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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
3vr8RQXSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3vr8RQXSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/1.000
3vr8RQXCytochrome b-large subunit/1.000
5c3jUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.587
5c3jUQ1Succinate dehydrogenase cytochrome b560/0.587
3vrbFTNSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.578
3vrbFTNCytochrome b-large subunit/0.578
4ytnFD8Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial/0.565
4ytnFD8Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial/0.565
4ytnFD8Succinate dehydrogenase cytochrome b560/0.565
2fbwCBESuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.551
2fbwCBESuccinate dehydrogenase cytochrome b, large subunit/0.551
1zoyUQ1Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.525
1zoyUQ1Succinate dehydrogenase cytochrome b560 subunit, mitochondrial/0.525
3ae4N1MSuccinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial1.3.5.10.498
3ae4N1MSuccinate dehydrogenase cytochrome b560 subunit, mitochondrial/0.498
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.497
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.497
5djtFMNNPH1-2/0.489
3eblGA4Gibberellin receptor GID1/0.487
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.486
1ot7IU5Bile acid receptor/0.486
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.483
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.482
5iqdGNPBifunctional AAC/APH2.3.10.477
1jqiCAAShort-chain specific acyl-CoA dehydrogenase, mitochondrial/0.476
1kqwRTLCellular retinol-binding protein type II/0.475
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.473
2x3jATPAcsD/0.473
3sp9IL2Peroxisome proliferator-activated receptor delta/0.473
4xgxADPFAD:protein FMN transferase/0.473
2zbaZBATrichothecene 3-O-acetyltransferase/0.472
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.471
3jpuTY4Transcriptional activator protein LasR/0.471
3tqaNDPDihydrofolate reductase/0.471
4ku2MYA3-oxoacyl-[ACP] synthase III/0.471
2rlcCHDCholoylglycine hydrolase3.5.1.240.470
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.470
2bu9HFVIsopenicillin N synthase1.21.3.10.469
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.469
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.467
1pdhFASp-hydroxybenzoate hydroxylase/0.466
3h3r14HCollagen type IV alpha-3-binding protein/0.466
1ia1NDPDihydrofolate reductase1.5.1.30.465
2uzwSS4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.465
3vmmP0DAlanine--anticapsin ligase/0.465
1ur5NADMalate dehydrogenase/0.464
2gjlFMNNitronate monooxygenase1.13.12.160.464
4jldADPAdenylate kinase/0.464
2v1aFMNNPH1-1/0.463
1qknRALEstrogen receptor beta/0.462
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.462
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.462
4ambDUDPutative glycosyl transferase/0.462
4s1hADPPyridoxal kinase, putative/0.462
2czfXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.461
2wdqCBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.461
2wdqCBESuccinate dehydrogenase cytochrome b556 subunit/0.461
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.461
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.461
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.461
5i4nATPTyrosine-protein kinase JAK2/0.461
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.460
1upw444Oxysterols receptor LXR-beta/0.460
2po7CHDFerrochelatase, mitochondrial4.99.1.10.460
3mwuBK3Calmodulin-domain protein kinase 1, putative/0.460
4g210VPVitamin D3 receptor A/0.460
4jzr4JREgl nine homolog 1/0.460
1u1gBBBUridine phosphorylase2.4.2.30.459
3q7fED2Uncharacterized protein/0.459
4m52M52Dihydrolipoyl dehydrogenase1.8.1.40.459
1fnnADPORC1-type DNA replication protein/0.458
1pq944BOxysterols receptor LXR-beta/0.458
2q0kNAPThioredoxin reductase1.8.1.90.458
3b2sB2STrichothecene 3-O-acetyltransferase/0.458
3bgxTMPThymidylate synthase/0.458
3ed1GA3Gibberellin receptor GID1/0.458
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.458
3w0iO11Vitamin D3 receptor/0.458
4a81DXCMajor pollen allergen Bet v 1-A/0.458
2gjnFMNNitronate monooxygenase1.13.12.160.457
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.457
3p3zP3ZPutative cytochrome P450/0.457
4fvqATPTyrosine-protein kinase JAK2/0.457
4h4zFADBiphenyl dioxygenase ferredoxin reductase subunit/0.457
2g9uG27Glycogen phosphorylase, muscle form2.4.1.10.456
2vigCOSShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.456
3dl0AP5Adenylate kinase/0.456
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.455
1obnASVIsopenicillin N synthase1.21.3.10.455
1ve3SAMUncharacterized protein/0.455
2ea2F77Methionine aminopeptidase 2/0.455
2emuSAHDiphthine synthase/0.455
3f3sNADLambda-crystallin homolog/0.455
3gfbNADL-threonine 3-dehydrogenase/0.455
3qvpFADGlucose oxidase1.1.3.40.455
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.454
2c3qGTXGlutathione S-transferase theta-12.5.1.180.454
3aosJH2Hemolymph juvenile hormone binding protein/0.454
3cvyFADRE11660p/0.454
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.454
4p13FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.454
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.453
3hj9FMNUncharacterized protein/0.453
3vt5YI2Vitamin D3 receptor/0.453
5djuFMNNPH1-2/0.453
1hk2T44Serum albumin/0.452
1jstATPCyclin-dependent kinase 22.7.11.220.452
1rc1KT3Trifunctional purine biosynthetic protein adenosine-32.1.2.20.452
1tehNADAlcohol dehydrogenase class-31.1.1.10.452
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.452
2ft9CHDFatty acid-binding protein 2, liver/0.452
2gr0FADFerredoxin reductase/0.452
3njuANNAcidic phospholipase A2 33.1.1.40.452
3pyzANPDihydrofolate synthase/folylpolyglutamate synthase/0.452
4y8vADPAcyl-CoA synthetase (NDP forming)/0.452
4ycpFMNtRNA-dihydrouridine(16) synthase/0.452
1culFOKAdenylate cyclase type 2/0.451
1culFOKAdenylate cyclase type 5/0.451
1yqzCOACoenzyme A disulfide reductase/0.451
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.451
3junAJDPhenazine biosynthesis protein A/B/0.451
3qttANPPantothenate synthetase/0.451
3vt3VDXVitamin D3 receptor/0.451
4eu9COASuccinyl-CoA:acetate CoA-transferase/0.451
1akeAP5Adenylate kinase/0.450
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.450
1mczRMNBenzoylformate decarboxylase4.1.1.70.450
1orrCDPCDP-paratose 2-epimerase/0.450
1tysTMPThymidylate synthase/0.450
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2gr1FADFerredoxin reductase/0.450
2qo6CHDFatty acid-binding protein 10-A, liver basic/0.450
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2y60M8FIsopenicillin N synthase1.21.3.10.450
4jl5ADPAdenylate kinase/0.450
1kquBR4Phospholipase A2, membrane associated/0.449
1szgFNSCytochrome b2, mitochondrial1.1.2.30.449
2cduFADNADH oxidase/0.449
2ea4F79Methionine aminopeptidase 2/0.449
2uyyNA7Putative oxidoreductase GLYR110.449
3cgtBCDCyclomaltodextrin glucanotransferase2.4.1.190.449
3ih0ANPUncharacterized sugar kinase PH14592.7.10.449
3keuATPPyridoxal kinase2.7.1.350.449
3otwCOAPhosphopantetheine adenylyltransferase/0.449
4cmfPXGUncharacterized protein/0.449
4nu6NADPhosphonate dehydrogenase1.20.1.10.449
1p8dCO1Oxysterols receptor LXR-beta/0.448
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.448
2c29NAPDihydroflavonol 4-reductase/0.448
2x06NADL-sulfolactate dehydrogenase/0.448
2y6fM9FIsopenicillin N synthase1.21.3.10.448
3g8dADPBiotin carboxylase6.3.4.140.448
3vqsJT1Genome polyprotein/0.448
4bb3KKAIsopenicillin N synthase1.21.3.10.448
4e9aQAPPeptide deformylase/0.448
4h4tFADBiphenyl dioxygenase ferredoxin reductase subunit/0.448
4iacACPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
1dr2TAPDihydrofolate reductase1.5.1.30.447
1i2cUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.447
1n2eAPCPantothenate synthetase6.3.2.10.447
1z3cSA8mRNA cap guanine-N7 methyltransferase2.1.1.560.447
2an9GDPGuanylate kinase2.7.4.80.447
2cjfRP43-dehydroquinate dehydratase4.2.1.100.447
3iaeD7KBenzaldehyde lyase/0.447
3juqAJDPhenazine biosynthesis protein A/B/0.447
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.447
4an4DUDPutative glycosyl transferase/0.447
4bcsBTNAvidin-related protein 4/5/0.447
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4oa9ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.447
1i2lDCSAminodeoxychorismate lyase4.1.3.380.446
1z6tADPApoptotic protease-activating factor 1/0.446
2daaDCSD-alanine aminotransferase2.6.1.210.446
2fonFADAcyl-coenzyme A oxidase/0.446
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.446
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
4b63NAPL-ornithine N(5)-monooxygenase/0.446
4bfvZVVPantothenate kinase2.7.1.330.446
4eqrCOACoenzyme A disulfide reductase/0.446
4kxjP34Nucleoprotein/0.446
4tyqAP5Adenylate kinase/0.446
4xfjANPArgininosuccinate synthase/0.446
5hs1VORLanosterol 14-alpha demethylase/0.446
1h50FMNPentaerythritol tetranitrate reductase/0.445
1i7lATPSynapsin-2/0.445
1qiqACCIsopenicillin N synthase1.21.3.10.445
1rjkVDZVitamin D3 receptor/0.445
2izfBTNStreptavidin/0.445
3b9lAZZSerum albumin/0.445
3h3sH15Collagen type IV alpha-3-binding protein/0.445
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.445
3sfy3FYUncharacterized protein/0.445
4a802ANMajor pollen allergen Bet v 1-A/0.445
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.445
4i1nFOLDihydrofolate reductase1.5.1.30.445
4oznATPAmmonium transporter/0.445
4qzuRTLRetinol-binding protein 2/0.445
5eoxADPType 4 fimbrial biogenesis protein PilM/0.445
1b5eDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.444
1kvkATPMevalonate kinase2.7.1.360.444
1tqf32PBeta-secretase 13.4.23.460.444
1u2yGOXPancreatic alpha-amylase/0.444
2ij7TPFMycocyclosin synthase1.14.21.90.444
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2y3sTIRTamL/0.444
3o26NDPSalutaridine reductase/0.444
3p62FMNPentaerythritol tetranitrate reductase/0.444
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
3zh8C58Protein kinase C iota type2.7.11.130.444
3zxsFADDeoxyribodipyrimidine photolyase-related protein/0.444
4df2FMNNADPH dehydrogenase/0.444
4g1cCNANAD-dependent protein deacylase sirtuin-5, mitochondrial/0.444
4ikeADPAdenylate kinase/0.444
4twnB96Ephrin type-A receptor 32.7.10.10.444
4up3NDPThioredoxin reductase/0.444
1fm4DXCMajor pollen allergen Bet v 1-L/0.443
1m6iFADApoptosis-inducing factor 1, mitochondrial1.1.10.443
1m78NDPDihydrofolate reductase1.5.1.30.443
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.443
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.443
2aclL05Oxysterols receptor LXR-alpha/0.443
2bjfDXCCholoylglycine hydrolase3.5.1.240.443
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.443
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.443
4nmbFADBifunctional protein PutA/0.443
1bwsNDPGDP-L-fucose synthase/0.442
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.442
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1ja1NAPNADPH--cytochrome P450 reductase/0.442
1umaIN2Prothrombin3.4.21.50.442
2ehlSAHDiphthine synthase/0.442
2ojf4PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2w2lNADD-mandelate dehydrogenase/0.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.442
5irnADPNucleotide binding oligomerization domain containing 2/0.442
1ei1ANPDNA gyrase subunit B/0.441
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.441
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.441
2p6dSAHDiphthine synthase/0.441
2pmlANPUncharacterized protein/0.441
2wzwFMNNitroreductase NfnB/0.441
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.441
3g8cADPBiotin carboxylase6.3.4.140.441
3qxpX64Cyclin-dependent kinase 22.7.11.220.441
3v2uATPProtein GAL3/0.441
4bio8XQHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.441
4dc0NDPPutative ketoacyl reductase1.3.10.441
4husVIRVirginiamycin A acetyltransferase2.3.10.441
4jx1CAHCamphor 5-monooxygenase1.14.15.10.441
4nt3ZAWLactoperoxidase1.11.1.70.441
4opiFDAConserved Archaeal protein/0.441
4r1fADPDNA topoisomerase 2-alpha5.99.1.30.441
4rujVDXVitamin D3 receptor A/0.441
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.440
1hb1OCVIsopenicillin N synthase1.21.3.10.440
1n2iPAJPantothenate synthetase6.3.2.10.440
1o5iNAD3-oxoacyl-(Acyl carrier protein) reductase/0.440
1okkGCPSignal recognition particle protein/0.440
1okkGCPSignal recognition particle receptor FtsY/0.440
2dxdANPNucleoside diphosphate kinase2.7.4.60.440
2he5NDPAldo-keto reductase family 1 member C211.1.10.440
2owkSAHDiphthine synthase/0.440
2pdtFADVivid PAS protein VVD/0.440
2xpvMIYTetracycline repressor protein class D/0.440
3af1GDPPantothenate kinase2.7.1.330.440
3bv2P38Mitogen-activated protein kinase 14/0.440
3c1tMYCDihydroflavonol 4-reductase1.1.1.2190.440
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.440
3ipq965Oxysterols receptor LXR-alpha/0.440
3lnmNAPVoltage-gated potassium channel subunit beta-2/0.440
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3tjlFMNNADPH dehydrogenase/0.440
4a4vYFDPeroxisome proliferator-activated receptor gamma/0.440
4bizADPSensor histidine kinase CpxA/0.440
4d5gFADCyclohexane-1,2-dione hydrolase3.7.1.110.440
4e2xTYDMethyltransferase/0.440
5l3rGCPCell division protein FtsY homolog, chloroplastic/0.440