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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
4tuyGTPTubulin alpha-1B chain

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4tuyGTPTubulin alpha-1B chain/1.000
4wbnGTPTubulin alpha-1B chain/0.843
4tv9GTPTubulin alpha-1B chain/0.818
4ihjGTPTubulin alpha-1B chain/0.809
5la6GTPTubulin alpha-1B chain/0.803
4o4iGTPTubulin alpha-1B chain/0.703
4zolGTPTubulin alpha-1B chain/0.639
5jqgGTPTubulin alpha-1B chain/0.627
4iijGTPTubulin alpha-1B chain/0.624
3ryhGTPTubulin alpha chain/0.616
4o4lGTPTubulin alpha-1B chain/0.605
4ffbGTPTubulin alpha-1 chain/0.589
3u9eCOALmo1369 protein/0.549
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.499
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.496
4kgkGTPUncharacterized protein/0.490
1xdpATPPolyphosphate kinase/0.488
4f6rGDPTubulin beta chain/0.487
4u3jGTPTubulin beta chain/0.486
1ib0NADNADH-cytochrome b5 reductase 31.6.2.20.484
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.481
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.480
2z4sADPChromosomal replication initiator protein DnaA/0.479
5la6GDPTubulin beta-2B chain/0.479
2x3jATPAcsD/0.473
3d3wNAPL-xylulose reductase1.1.1.100.473
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.473
3qt62P0Mevalonate diphosphate decarboxylase/0.470
4b63NAPL-ornithine N(5)-monooxygenase/0.470
4yj2GTPTubulin alpha-1B chain/0.470
1njfADPDNA polymerase III subunit tau2.7.7.70.468
2qenADPWalker-Type ATPase/0.468
3cb2GDPTubulin gamma-1 chain/0.468
2abaSTRPentaerythritol tetranitrate reductase/0.467
3nxxNDPDihydrofolate reductase1.5.1.30.467
4bfxZVXPantothenate kinase2.7.1.330.467
4p9dTMPDeoxycytidylate deaminase/0.467
5itzGTPTubulin alpha-1B chain/0.466
2iko7IGRenin3.4.23.150.465
1xddAAYIntegrin alpha-L/0.464
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.464
1qx4FADNADH-cytochrome b5 reductase 31.6.2.20.463
1vbiNADMalate/L-lactate dehydrogenase family protein/0.463
2ifaFMNUncharacterized protein/0.463
3f7bAG5Carbonic anhydrase 44.2.1.10.463
2i7pACOPantothenate kinase 32.7.1.330.462
2r59PH0Leukotriene A-4 hydrolase3.3.2.60.462
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.462
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.461
4j75TYMTryptophan--tRNA ligase/0.461
1okkGCPSignal recognition particle protein/0.460
1okkGCPSignal recognition particle receptor FtsY/0.460
3v2uATPProtein GAL3/0.460
4dpy2P0Mevalonate diphosphate decarboxylase/0.460
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.460
2a94AP0L-lactate dehydrogenase1.1.1.270.459
2xveFADPutative flavin-containing monooxygenase/0.459
2xw7NDPDihydrofolate reductase/0.459
1a5bIGPTryptophan synthase alpha chain/0.458
2xfyACXBeta-amylase3.2.1.20.458
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.458
3w2eNADNADH-cytochrome b5 reductase 31.6.2.20.458
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.458
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.457
1f8fNADBenzyl alcohol dehydrogenase/0.457
1tehNADAlcohol dehydrogenase class-31.1.1.10.457
1z5vGSPTubulin gamma-1 chain/0.457
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.457
2dxdANPNucleoside diphosphate kinase2.7.4.60.457
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.457
4ej0NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.457
4xnw2IDP2Y purinoceptor 1/0.457
1vl8NAPOxidoreductase, short chain dehydrogenase/reductase family/0.456
2g1r3IGRenin3.4.23.150.456
3cid318Beta-secretase 13.4.23.460.456
3iahNAPPutative oxoacyl-(Acyl carrier protein) reductase/0.456
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.456
4hmxFMNPyridoxamine 5'-phosphate oxidase/0.456
4lj9ACPChaperone protein ClpB/0.456
1x1aSAMC-20 methyltransferase/0.455
2nniMTKCytochrome P450 2C8/0.455
3ivgFG5Pantothenate synthetase6.3.2.10.455
3l77NJPShort-chain alcohol dehydrogenase/0.455
3r7kFDAProbable acyl CoA dehydrogenase/0.455
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.455
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.455
4rvfTYDD-mycarose 3-C-methyltransferase/0.455
5dw60T1Succinyl-CoA:acetate CoA-transferase/0.455
2ahrNAPPyrroline-5-carboxylate reductase/0.454
2o12FMNChorismate synthase/0.454
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.454
3dogNNNCyclin-dependent kinase 22.7.11.220.454
3dv5BAVBeta-secretase 13.4.23.460.454
3iaaTYDCalG2/0.454
3vvpBNUUncharacterized protein/0.454
4rphGDUUDP-galactopyranose mutase5.4.99.90.454
1a9zUPGUDP-glucose 4-epimerase5.1.3.20.453
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.453
1txzAPRProbable ADP-ribose 1''-phosphate phosphatase YML087W3.1.3.840.453
1uxyEPUUDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.453
2el0SAHDiphthine synthase/0.453
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.453
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
3lqfNADGalactitol dehydrogenase/0.453
4rvgTYDD-mycarose 3-C-methyltransferase/0.453
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.453
1n95HFPProtein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.452
1n95HFPProtein farnesyltransferase subunit beta2.5.1.580.452
1u1iNADMyo-inositol-1-phosphate synthase (Ino1)/0.452
2rlcCHDCholoylglycine hydrolase3.5.1.240.452
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.452
3ed1GA3Gibberellin receptor GID1/0.452
3fr5I4AFatty acid-binding protein, adipocyte/0.452
4e32DWNMethyltransferase/0.452
4lxa1YSBeta-secretase 13.4.23.460.452
1kp3ATPArgininosuccinate synthase6.3.4.50.451
2a87FADThioredoxin reductase1.8.1.90.451
2p5nNDPAldo-keto reductase family 1 member C211.1.10.451
2r8pT6FTransketolase 1/0.451
2w14WR2Snake venom metalloproteinase BaP13.4.240.451
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.451
2y0mACOHistone acetyltransferase KAT8/0.451
3dhbC6LN-acyl homoserine lactonase AiiA3.1.1.810.451
4dpuAGSMevalonate diphosphate decarboxylase/0.451
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.451
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.451
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.450
1yb5NAPQuinone oxidoreductase1.6.5.50.450
1zrzBI1Protein kinase C iota type2.7.11.130.450
2c29NAPDihydroflavonol 4-reductase/0.450
2gesCOKPantothenate kinase2.7.1.330.450
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.450
2o7oDXTTetracycline repressor protein class D/0.450
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.450
4eb7PLPCysteine desulfurase IscS 2/0.450
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.449
1nl4HFPProtein farnesyltransferase subunit beta2.5.1.580.449
2bkjFMNNADPH-flavin oxidoreductase/0.449
2hunNAD336aa long hypothetical dTDP-glucose 4,6-dehydratase/0.449
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.449
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3b6zCO7Enoyl reductase LovC10.449
3gfbNADL-threonine 3-dehydrogenase/0.449
3pdnSFGHistone-lysine N-methyltransferase SMYD32.1.1.430.449
4dldTZGGlutamate receptor ionotropic, kainate 1/0.449
4hiaFMNLOV protein/0.449
4pzrCOAHistone acetyltransferase p300/0.449
4up3NDPThioredoxin reductase/0.449
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.449
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.449
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.448
1n2iPAJPantothenate synthetase6.3.2.10.448
1udaUFGUDP-glucose 4-epimerase5.1.3.20.448
2ikuLIYRenin3.4.23.150.448
3e8xNAPBH1520 protein/0.448
4bmsNAPAlclohol dehydrogenase/short-chain dehydrogenase/0.448
4dfg0JVGag-Pol polyprotein3.4.23.160.448
4dh60KNBeta-secretase 13.4.23.460.448
4r1lADPPhenylacetate-coenzyme A ligase/0.448
5js6NAD17-beta-hydroxysteroid dehydrogenase 141.1.10.448
1rp0AHZThiamine thiazole synthase, chloroplastic/0.447
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.447
2ignFADPyranose 2-oxidase/0.447
2qs3UBEGlutamate receptor ionotropic, kainate 1/0.447
2rcyNAPPyrroline-5-carboxylate reductase/0.447
3ig6438Urokinase-type plasminogen activator3.4.21.730.447
3to3ATPPetrobactin biosynthesis protein AsbB/0.447
4b4w9L9Bifunctional protein FolD/0.447
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
4i8x6P3L-lactate dehydrogenase A chain1.1.1.270.447
5dozNDPJamJ/0.447
1jkx138Phosphoribosylglycinamide formyltransferase/0.446
1tqf32PBeta-secretase 13.4.23.460.446
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.446
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.446
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.446
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.446
3mx5UTPNucleoprotein/0.446
4ef8FMNDihydroorotate dehydrogenase (fumarate)/0.446
4g3jVNTLanosterol 14-alpha-demethylase/0.446
4hmwFMNPyridoxamine 5'-phosphate oxidase/0.446
4mlp2CXCryptochrome-2/0.446
4wudANPDNA gyrase subunit B/0.446
1bmdNADMalate dehydrogenase/0.445
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.445
1qrpHH0Pepsin A-43.4.23.10.445
2g1y5IGRenin3.4.23.150.445
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.445
2z1mNDPGDP-mannose 4,6-dehydratase/0.445
3fstFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.445
3rdqDTBStreptavidin/0.445
4cdmFO1Deoxyribodipyrimidine photolyase/0.445
4rheFMNFlavin prenyltransferase UbiX/0.445
4wucANPDNA gyrase subunit B/0.445
5irnADPNucleotide binding oligomerization domain containing 2/0.445
6gsuGPSGlutathione S-transferase Mu 12.5.1.180.445
1ae1NAPTropinone reductase 1/0.444
1nytNAPShikimate dehydrogenase (NADP(+))/0.444
1t2cNAIL-lactate dehydrogenase1.1.1.270.444
1xe55FEPlasmepsin-23.4.23.390.444
1xkvATPPhosphoenolpyruvate carboxykinase (ATP)/0.444
2getCOKPantothenate kinase2.7.1.330.444
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.444
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.444
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3ioeA7DPantothenate synthetase6.3.2.10.444
3lpkZ76Beta-secretase 13.4.23.460.444
3p62FMNPentaerythritol tetranitrate reductase/0.444
3qwbNDPProbable quinone oxidoreductase1.6.5.50.444
3up5FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.444
4bznUGXSerine/threonine-protein kinase pim-12.7.11.10.444
4k9oTPPBenzoylformate decarboxylase4.1.1.70.444
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1kqcFMNOxygen-insensitive NAD(P)H nitroreductase/0.443
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.443
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.443
2fxfACODiamine acetyltransferase 1/0.443
2gnaGDUUDP-N-acetylglucosamine 4,6-dehydratase (inverting)4.2.1.1150.443
2vwqNAPGlucose 1-dehydrogenase/0.443
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.443
3c34KAIGlutamate receptor ionotropic, kainate 1/0.443
3cic316Beta-secretase 13.4.23.460.443
3gbuATPUncharacterized sugar kinase PH14592.7.10.443
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.443
3udq09EBeta-secretase 13.4.23.460.443
4bizADPSensor histidine kinase CpxA/0.443
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.443
4j16NADNAD/NADP transhydrogenase alpha subunit 1/0.443
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.443
4l4xNDPAmphI/0.443
4lcg1WMUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.443
1ay0TPPTransketolase 12.2.1.10.442
1f0yNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
1i59ANPChemotaxis protein CheA2.7.13.30.442
1rfuADPPyridoxal kinase2.7.1.350.442
1ve3SAMUncharacterized protein/0.442
3ibqATPPyridoxal kinase/0.442
3swqEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.442
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.442
4xr9NADCalS8/0.442
4yxm2BADNA integrity scanning protein DisA/0.442
5fm6ADPRuvB-like helicase/0.442
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.441
2e16SAHDiphthine synthase/0.441
2fhnBNIAvidin-related protein 4/5/0.441
2igoFADPyranose 2-oxidase/0.441
2pb4SAHDiphthine synthase/0.441
2q5g1FAPeroxisome proliferator-activated receptor delta/0.441
3h7rNAPAldo-keto reductase family 4 member C8/0.441
3hu1AGSTransitional endoplasmic reticulum ATPase3.6.4.60.441
3iqiASN_GLU_ASN_ILECysteine synthase2.5.1.470.441
3junAKDPhenazine biosynthesis protein A/B/0.441
3p74FMNPentaerythritol tetranitrate reductase/0.441
4du82P0Mevalonate diphosphate decarboxylase/0.441
4fkzUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.441
4gsuDWZL,D-transpeptidase 22.3.20.441
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.441
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.441
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.441
1e2nRCAThymidine kinase/0.440
1g6oADPCag alpha/0.440
1nhhANPDNA mismatch repair protein MutL/0.440
1zxmANPDNA topoisomerase 2-alpha5.99.1.30.440
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.440
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.440
2cwfNDPDelta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase/0.440
2dvlFADAcyl-CoA dehydrogenase/0.440
2f3rG5PGuanylate kinase2.7.4.80.440
2gjnFMNNitronate monooxygenase1.13.12.160.440
2tctCTCTetracycline repressor protein class D/0.440
2v59LZKBiotin carboxylase6.3.4.140.440
2w02ATPAcsD/0.440
2ylrNAPPhenylacetone monooxygenase1.14.13.920.440
2z6cFMNPhototropin-12.7.11.10.440
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.440
3af3GCPPantothenate kinase2.7.1.330.440
3af4GCPPantothenate kinase2.7.1.330.440
3c35KAIGlutamate receptor ionotropic, kainate 1/0.440
3c36KAIGlutamate receptor ionotropic, kainate 1/0.440
3hu2AGSTransitional endoplasmic reticulum ATPase3.6.4.60.440
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.440
3l7dDK5Glycogen phosphorylase, muscle form2.4.1.10.440
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3sufSUEPolyprotein/0.440
4b45GSPTubulin-like protein CetZ2/0.440
4g95OAGDihydrofolate reductase1.5.1.30.440
5czySAMEukaryotic huntingtin interacting protein B/0.440