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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
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/1.000
5c3jUQ1Succinate dehydrogenase cytochrome b560/1.000
4ytnFD8Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.576
4ytnFD8Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial/0.576
4ytnFD8Succinate dehydrogenase cytochrome b560/0.576
3vr8RQXSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.566
3vr8RQXCytochrome b-large subunit/0.566
3vrbFTNSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.528
3vrbFTNCytochrome b-large subunit/0.528
1zoyUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.509
1zoyUQ1Succinate dehydrogenase cytochrome b560 subunit, mitochondrial/0.509
1ppjANYCytochrome b/0.504
2x06NADL-sulfolactate dehydrogenase/0.501
2rlcCHDCholoylglycine hydrolase3.5.1.240.490
3ae4N1MSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.490
3ae4N1MSuccinate dehydrogenase cytochrome b560 subunit, mitochondrial/0.490
3b2sB2STrichothecene 3-O-acetyltransferase/0.483
2fbwCBESuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.482
2fbwCBESuccinate dehydrogenase cytochrome b, large subunit/0.482
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.481
4bfuZVUPantothenate kinase2.7.1.330.481
2rqfJH3Hemolymph juvenile hormone binding protein/0.479
1qiqACCIsopenicillin N synthase1.21.3.10.478
2bu9HFVIsopenicillin N synthase1.21.3.10.476
4dbzNDPPutative ketoacyl reductase1.3.10.476
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.475
2gjlFMNNitronate monooxygenase1.13.12.160.474
4gl4NAIAlcohol dehydrogenase class-3/0.474
2c29NAPDihydroflavonol 4-reductase/0.473
3junAJDPhenazine biosynthesis protein A/B/0.472
4ure1PSCyclohexanol dehydrogenase/0.472
1o01NADAldehyde dehydrogenase, mitochondrial1.2.1.30.471
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.471
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.470
4bfzZVZPantothenate kinase2.7.1.330.470
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.470
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.469
3maaFKPAdenylate cyclase type 2/0.469
3maaFKPAdenylate cyclase type 5/0.469
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.467
1u1gBBBUridine phosphorylase2.4.2.30.467
2y6fM9FIsopenicillin N synthase1.21.3.10.466
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.466
4dc0NDPPutative ketoacyl reductase1.3.10.466
1n83CLRNuclear receptor ROR-alpha/0.465
3a0tADPSensor histidine kinase/0.465
3own3OWRenin3.4.23.150.465
3vqsJT1Genome polyprotein/0.465
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.464
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.463
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.463
2g8yNADHydroxycarboxylate dehydrogenase B/0.463
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.463
3lqfNADGalactitol dehydrogenase/0.463
4m4922YL-lactate dehydrogenase A chain1.1.1.270.463
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.462
2fonFADAcyl-coenzyme A oxidase/0.462
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.462
2xc3RT8Steroid C26-monooxygenase1.14.13.1410.462
3wv9FEGHmd co-occurring protein HcgE/0.462
1culFOKAdenylate cyclase type 2/0.461
1culFOKAdenylate cyclase type 5/0.461
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.461
4an4DUDPutative glycosyl transferase/0.461
2bjfDXCCholoylglycine hydrolase3.5.1.240.460
2ejzSAHDiphthine synthase/0.460
1e2nRCAThymidine kinase/0.459
1obnASVIsopenicillin N synthase1.21.3.10.459
2gjnFMNNitronate monooxygenase1.13.12.160.459
2iypNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.459
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.459
2ft9CHDFatty acid-binding protein 2, liver/0.458
2wmvZYVSerine/threonine-protein kinase Chk12.7.11.10.458
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.458
1blzACVIsopenicillin N synthase1.21.3.10.457
1c7oPPGHemolysin/0.457
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.457
3e2sFADBifunctional protein PutA1.5.5.20.457
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.457
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.457
4hdhATPGenome polyprotein2.7.7.480.457
4o8aFADBifunctional protein PutA1.2.1.880.457
1beuIPLTryptophan synthase alpha chain/0.456
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
3mdmFJZCholesterol 24-hydroxylase/0.456
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.456
4du82P0Mevalonate diphosphate decarboxylase/0.456
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.455
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.455
2bpoNAPNADPH--cytochrome P450 reductase/0.455
2fb35ADGTP 3',8-cyclase4.1.99.180.455
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.455
2qbuSAHPrecorrin-2 methyltransferase/0.455
3f3sNADLambda-crystallin homolog/0.455
3vtdTKDVitamin D3 receptor/0.455
1pqc444Oxysterols receptor LXR-beta/0.454
1qjfACSIsopenicillin N synthase1.21.3.10.454
3phiNDPShikimate dehydrogenase (NADP(+))/0.454
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.454
4bb3KKAIsopenicillin N synthase1.21.3.10.454
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.454
4yntFDAGlucose oxidase, putative/0.454
1dg8NDPDihydrofolate reductase1.5.1.30.453
1jg0DDTThymidylate synthase/0.453
1rfgGMPPurine nucleoside phosphorylase2.4.2.10.453
1vf2GTXGlutathione S-transferase 32.5.1.180.453
4a8v2ANMajor pollen allergen Bet v 1-J/0.453
4ipw1G7Mycocyclosin synthase1.14.21.90.453
4ke11R6Beta-secretase 13.4.23.460.453
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.452
1ykdCMPAdenylate cyclase/0.452
2a94AP0L-lactate dehydrogenase1.1.1.270.452
2qimZEAClass 10 plant pathogenesis-related protein/0.452
3b9lAZZSerum albumin/0.452
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.452
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.452
3s55NADPutative short-chain dehydrogenase/reductase/0.452
3zxsFADDeoxyribodipyrimidine photolyase-related protein/0.452
4bfxZVXPantothenate kinase2.7.1.330.452
4brgGNPEctonucleoside triphosphate diphosphohydrolase I/0.452
1nenDNTSuccinate dehydrogenase iron-sulfur subunit1.3.5.10.451
1nenDNTSuccinate dehydrogenase cytochrome b556 subunit/0.451
1t90NADMalonate-semialdehyde dehydrogenase1.2.1.270.451
2briANPUridylate kinase2.7.4.220.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
4g3jVNTLanosterol 14-alpha-demethylase/0.451
4mk828QGenome polyprotein2.7.7.480.451
4q73FADBifunctional protein PutA/0.451
2g1n1IGRenin3.4.23.150.450
2gv8NDPThiol-specific monooxygenase1.14.130.450
2lfoGCHFatty acid-binding protein, liver/0.450
2xbmSAHGenome polyprotein/0.450
2ylzFADPhenylacetone monooxygenase1.14.13.920.450
3ibqATPPyridoxal kinase/0.450
3junAKDPhenazine biosynthesis protein A/B/0.450
4m9aFDAAcyl-CoA dehydrogenase/0.450
4p9dTMPDeoxycytidylate deaminase/0.450
1guyNADMalate dehydrogenase/0.449
1m6iFADApoptosis-inducing factor 1, mitochondrial1.1.10.449
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.449
2i4qUA4Renin3.4.23.150.449
2xtnGTPGTPase IMAP family member 2/0.449
2zvbSAHPrecorrin-3 C17-methyltransferase/0.449
3cblSTUTyrosine-protein kinase Fes/Fps2.7.10.20.449
3oqkS52Renin3.4.23.150.449
4k6fNAPPutative Acetoacetyl-CoA reductase/0.449
4ycpFMNtRNA-dihydrouridine(16) synthase/0.449
1oc1ASVIsopenicillin N synthase1.21.3.10.448
1xe65FPPlasmepsin-23.4.23.390.448
2ea2F77Methionine aminopeptidase 2/0.448
2ibzUQ6Cytochrome b/0.448
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
2qw034Z4-chlorobenzoyl CoA ligase/0.448
2vbdV10Isopenicillin N synthase1.21.3.10.448
2y60M8FIsopenicillin N synthase1.21.3.10.448
3jziJZLBiotin carboxylase6.3.4.140.448
3qlsNDPDihydrofolate reductase1.5.1.30.448
3qt62P0Mevalonate diphosphate decarboxylase/0.448
3vt7VDXVitamin D3 receptor/0.448
4g7gVFVLanosterol 14-alpha-demethylase/0.448
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.448
4twnB96Ephrin type-A receptor 32.7.10.10.448
5i4nATPTyrosine-protein kinase JAK2/0.448
1a8rGTPGTP cyclohydrolase 13.5.4.160.447
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.447
1vbiNADMalate/L-lactate dehydrogenase family protein/0.447
2iodMYCDihydroflavonol 4-reductase1.1.1.2190.447
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.447
3c16FOKAdenylate cyclase type 2/0.447
3c16FOKAdenylate cyclase type 5/0.447
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.447
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.447
3fpzAHZThiamine thiazole synthase/0.447
3h3sH15Collagen type IV alpha-3-binding protein/0.447
3nbvANPKetohexokinase/0.447
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.447
3wb2YGPUncharacterized protein MJ0488/0.447
4ambDUDPutative glycosyl transferase/0.447
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.446
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.446
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.446
1o04NADAldehyde dehydrogenase, mitochondrial1.2.1.30.446
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.446
1z4uPH9Polyprotein/0.446
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.446
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.446
2omeNADC-terminal-binding protein 2/0.446
2y0mACOHistone acetyltransferase KAT8/0.446
2znoS44Peroxisome proliferator-activated receptor gamma/0.446
3ddw055Glycogen phosphorylase, liver form2.4.1.10.446
3pqbVGPPutative oxidoreductase/0.446
4b63NAPL-ornithine N(5)-monooxygenase/0.446
4bfwZVWPantothenate kinase2.7.1.330.446
4ekl0RFRAC-alpha serine/threonine-protein kinase2.7.11.10.446
4nxxGDPMitochondrial dynamics protein MID51/0.446
4oztP1AEcdysone receptor, putative/0.446
1bk0ACVIsopenicillin N synthase1.21.3.10.445
1hb1OCVIsopenicillin N synthase1.21.3.10.445
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1kvkATPMevalonate kinase2.7.1.360.445
1ot7IU5Bile acid receptor/0.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
1w6hTITPlasmepsin-23.4.23.390.445
1xddAAYIntegrin alpha-L/0.445
2eklNADD-3-phosphoglycerate dehydrogenase/0.445
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.445
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2onmADPAldehyde dehydrogenase, mitochondrial1.2.1.30.445
3b70NAPEnoyl reductase LovC10.445
3h3r14HCollagen type IV alpha-3-binding protein/0.445
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.445
3toxNAPPutative oxidoreductase/0.445
4a83DXCMajor pollen allergen Bet v 1-A/0.445
4h2nFAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.445
4iji99TGlutathione S-transferase-like protein YibF/0.445
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.444
1cs4FOKAdenylate cyclase type 2/0.444
1cs4FOKAdenylate cyclase type 5/0.444
1ek5NADUDP-glucose 4-epimerase/0.444
1ia1NDPDihydrofolate reductase1.5.1.30.444
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.444
1tj0FADBifunctional protein PutA1.5.5.20.444
1tj1FADBifunctional protein PutA1.5.5.20.444
1u1f183Uridine phosphorylase2.4.2.30.444
1u7tNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.444
2rhgIGPTryptophan synthase alpha chain/0.444
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.444
3iaaTYDCalG2/0.444
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.444
4i1iNADMalate dehydrogenase/0.444
4l0qNADAlcohol dehydrogenase class-3/0.444
4qxq1YEStimulator of interferon genes protein/0.444
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.444
1f20FADNitric oxide synthase, brain1.14.13.390.443
1ipeNDPTropinone reductase 21.1.1.2360.443
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.443
2y3rTRKTamL/0.443
3c14FOKAdenylate cyclase type 2/0.443
3c14FOKAdenylate cyclase type 5/0.443
3h3t16HCollagen type IV alpha-3-binding protein/0.443
3qiyQI1Botulinum neurotoxin type A3.4.24.690.443
3ziaADPATP synthase subunit beta, mitochondrial3.6.3.140.443
4bfvZVVPantothenate kinase2.7.1.330.443
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4opgFDAConserved Archaeal protein/0.443
5stdUNNScytalone dehydratase4.2.1.940.443
1h60STRPentaerythritol tetranitrate reductase/0.442
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.442
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.442
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.442
2aq8NAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
3gw9VNILanosterol 14-alpha-demethylase/0.442
3h3qH13Collagen type IV alpha-3-binding protein/0.442
3oafOAGDihydrofolate reductase1.5.1.30.442
3oqfS51Renin3.4.23.150.442
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.442
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.442
4d9eLCSD-cysteine desulfhydrase/0.442
4dpuAGSMevalonate diphosphate decarboxylase/0.442
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.442
4jzr4JREgl nine homolog 1/0.442
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.442
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.442
1il0NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1m78NDPDihydrofolate reductase1.5.1.30.441
2daaDCSD-alanine aminotransferase2.6.1.210.441
2dxdANPNucleoside diphosphate kinase2.7.4.60.441
2egsSAHDiphthine synthase/0.441
2g1r3IGRenin3.4.23.150.441
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.441
2wdzNADGalactitol dehydrogenase/0.441
3co93MSGenome polyprotein2.7.7.480.441
3d84NDPDihydrofolate reductase1.5.1.30.441
3jpuTY4Transcriptional activator protein LasR/0.441
3zoiM2WIsopenicillin N synthase1.21.3.10.441
4b4vL34Bifunctional protein FolD/0.441
4ead0NPThymidine phosphorylase2.4.2.40.441
4eaw0NQGenome polyprotein2.7.7.480.441
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.441
4tyqAP5Adenylate kinase/0.441
5dcyNAPIridoid synthase1.3.1.990.441
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.440
1f8fNADBenzyl alcohol dehydrogenase/0.440
1f8wFADNADH peroxidase1.11.1.10.440
1g41ADPATP-dependent protease ATPase subunit HslU/0.440
1kfbIGPTryptophan synthase alpha chain/0.440
1ma0NADAlcohol dehydrogenase class-31.1.1.10.440
1rzuADPGlycogen synthase 12.4.1.210.440
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.440
2jdtI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2pchSAHDiphthine synthase/0.440
3a28NADL-2,3-butanediol dehydrogenase1.1.1.760.440
3f03FMNPentaerythritol tetranitrate reductase/0.440
3gnvXNZGenome polyprotein2.7.7.480.440
3i0pNADMalate dehydrogenase, putative/0.440
3mjrAC2Deoxycytidine kinase2.7.1.740.440
4b4w9L9Bifunctional protein FolD/0.440
4exg916Beta-secretase 13.4.23.460.440
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
5a3bAPRSIR2 family protein/0.440
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.440
6gsuGPSGlutathione S-transferase Mu 12.5.1.180.440