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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
2ax4ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 22.7.1.25

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2ax4ADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 22.7.1.251.000
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.583
2oapANPType II secretion system protein (GspE-2)/0.521
3w8rACPUridine kinase/0.512
4yxm2BADNA integrity scanning protein DisA/0.505
3s87ADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.503
4n9iPCGCatabolite expression activator/0.500
5cnsDATRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.500
4bzqADPBifunctional enzyme CysN/CysC2.7.1.250.499
1joaFADNADH peroxidase1.11.1.10.497
2b4rAESGlyceraldehyde-3-phosphate dehydrogenase/0.495
4hmvWUBPhenazine biosynthesis protein PhzG1.40.495
3s5wNAPL-ornithine N(5)-monooxygenase/0.491
2q46NAPUncharacterized protein At5g02240/0.487
3mx5UTPNucleoprotein/0.487
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.487
2gesCOKPantothenate kinase2.7.1.330.486
2npxFADNADH peroxidase1.11.1.10.486
1i6lTYMTryptophan--tRNA ligase6.1.1.20.483
2getCOKPantothenate kinase2.7.1.330.481
3hdyGDUUDP-galactopyranose mutase/0.481
3tjzGNPADP-ribosylation factor 1/0.480
4djaFAD(6-4) photolyase/0.480
3c1y2BADNA integrity scanning protein DisA/0.479
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.477
4bfsZVSPantothenate kinase2.7.1.330.477
4ipw1G7Mycocyclosin synthase1.14.21.90.477
1omoNADAlanine dehydrogenase/0.476
2g89UMPThymidylate synthase/0.476
4yvz3ATDNA integrity scanning protein DisA/0.476
1jedADPSulfate adenylyltransferase/0.475
2briANPUridylate kinase2.7.4.220.475
2c29NAPDihydroflavonol 4-reductase/0.475
3cisATPUniversal stress protein Rv2623/0.475
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.474
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.473
2qw034Z4-chlorobenzoyl CoA ligase/0.472
2f3rG5PGuanylate kinase2.7.4.80.470
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.470
1zp9ATPRIO-type serine/threonine-protein kinase Rio12.7.11.10.469
2nnqT4BFatty acid-binding protein, adipocyte/0.469
3c212BADNA integrity scanning protein DisA/0.469
4tyqAP5Adenylate kinase/0.469
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.469
1nhqFADNADH peroxidase1.11.1.10.468
1x27ASP_TYR_VAL_HIS_PTRTyrosine-protein kinase Lck2.7.10.20.468
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.468
2dftADPShikimate kinase2.7.1.710.468
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.468
4wsoNADProbable nicotinate-nucleotide adenylyltransferase/0.468
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.468
3nl6TPSUncharacterized protein/0.467
4g8jTHMUridine phosphorylase/0.467
2ft9CHDFatty acid-binding protein 2, liver/0.466
2g1s4IGRenin3.4.23.150.466
2qbuSAHPrecorrin-2 methyltransferase/0.466
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.466
1nzfUPGDNA beta-glucosyltransferase/0.465
1u1iNADMyo-inositol-1-phosphate synthase (Ino1)/0.465
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.465
3enkUPGUDP-glucose 4-epimerase/0.465
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.465
3opxU5PSuppressor of disruption of TFIIS/0.465
3tr05GPGuanylate kinase/0.465
3gfbNADL-threonine 3-dehydrogenase/0.464
4dpuAGSMevalonate diphosphate decarboxylase/0.464
4ohxADPProtein clpf-1/0.464
1nhsFADNADH peroxidase1.11.1.10.463
1towCRZFatty acid-binding protein, adipocyte/0.463
2ag5NAD3-hydroxybutyrate dehydrogenase type 2/0.463
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.463
2rlcCHDCholoylglycine hydrolase3.5.1.240.463
4wxlBB2Peptide deformylase/0.463
1nhpFADNADH peroxidase1.11.1.10.462
2xfsJ01Uncharacterized protein/0.462
3h86AP5Adenylate kinase/0.462
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.462
5fklTDCTetracycline repressor protein class D/0.462
1c9k5GPBifunctional adenosylcobalamin biosynthesis protein CobU/0.461
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.461
2gjnFMNNitronate monooxygenase1.13.12.160.461
2hu2NADC-terminal binding protein 1/0.461
3hyoADPPyridoxal kinase/0.461
3ixp834Ecdysone receptor/0.461
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.461
4ycoFMNtRNA-dihydrouridine(16) synthase/0.461
5agaANPDNA polymerase theta/0.461
1jueFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.460
2gjlFMNNitronate monooxygenase1.13.12.160.460
2x0rNADMalate dehydrogenase/0.460
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.460
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.460
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.460
1i3mUD1UDP-glucose 4-epimerase/0.459
2rl1UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.459
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.459
3phiNDPShikimate dehydrogenase (NADP(+))/0.459
3qt62P0Mevalonate diphosphate decarboxylase/0.459
4gcmNAPThioredoxin reductase1.8.1.90.459
4ohwATPProtein clpf-1/0.459
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.458
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.458
2g8aUMPThymidylate synthase/0.458
2hutSAHDiphthine synthase/0.458
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.458
3h4lANPDNA mismatch repair protein PMS1/0.458
3r9iADPSeptum site-determining protein MinD/0.458
4ku2MYA3-oxoacyl-[ACP] synthase III/0.458
4opgFDAConserved Archaeal protein/0.458
4yp12BAStimulator of interferon genes protein/0.458
1nhrFADNADH peroxidase1.11.1.10.457
1pdhFASp-hydroxybenzoate hydroxylase/0.457
2ejvNADL-threonine 3-dehydrogenase/0.457
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.457
2zsaADPPantothenate kinase2.7.1.330.457
3m9vTYDFAD-dependent oxidoreductase/0.457
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.457
4lutDCSAlanine racemase/0.457
1f8wFADNADH peroxidase1.11.1.10.456
1gv0NADMalate dehydrogenase/0.456
1hdgNADGlyceraldehyde-3-phosphate dehydrogenase/0.456
1p9wANPType II secretion system protein E/0.456
1w0kADPATP synthase subunit alpha, mitochondrial/0.456
1w0kADPATP synthase subunit beta, mitochondrial3.6.3.140.456
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.456
2x3jATPAcsD/0.456
2z4sADPChromosomal replication initiator protein DnaA/0.456
3f3sNADLambda-crystallin homolog/0.456
3lqfNADGalactitol dehydrogenase/0.456
4briUNPEctonucleoside triphosphate diphosphohydrolase I/0.456
1ascNPLAspartate aminotransferase2.6.1.10.455
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.455
1xe55FEPlasmepsin-23.4.23.390.455
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.455
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.455
2yylFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.455
3oqkS52Renin3.4.23.150.455
3v0o4GWHisto-blood group ABO system transferase/0.455
4dpy2P0Mevalonate diphosphate decarboxylase/0.455
4lrlTTPHD domain protein/0.455
4m4922YL-lactate dehydrogenase A chain1.1.1.270.455
4mvcCDCCholine-phosphate cytidylyltransferase A/0.455
4wpuGDPPhosphoenolpyruvate carboxykinase [GTP]/0.455
1a5uATPPyruvate kinase PKM2.7.1.400.454
1hkuNADC-terminal-binding protein 11.1.10.454
1kh3ANPArgininosuccinate synthase/0.454
1udaUFGUDP-glucose 4-epimerase5.1.3.20.454
2i4qUA4Renin3.4.23.150.454
2qo9ANPEphrin type-A receptor 32.7.10.10.454
2vkvTDCTetracycline repressor protein class D/0.454
4a99FADTetX family tetracycline inactivation enzyme/0.454
4f5dC2EStimulator of interferon genes protein/0.454
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.454
4loh1SYStimulator of interferon genes protein/0.454
1e0jANPDNA primase/helicase2.7.70.453
1nhhANPDNA mismatch repair protein MutL/0.453
1vjtNADAlpha-glucosidase, putative/0.453
3etgNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.453
3koqFMNPutative nitroreductase/0.453
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.453
4eetFMNPhototropin-22.7.11.10.453
4gxs0YSGlutamate receptor 2/0.453
1h63FMNPentaerythritol tetranitrate reductase/0.452
1lbcCYZGlutamate receptor 2/0.452
1npxFADNADH peroxidase1.11.1.10.452
2a94AP0L-lactate dehydrogenase1.1.1.270.452
2geuCOKPantothenate kinase2.7.1.330.452
3fr5I4AFatty acid-binding protein, adipocyte/0.452
3sxpNADADP-L-glycero-D-mannoheptose-6-epimerase/0.452
5fkoTDCTetracycline repressor protein class D/0.452
1e2nRCAThymidine kinase/0.451
1icuFMNOxygen-insensitive NAD(P)H nitroreductase/0.451
1qwjNCCN-acylneuraminate cytidylyltransferase2.7.7.430.451
3toxNAPPutative oxidoreductase/0.451
4g9kFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.451
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.451
4lcjNADC-terminal-binding protein 2/0.451
4loi1YCStimulator of interferon genes protein/0.451
4oi2ADPProtein clpf-1/0.451
5ftcADPTPR domain protein/0.451
1u1gBBBUridine phosphorylase2.4.2.30.450
2abbFMNPentaerythritol tetranitrate reductase/0.450
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.450
3kb1ADPIron-sulfur cluster carrier protein/0.450
3q1kADPD-alanine--D-alanine ligase A6.3.2.40.450
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4b3aTACTetracycline repressor protein class D/0.450
4gl4NAIAlcohol dehydrogenase class-3/0.450
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.450
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.449
1kvsUPGUDP-glucose 4-epimerase5.1.3.20.449
1x2hLPALipoate-protein ligase A6.3.1.200.449
1yb5NAPQuinone oxidoreductase1.6.5.50.449
3cluFADElectron transfer flavoprotein subunit alpha/0.449
4dieC5PCytidylate kinase/0.449
4isuIKMGlutamate receptor 2/0.449
4m2bUPGUDP-glucose pyrophosphorylase/0.449
4oaqNDPR-specific carbonyl reductase/0.449
4ohvANPProtein clpf-1/0.449
4zohFADPutative oxidoreductase FAD-binding subunit/0.449
4z36ON3Lysophosphatidic acid receptor 1/0.449
1b5dDCMDeoxycytidylate 5-hydroxymethyltransferase2.1.2.80.448
1noiNTZGlycogen phosphorylase, muscle form2.4.1.10.448
1ytmATPPhosphoenolpyruvate carboxykinase (ATP)/0.448
2cmoM1LGlutamate receptor 2/0.448
2hk9NAPShikimate dehydrogenase (NADP(+))/0.448
2oorNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.448
2ylrNAPPhenylacetone monooxygenase1.14.13.920.448
3h2sNDPPutative NADH-flavin reductase/0.448
3kb6NADD-lactate dehydrogenase/0.448
3nbvANPKetohexokinase/0.448
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.448
4jxxATPGlutamine--tRNA ligase6.1.1.180.448
4z54GDPNeuronal-specific septin-3/0.448
5fkmTDCTetracycline repressor protein class D/0.448
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.447
1mjaCOAHistone acetyltransferase ESA1/0.447
1t09NAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.447
1tsxUMPThymidylate synthase/0.447
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.447
2e1zB4PPropionate kinase/0.447
2ggqTTPDual sugar-1-phosphate nucleotidylyltransferase/0.447
3apwDP0Alpha-1-acid glycoprotein 2/0.447
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
3r1rATPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.447
3sopGDPNeuronal-specific septin-3/0.447
4a0rDTBBifunctional dethiobiotin synthetase/7,8-diamino-pelargonic acid aminotransferase, mitochondrial6.3.3.30.447
4a6nFADTetX family tetracycline inactivation enzyme/0.447
4bfxZVXPantothenate kinase2.7.1.330.447
4dptAGSMevalonate diphosphate decarboxylase/0.447
4l0qNADAlcohol dehydrogenase class-3/0.447
1esvLARActin, alpha skeletal muscle/0.446
1njfADPDNA polymerase III subunit tau2.7.7.70.446
1pjcNADAlanine dehydrogenase/0.446
1tqf32PBeta-secretase 13.4.23.460.446
2g1y5IGRenin3.4.23.150.446
2q14ADPPhosphohydrolase/0.446
2r0cFADPutative FAD-monooxygenase/0.446
2xpuTDCTetracycline repressor protein class D/0.446
3fwyADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein/0.446
3gbuATPUncharacterized sugar kinase PH14592.7.10.446
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.446
3otwCOAPhosphopantetheine adenylyltransferase/0.446
4a862ANMajor pollen allergen Bet v 1-A/0.446
4du82P0Mevalonate diphosphate decarboxylase/0.446
4k6fNAPPutative Acetoacetyl-CoA reductase/0.446
5k5zANPUncharacterized protein/0.446
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
3jzdNADMaleylacetate reductase/0.445
3ty3GGGHomoisocitrate dehydrogenase1.1.1.870.445
4esoNAPPutative oxidoreductase/0.445
4l4xNDPAmphI/0.445
1h73ANPHomoserine kinase2.7.1.390.444
1mezGDPAdenylosuccinate synthetase isozyme 1/0.444
1n2eAPCPantothenate synthetase6.3.2.10.444
1t2cNAIL-lactate dehydrogenase1.1.1.270.444
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.444
2g1r3IGRenin3.4.23.150.444
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.444
2x06NADL-sulfolactate dehydrogenase/0.444
2zsbADPPantothenate kinase2.7.1.330.444
3k6l2BBPeptide deformylase3.5.1.880.444
4giu636Anthranilate phosphoribosyltransferase/0.444
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.444
4la1FADThioredoxin glutathione reductase/0.444
4m83ERYOleandomycin glycosyltransferase2.4.10.444
5eioNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.444
1ds7FMNOxygen-insensitive NAD(P)H nitroreductase/0.443
1ffuFADCarbon monoxide dehydrogenase medium chain/0.443
1qm5PLPMaltodextrin phosphorylase2.4.1.10.443
1xe65FPPlasmepsin-23.4.23.390.443
2a84ATPPantothenate synthetase6.3.2.10.443
2iko7IGRenin3.4.23.150.443
2qtrNXXProbable nicotinate-nucleotide adenylyltransferase/0.443
3fhyATPPyridoxal kinase2.7.1.350.443
3fpaDTBATP-dependent dethiobiotin synthetase BioD/0.443
3s1dZIRCytokinin dehydrogenase 11.5.99.120.443
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.443
3uu114BAnthranilate phosphoribosyltransferase/0.443
4dc0NDPPutative ketoacyl reductase1.3.10.443
4f9fGDPPutative glycosyltransferase/0.443
4g3jVNTLanosterol 14-alpha-demethylase/0.443
4jxzATPGlutamine--tRNA ligase6.1.1.180.443
4qxq1YEStimulator of interferon genes protein/0.443
4u07ATPAdenosine monophosphate-protein transferase FICD2.7.7.n10.443
5f54TMPSingle-stranded-DNA-specific exonuclease/0.443
5fl3ADPPili retraction protein PilT/0.443
1kqbFMNOxygen-insensitive NAD(P)H nitroreductase/0.442
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.442
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.442
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.442
2vkeTACTetracycline repressor protein class D/0.442
3a0tADPSensor histidine kinase/0.442
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3f03FMNPentaerythritol tetranitrate reductase/0.442
3fd6ADPSelenide, water dikinase 12.7.9.30.442
3h3cP1EProtein-tyrosine kinase 2-beta2.7.10.20.442
3s5wFADL-ornithine N(5)-monooxygenase/0.442
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.442
4d03NAPPhenylacetone monooxygenase1.14.13.920.442
4u03GTPCyclic GMP-AMP synthase/0.442
4wouGDPPhosphoenolpyruvate carboxykinase [GTP]/0.442
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
1hygNAPL-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))/0.441
1qbqHFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.441
1qbqHFPProtein farnesyltransferase subunit beta2.5.1.580.441
2b53D23Cyclin-dependent kinase 22.7.11.220.441
2c27ACOMycothiol acetyltransferase2.3.1.1890.441
2gksADPProbable bifunctional SAT/APS kinase2.7.1.250.441
2nniMTKCytochrome P450 2C8/0.441
2rabFADGlutathione amide reductase/0.441
3ahiHTLProbable phosphoketolase/0.441
3p82FMNPentaerythritol tetranitrate reductase/0.441
4a8v2ANMajor pollen allergen Bet v 1-J/0.441
4egbNADdTDP-glucose 4,6-dehydratase/0.441
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.441
4rx6ATPNitrogen regulatory PII-like protein/0.441
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
1i59ANPChemotaxis protein CheA2.7.13.30.440
1kvuUPGUDP-glucose 4-epimerase5.1.3.20.440
1msmJE2Gag-Pol polyprotein3.4.23.160.440
1s64778Geranylgeranyl transferase type-1 subunit beta2.5.1.590.440
1vyrFMNPentaerythritol tetranitrate reductase/0.440
2bjfDXCCholoylglycine hydrolase3.5.1.240.440
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.440
2zkjADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.440
4bfzZVZPantothenate kinase2.7.1.330.440
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.440
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.440
4hj6FMNLOV protein/0.440
4mlp2CXCryptochrome-2/0.440