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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
3ae4N1MSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3ae4N1MSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.11.000
3ae4N1MSuccinate dehydrogenase cytochrome b560 subunit, mitochondrial/1.000
1zoyUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.547
1zoyUQ1Succinate dehydrogenase cytochrome b560 subunit, mitochondrial/0.547
3vrbFTNSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.543
3vrbFTNCytochrome b-large subunit/0.543
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.525
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.525
2fbwCBESuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.494
2fbwCBESuccinate dehydrogenase cytochrome b, large subunit/0.494
3sp9IL2Peroxisome proliferator-activated receptor delta/0.492
3vr8RQXSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.488
3vr8RQXCytochrome b-large subunit/0.488
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.488
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.488
3v0p4GWHisto-blood group ABO system transferase/0.486
4qzuRTLRetinol-binding protein 2/0.481
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.480
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.477
1tehNADAlcohol dehydrogenase class-31.1.1.10.476
4bb3KKAIsopenicillin N synthase1.21.3.10.476
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.472
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.471
1u1gBBBUridine phosphorylase2.4.2.30.471
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.470
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.469
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.469
4nmdFDABifunctional protein PutA/0.469
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.467
3zlmANPAdenosine monophosphate-protein transferase NmFic2.7.7.n10.467
3zoiM2WIsopenicillin N synthase1.21.3.10.467
1x14NADNAD(P) transhydrogenase subunit alpha1.6.1.20.466
1s19MC9Vitamin D3 receptor/0.465
1bk0ACVIsopenicillin N synthase1.21.3.10.464
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.463
5cpmFNRNADH:flavin oxidoreductase/0.463
2e15SAHDiphthine synthase/0.462
4jbsP52Endoplasmic reticulum aminopeptidase 23.4.110.462
4qe6JN3Bile acid receptor/0.461
1dv2ATPBiotin carboxylase6.3.4.140.460
1xe65FPPlasmepsin-23.4.23.390.460
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.460
4ia3BIVVitamin D3 receptor A/0.460
1m78NDPDihydrofolate reductase1.5.1.30.459
1pjkANPCasein kinase II subunit alpha2.7.11.10.459
5irnADPNucleotide binding oligomerization domain containing 2/0.459
2pb4SAHDiphthine synthase/0.458
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.458
3akm11DFatty acid-binding protein, intestinal/0.458
4dpuAGSMevalonate diphosphate decarboxylase/0.458
4i4b1CV3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.458
4l9q9TPSerum albumin/0.458
2emuSAHDiphthine synthase/0.457
4a87NARMajor pollen allergen Bet v 1-A/0.457
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.456
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.456
3sn6P0GBeta-2 adrenergic receptor/0.456
1cf3FADGlucose oxidase1.1.3.40.455
1ot7IU5Bile acid receptor/0.455
2bu9HFVIsopenicillin N synthase1.21.3.10.455
3b2sB2STrichothecene 3-O-acetyltransferase/0.455
3nwlNDPCatalase1.11.1.60.455
3zkyWT4Isopenicillin N synthase1.21.3.10.455
4cmfPXGUncharacterized protein/0.455
4gl4NAIAlcohol dehydrogenase class-3/0.455
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.455
1sq5ADPPantothenate kinase2.7.1.330.454
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
2jb4A14Isopenicillin N synthase1.21.3.10.454
2vbpVB1Isopenicillin N synthase1.21.3.10.454
2ej2PPEBranched-chain amino acid aminotransferase (IlvE)/0.453
2ek2SAHDiphthine synthase/0.453
2ft9CHDFatty acid-binding protein 2, liver/0.453
2x06NADL-sulfolactate dehydrogenase/0.453
3edjBCDCyclomaltodextrinase/0.453
3lu8IQXSerum albumin/0.453
1kevNDPNADP-dependent isopropanol dehydrogenase1.1.1.800.452
2dv5SAHDiphthine synthase/0.452
2emrSAHDiphthine synthase/0.452
3keuATPPyridoxal kinase2.7.1.350.452
4lva20MNicotinamide phosphoribosyltransferase2.4.2.120.452
5iqeGNPBifunctional AAC/APH2.3.10.452
1vceSAHDiphthine synthase/0.451
1x1aSAMC-20 methyltransferase/0.451
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.451
2huvSAHDiphthine synthase/0.451
3p6pA6BCamphor 5-monooxygenase1.14.15.10.451
4ytnFD8Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.451
4ytnFD8Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial/0.451
4ytnFD8Succinate dehydrogenase cytochrome b560/0.451
1ma0NADAlcohol dehydrogenase class-31.1.1.10.450
3jpuTY4Transcriptional activator protein LasR/0.450
3qlrNDPDihydrofolate reductase1.5.1.30.450
4f9fGDPPutative glycosyltransferase/0.450
4jldADPAdenylate kinase/0.450
1eioGCHGastrotropin/0.449
1fm4DXCMajor pollen allergen Bet v 1-L/0.449
1hb3SCVIsopenicillin N synthase1.21.3.10.449
3junAKDPhenazine biosynthesis protein A/B/0.449
4ldeP0GBeta-2 adrenergic receptor/0.449
1kvkATPMevalonate kinase2.7.1.360.448
1obnASVIsopenicillin N synthase1.21.3.10.448
2gjlFMNNitronate monooxygenase1.13.12.160.448
2jdtI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
2npfMOUElongation factor 2/0.448
3akn11DFatty acid-binding protein, intestinal/0.448
3g8dADPBiotin carboxylase6.3.4.140.448
3vf60H6Glucokinase2.7.1.20.448
4a83DXCMajor pollen allergen Bet v 1-A/0.448
4oztP1AEcdysone receptor, putative/0.448
4rupH97Vitamin D3 receptor A/0.448
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.447
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.447
5eccNAPDehydrofolate reductase type I/0.447
2vcmM11Isopenicillin N synthase1.21.3.10.446
2z4sADPChromosomal replication initiator protein DnaA/0.446
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.446
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
2ek7SAHDiphthine synthase/0.445
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.445
2z9dFMNFMN-dependent NADH-azoreductase/0.445
3b9lAZZSerum albumin/0.445
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.445
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.445
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.445
5iqdGNPBifunctional AAC/APH2.3.10.445
5dhhDGWNociceptin receptor/0.445
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.444
2egbSAHDiphthine synthase/0.444
2po7CHDFerrochelatase, mitochondrial4.99.1.10.444
2qbuSAHPrecorrin-2 methyltransferase/0.444
2wpxACOOrf14/0.444
2y60M8FIsopenicillin N synthase1.21.3.10.444
3h3qH13Collagen type IV alpha-3-binding protein/0.444
3ox4NADAlcohol dehydrogenase 21.1.1.10.444
4jhz1KVBeta-glucuronidase3.2.1.310.444
4l0qNADAlcohol dehydrogenase class-3/0.444
1fmjRTLRetinol dehydratase/0.443
1wngSAHDiphthine synthase/0.443
1y0s331Peroxisome proliferator-activated receptor delta/0.443
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.443
2fj1CTCTetracycline repressor protein class D/0.443
2p6dSAHDiphthine synthase/0.443
3lpfZ77Beta-glucuronidase3.2.1.310.443
4du82P0Mevalonate diphosphate decarboxylase/0.443
4o4iACPTubulin tyrosine ligase/0.443
4v2gITCTetracycline repressor protein class D/0.443
5er0FADUncharacterized NAD(FAD)-dependent dehydrogenase/0.443
1bdbNADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase/0.442
1dr2TAPDihydrofolate reductase1.5.1.30.442
1ia1NDPDihydrofolate reductase1.5.1.30.442
1uofPNNDeacetoxycephalosporin C synthase1.14.20.10.442
2b9yFADPutative aminooxidase/0.442
2ehlSAHDiphthine synthase/0.442
2ejzSAHDiphthine synthase/0.442
2eleSAHDiphthine synthase/0.442
2pciSAHDiphthine synthase/0.442
2xgs44PUncharacterized protein/0.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.442
3qvpFADGlucose oxidase1.1.3.40.442
3tqcADPPantothenate kinase/0.442
3zxsFADDeoxyribodipyrimidine photolyase-related protein/0.442
4ejmNAPPutative zinc-binding dehydrogenase/0.442
7catNDPCatalase1.11.1.60.442
3p0gP0GBeta-2 adrenergic receptor/0.442
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1nenDNTSuccinate dehydrogenase iron-sulfur subunit1.3.5.10.441
1nenDNTSuccinate dehydrogenase cytochrome b556 subunit/0.441
2dsgSAHDiphthine synthase/0.441
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.441
2oapANPType II secretion system protein (GspE-2)/0.441
2p5cSAHDiphthine synthase/0.441
4fhh0U3Vitamin D3 receptor A/0.441
4h9tHL4Phosphotriesterase/0.441
4jtqNAPAldo-keto reductase family 1 member C2/0.441
4lvb20NNicotinamide phosphoribosyltransferase2.4.2.120.441
8catNDPCatalase1.11.1.60.441
1rx1NAPDihydrofolate reductase1.5.1.30.440
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.440
2fonFADAcyl-coenzyme A oxidase/0.440
2owkSAHDiphthine synthase/0.440
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.440
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.440
3mwuBK3Calmodulin-domain protein kinase 1, putative/0.440
3uoyFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
4a6nFADTetX family tetracycline inactivation enzyme/0.440
4en4ATPPyridoxal kinase2.7.1.350.440
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440