-22.4.2.300.446
4z24FADPutative GMC-type oxidoreductase R13510.446
5hbsRTLRetinol-binding protein 1/0.446
1ie8KH1Vitamin D3 receptor/0.445
1o97FADElectron transfer flavoprotein subunit alpha/0.445
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.445
1u1gBBBUridine phosphorylase2.4.2.30.445
1upw444Oxysterols receptor LXR-beta/0.445
1vbiNADMalate/L-lactate dehydrogenase family protein/0.445
2bu9HFVIsopenicillin N synthase1.21.3.10.445
2hl2SSAThreonine--tRNA ligase6.1.1.30.445
2xlsFADPutative flavin-containing monooxygenase/0.445
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.445
3c3dFO12-phospho-L-lactate transferase/0.445
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
3pqbVGPPutative oxidoreductase/0.445
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.445
3wypBSOStreptavidin/0.445
4bfyZVYPantothenate kinase2.7.1.330.445
5iu4ZMAAdenosine receptor A2a/0.445
1ia1NDPDihydrofolate reductase1.5.1.30.444
1qknRALEstrogen receptor beta/0.444
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.444
1rxjBNIStreptavidin/0.444
1tkbN1TTransketolase 12.2.1.10.444
1tl1H18Gag-Pol polyprotein2.7.7.490.444
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3h3qH13Collagen type IV alpha-3-binding protein/0.444
3pm9FADPutative oxidoreductase/0.444
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.444
4ap3FADSteroid monooxygenase/0.444
4b4w9L9Bifunctional protein FolD/0.444
4ejh0QACytochrome P450 2A131.14.14.10.444
4mihFADPyranose 2-oxidase1.1.3.100.444
5g53NECAdenosine receptor A2a/0.444
1axwMTXThymidylate synthase/0.443
1bk0ACVIsopenicillin N synthase1.21.3.10.443
1o6qR17Squalene--hopene cyclase4.2.1.1290.443
1obnASVIsopenicillin N synthase1.21.3.10.443
2b03TUDPhospholipase A2, major isoenzyme3.1.1.40.443
2pdlTOLAldose reductase1.1.1.210.443
2r0pK2CPutative FAD-monooxygenase/0.443
2xveFADPutative flavin-containing monooxygenase/0.443
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.443
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
3ipuO40Oxysterols receptor LXR-alpha/0.443
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.443
3oafOAGDihydrofolate reductase1.5.1.30.443
3vtdTKDVitamin D3 receptor/0.443
4b1hAR6Poly(ADP-ribose) glycohydrolase3.2.1.1430.443
4caxMYAGlycylpeptide N-tetradecanoyltransferase2.3.1.970.443
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.443
4jlj1NMDeoxycytidine kinase2.7.1.740.443
4k9nTZDBenzoylformate decarboxylase4.1.1.70.443
5hwqCAAHydroxymethylglutaryl-CoA synthase/0.443
5d5aCAUBeta-2 adrenergic receptor/0.443
1e26GPBDihydrofolate reductase1.5.1.30.442
1gky5GPGuanylate kinase2.7.4.80.442
1rx1NAPDihydrofolate reductase1.5.1.30.442
1thnADPAnti-sigma F factor/0.442
2ieaTDPPyruvate dehydrogenase E1 component1.2.4.10.442
2vosADPFolylpolyglutamate synthase/0.442
3c1kT15Prothrombin3.4.21.50.442
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.442
3q7fED2Uncharacterized protein/0.442
3up0D7SaceDAF-12/0.442
4blcNDPCatalase1.11.1.60.442
4c49HCYCorticosteroid-binding globulin/0.442
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4kxjP34Nucleoprotein/0.442
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
5irnADPNucleotide binding oligomerization domain containing 2/0.442
4s0vSUVOrexin receptor type 2/0.442
3p0gP0GBeta-2 adrenergic receptor/0.442
1bsvNDPGDP-L-fucose synthase/0.441
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.441
1hvyD16Thymidylate synthase2.1.1.450.441
1ldqSHMAvidin/0.441
1qorNDPQuinone oxidoreductase 1/0.441
1wp4NDP3-hydroxyisobutyrate dehydrogenase/0.441
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.441
2j9lATPH(+)/Cl(-) exchange transporter 5/0.441
2p5uNADUDP-glucose 4-epimerase/0.441
2rm2W43Genome polyprotein/0.441
3bw4FMNPutative 2-nitropropane dioxygenase/0.441
3c14FOKAdenylate cyclase type 2/0.441
3c14FOKAdenylate cyclase type 5/0.441
3gkjHC3Niemann-Pick C1 protein/0.441
3gwfFADCyclohexanone monooxygenase/0.441
3lkhLT6Genome polyprotein2.7.7.480.441
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
4h9506UDihydrofolate reductase1.5.1.30.441
4ia1BIVVitamin D3 receptor A/0.441
4m9aFDAAcyl-CoA dehydrogenase/0.441
4psbGA3Cytokinin-specific binding protein/0.441
5dc5B3NHistone deacetylase 83.5.1.980.441
5eccNAPDehydrofolate reductase type I/0.441
1ae8AZLProthrombin3.4.21.50.440
1h35R01Squalene--hopene cyclase4.2.1.1290.440
1kt7RTLRetinol-binding protein 4/0.440
1mueCDDProthrombin3.4.21.50.440
1n2vBDIQueuine tRNA-ribosyltransferase2.4.2.290.440
1nhkCMPNucleoside diphosphate kinase2.7.4.60.440
1vgrCOAFormyl-CoA:oxalate CoA-transferase/0.440
1zgv501Prothrombin3.4.21.50.440
2bbqPFGThymidylate synthase/0.440
2bdyUNBProthrombin3.4.21.50.440
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2tscCB3Thymidylate synthase/0.440
3d7zGK5Mitogen-activated protein kinase 14/0.440
3h3sH15Collagen type IV alpha-3-binding protein/0.440
3sfi3SFHTH-type transcriptional regulator EthR/0.440
3uk6ADPRuvB-like 23.6.4.120.440
4aosFADSteroid monooxygenase/0.440
4c6uTLG3-oxoacyl-ACP synthase/0.440
4gevCB3Thymidylate synthase/0.440
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4jbtASDCytochrome P450 monooxygenase/0.440
4l0qNADAlcohol dehydrogenase class-3/0.440
4mryCEIObelin/0.440
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.440