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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
2ag0TPPBenzaldehyde lyase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
2ag0TPPBenzaldehyde lyase/1.000
2uz1TPPBenzaldehyde lyase/0.621
2ag1TPPBenzaldehyde lyase/0.577
3iafTPPBenzaldehyde lyase/0.531
2q5oTPWIndole-3-pyruvate decarboxylase4.1.1.740.514
2jlaTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.512
1mczTDPBenzoylformate decarboxylase4.1.1.70.511
2jlcTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.511
5ej8TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.503
2q5qTPWIndole-3-pyruvate decarboxylase4.1.1.740.498
4jubTPPBenzoylformate decarboxylase4.1.1.70.498
4k9oTPPBenzoylformate decarboxylase4.1.1.70.498
5esoTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.497
5ahkTPPAcetolactate synthase II, large subunit/0.496
2ihvTPPN(2)-(2-carboxyethyl)arginine synthase/0.495
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.492
4zp1TPPPyruvate decarboxylase4.1.1.10.491
2v3wTPPBenzoylformate decarboxylase4.1.1.70.489
2x7jTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.489
4jufTPPBenzoylformate decarboxylase4.1.1.70.489
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.489
5ej9TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.489
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.488
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.487
2w93TPPPyruvate decarboxylase isozyme 1/0.487
1ozhHE3Acetolactate synthase, catabolic2.2.1.60.484
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.482
5ej7TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.481
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.479
3iodA6DPantothenate synthetase6.3.2.10.479
5esdTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.476
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.475
3f03FMNPentaerythritol tetranitrate reductase/0.475
3r95ACOMccE protein/0.475
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.475
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.474
4k9nTZDBenzoylformate decarboxylase4.1.1.70.474
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.473
3eyaTDPPyruvate dehydrogenase [ubiquinone]1.2.5.10.473
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.473
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.472
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.472
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.471
5ej5TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.471
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.470
1tehNADAlcohol dehydrogenase class-31.1.1.10.469
2b7aIZATyrosine-protein kinase JAK2/0.468
4jb1FADUDP-N-acetylenolpyruvoylglucosamine reductase/0.467
5ejaTD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.467
2panTDPGlyoxylate carboligase4.1.1.470.466
2x7hPFNProstaglandin reductase 310.466
1h50FMNPentaerythritol tetranitrate reductase/0.465
2bbqPFGThymidylate synthase/0.465
3ln1CELProstaglandin G/H synthase 21.14.99.10.465
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.464
2xpuTDCTetracycline repressor protein class D/0.464
2ejvNADL-threonine 3-dehydrogenase/0.463
2p5uNADUDP-glucose 4-epimerase/0.463
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.463
3ijoB4DGlutamate receptor 2/0.463
1bw9NADPhenylalanine dehydrogenase/0.462
1vrwNAIEnoyl-ACP reductase/0.462
1y9dTPPPyruvate oxidase1.2.3.30.462
2z3uCRRCytochrome P450/0.462
3hwxTPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.462
3lsmSFDPyranose 2-oxidase/0.462
4ambDUDPutative glycosyl transferase/0.462
1ovmTPPIndole-3-pyruvate decarboxylase4.1.1.740.461
1vyrFMNPentaerythritol tetranitrate reductase/0.461
2fj1CTCTetracycline repressor protein class D/0.461
2tpsTPSThiamine-phosphate synthase/0.461
3q44D50M1 family aminopeptidase3.4.110.461
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.461
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.460
2ihuTP9N(2)-(2-carboxyethyl)arginine synthase/0.460
2qo9ANPEphrin type-A receptor 32.7.10.10.460
3a4vNADNDP-sugar epimerase/0.460
4gk3L87Ephrin type-A receptor 32.7.10.10.460
1hfqMOTDihydrofolate reductase1.5.1.30.459
1nvsUCMSerine/threonine-protein kinase Chk12.7.11.10.459
2z97CAMCamphor 5-monooxygenase1.14.15.10.459
1dxqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
1h51FMNPentaerythritol tetranitrate reductase/0.458
3d3wNAPL-xylulose reductase1.1.1.100.458
3ik6HCZGlutamate receptor 2/0.458
5dcyNAPIridoid synthase1.3.1.990.458
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.457
1uy7PU4Heat shock protein HSP 90-alpha/0.457
3a1nNADNDP-sugar epimerase/0.457
3mdmFJZCholesterol 24-hydroxylase/0.457
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.457
3p62FMNPentaerythritol tetranitrate reductase/0.457
3zkyWT4Isopenicillin N synthase1.21.3.10.457
4qnwFMNChanoclavine-I aldehyde reductase easA/0.457
1kekHTLPyruvate synthase/0.456
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.456
3fwgCAMCamphor 5-monooxygenase1.14.15.10.456
3kgcLY7Glutamate receptor 2/0.456
3p3zP3ZPutative cytochrome P450/0.456
3w6hAZMCarbonic anhydrase 14.2.1.10.456
4g7gVFVLanosterol 14-alpha-demethylase/0.456
4pzdNAD3-Hydroxyacyl-CoA dehydrogenase/0.456
1ie8KH1Vitamin D3 receptor/0.455
1rfvADPPyridoxal kinase2.7.1.350.455
1thnADPAnti-sigma F factor/0.455
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.455
4achKDIGlycogen synthase kinase-3 beta2.7.11.260.455
4k9pTPPBenzoylformate decarboxylase4.1.1.70.455
3lqfNADGalactitol dehydrogenase/0.454
3rj9NADAlcohol dehydrogenase1.1.1.10.454
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.454
5c4iTPPOxalate oxidoreductase subunit alpha/0.454
5c4iTPPOxalate oxidoreductase subunit beta/0.454
2pvnP63Casein kinase II subunit alpha2.7.11.10.453
2yeiXQIHeat shock protein HSP 90-alpha/0.453
3gw9VNILanosterol 14-alpha-demethylase/0.453
3ibqATPPyridoxal kinase/0.453
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.453
4l3q926Glucokinase2.7.1.20.453
1e7qNAPGDP-L-fucose synthase/0.452
1pr9NAPL-xylulose reductase1.1.1.100.452
2c3yHTLPyruvate synthase/0.452
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.452
2nr4FMNConserved protein/0.452
3d0bSNXHeat shock protein HSP 90-alpha/0.452
3drcMTXDihydrofolate reductase1.5.1.30.452
3lpkZ76Beta-secretase 13.4.23.460.452
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.452
4ead0NPThymidine phosphorylase2.4.2.40.452
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.452
1h63FMNPentaerythritol tetranitrate reductase/0.451
1m78NDPDihydrofolate reductase1.5.1.30.451
1pvdTPPPyruvate decarboxylase isozyme 1/0.451
1upaTPPN(2)-(2-carboxyethyl)arginine synthase/0.451
2eglSAHDiphthine synthase/0.451
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.451
2znq401Peroxisome proliferator-activated receptor delta/0.451
3lpjZ75Beta-secretase 13.4.23.460.451
4jucTPPBenzoylformate decarboxylase4.1.1.70.451
3a3bRBFLumazine protein/0.450
5eccNAPDehydrofolate reductase type I/0.450
1n83CLRNuclear receptor ROR-alpha/0.449
2vcmM11Isopenicillin N synthase1.21.3.10.449
2zshGA3Gibberellin receptor GID1A30.449
3oqkS52Renin3.4.23.150.449
3uleC69Actin-related protein 3/0.449
3w0pADPHygromycin-B 4-O-kinase2.7.1.1630.449
5a3bAPRSIR2 family protein/0.449
1iwjCAMCamphor 5-monooxygenase1.14.15.10.448
1mmaADPMyosin-2 heavy chain/0.448
2c42TPPPyruvate synthase/0.448
2g1r3IGRenin3.4.23.150.448
2q7vFADThioredoxin reductase/0.448
2zawCAMCamphor 5-monooxygenase1.14.15.10.448
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.447
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.447
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.447
3fwiCAMCamphor 5-monooxygenase1.14.15.10.447
4ji91M3Tyrosine-protein kinase JAK2/0.447
4nteFADDepH/0.447
4nxuADPMitochondrial dynamics protein MID51/0.447
5ej6TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.447
1e3eNAIAlcohol dehydrogenase 41.1.1.10.446
2p8uCOAHydroxymethylglutaryl-CoA synthase, cytoplasmic2.3.3.100.446
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3fp0FP015-O-acetyltransferase/0.446
3kb6NADD-lactate dehydrogenase/0.446
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.446
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.446
4dh60KNBeta-secretase 13.4.23.460.446
4u7wNDPMxaA/0.446
5a3cNADSIR2 family protein/0.446
1t88CAMCamphor 5-monooxygenase1.14.15.10.445
2ohjFMNType A flavoprotein FprA10.445
3fwjCAMCamphor 5-monooxygenase1.14.15.10.445
3h6vNS6Glutamate receptor 2/0.445
3owj1ELCasein kinase II subunit alpha2.7.11.10.445
3vvpBNUUncharacterized protein/0.445
4dpy2P0Mevalonate diphosphate decarboxylase/0.445
4h1e10JBeta-secretase 13.4.23.460.445
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.445
1bwsNDPGDP-L-fucose synthase/0.444
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.444
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.444
2abbFMNPentaerythritol tetranitrate reductase/0.444
2bxmIMNSerum albumin/0.444
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.444
2yn8STUEphrin type-B receptor 42.7.10.10.444
3e8r615Disintegrin and metalloproteinase domain-containing protein 173.4.24.860.444
3fql79ZGenome polyprotein2.7.7.480.444
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.444
3oqfS51Renin3.4.23.150.444
3vw6IM6Mitogen-activated protein kinase kinase kinase 52.7.11.250.444
4bb3KKAIsopenicillin N synthase1.21.3.10.444
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.444
5hs1VORLanosterol 14-alpha demethylase/0.444
1dz8CAMCamphor 5-monooxygenase1.14.15.10.443
1m2rMNYCasein kinase II subunit alpha2.7.11.10.443
1mg5NAIAlcohol dehydrogenase1.1.1.10.443
1vjy460TGF-beta receptor type-12.7.11.300.443
1y0s331Peroxisome proliferator-activated receptor delta/0.443
2d29FADAcyl-CoA dehydrogenase/0.443
2ejzSAHDiphthine synthase/0.443
2kceD16Thymidylate synthase/0.443
2npaMMBPeroxisome proliferator-activated receptor alpha/0.443
3h06VBPGlutamate receptor 2/0.443
3il1B5DGlutamate receptor 2/0.443
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.443
4jq8KJ8Epidermal growth factor receptor2.7.10.10.443
6cp4CAMCamphor 5-monooxygenase1.14.15.10.443
1dhiMTXDihydrofolate reductase1.5.1.30.442
1drhNAPDihydrofolate reductase1.5.1.30.442
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
1upbTPPN(2)-(2-carboxyethyl)arginine synthase/0.442
2jcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.442
2v59LZKBiotin carboxylase6.3.4.140.442
2vk4TPPPyruvate decarboxylase4.1.1.10.442
2xh9J01Uncharacterized protein/0.442
2zbaZBATrichothecene 3-O-acetyltransferase/0.442
3d8vUD1Bifunctional protein GlmU/0.442
3flwFLWMitogen-activated protein kinase 14/0.442
3lsiFADPyranose 2-oxidase/0.442
3lu8IQXSerum albumin/0.442
3mjhGTPRas-related protein Rab-5A/0.442
3tm5SFGUncharacterized protein/0.442
3u9eCOALmo1369 protein/0.442
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.442
4jjiNADAlcohol dehydrogenase class-3/0.442
1l4kNCNNicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase2.4.2.210.441
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.441
2bfrADP[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.441
2rioADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.441
2x0iNAIMalate dehydrogenase/0.441
3d7kD7KBenzaldehyde lyase/0.441
3l0lHC3Nuclear receptor ROR-gamma/0.441
3opdHIEHeat shock protein 83/0.441
3pgqGY3Acetyl-CoA carboxylase/0.441
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4c04SFGProtein arginine N-methyltransferase 6/0.441
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.441
1cf3FADGlucose oxidase1.1.3.40.440
1dr3HBIDihydrofolate reductase1.5.1.30.440
1iqeXMBCoagulation factor X3.4.21.60.440
1tj0FADBifunctional protein PutA1.5.5.20.440
1ygkRRCPyridoxal kinase2.7.1.350.440
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2cx8SAHRibosomal RNA small subunit methyltransferase E/0.440
2w6oOA3Biotin carboxylase6.3.4.140.440
2wotZZGTGF-beta receptor type-12.7.11.300.440
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.440
2xvv9DNSerum albumin/0.440
3gwfFADCyclohexanone monooxygenase/0.440
3p8jFMNPentaerythritol tetranitrate reductase/0.440
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.440
4b7zQ4QAcetylcholinesterase3.1.1.70.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4l1fCOSAcyl-CoA dehydrogenase domain protein/0.440
4m83ERYOleandomycin glycosyltransferase2.4.10.440
4nxwADPMitochondrial dynamics protein MID51/0.440
5cp4CAMCamphor 5-monooxygenase1.14.15.10.440