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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
3wtkTH4Acetylcholine-binding protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3wtkTH4Acetylcholine-binding protein/1.000
3wthIM4Acetylcholine-binding protein/0.596
2zjuIM4Acetylcholine-binding protein/0.580
3wtiCT4Acetylcholine-binding protein/0.528
4alxIZNAcetylcholine-binding protein/0.506
2anmCDOProthrombin3.4.21.50.503
3sf6FDAGlutaryl-CoA dehydrogenase/0.503
1nm6L86Prothrombin3.4.21.50.487
4bb3KKAIsopenicillin N synthase1.21.3.10.487
2zi224UProthrombin3.4.21.50.484
1pqc444Oxysterols receptor LXR-beta/0.479
4ax9N5NProthrombin3.4.21.50.476
2d29FADAcyl-CoA dehydrogenase/0.475
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.473
4bfxZVXPantothenate kinase2.7.1.330.471
4lxb7R9Prothrombin3.4.21.50.471
4ryvZEAProtein LlR18A/0.471
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.470
1ta6177Prothrombin3.4.21.50.470
2znk31UProthrombin3.4.21.50.470
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
1ypmRA4Prothrombin3.4.21.50.469
2xlsFADPutative flavin-containing monooxygenase/0.468
2zda32UProthrombin3.4.21.50.468
2zfq45UProthrombin3.4.21.50.468
2zhe13UProthrombin3.4.21.50.468
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
2vkeTACTetracycline repressor protein class D/0.466
3fhxPXLPyridoxal kinase2.7.1.350.466
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.466
3zdhXRSAcetylcholine-binding protein/0.466
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.466
2dvlFADAcyl-CoA dehydrogenase/0.465
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.465
2ignFADPyranose 2-oxidase/0.465
2jh5895Prothrombin3.4.21.50.465
2zc922UProthrombin3.4.21.50.465
3adaNADSubunit alpha of sarocosine oxidase/0.465
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.465
1ypeUIPProthrombin3.4.21.50.464
1zgi382Prothrombin3.4.21.50.464
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.464
5hs1VORLanosterol 14-alpha demethylase/0.464
1d3pBT3Prothrombin3.4.21.50.463
1fmlRTLRetinol dehydratase/0.463
2q7vFADThioredoxin reductase/0.463
2zhq27UProthrombin3.4.21.50.463
3h2sNDPPutative NADH-flavin reductase/0.463
4hy6FJ1Heat shock protein HSP 90-alpha/0.463
4kbyC2EStimulator of interferon genes protein/0.463
1afeALZProthrombin3.4.21.50.462
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1mueCDDProthrombin3.4.21.50.462
1t4v14AProthrombin3.4.21.50.462
4dpf0LGBeta-secretase 13.4.23.460.462
1uy6PU3Heat shock protein HSP 90-alpha/0.461
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
2bdyUNBProthrombin3.4.21.50.461
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.461
2jh0701Prothrombin3.4.21.50.461
3c1kT15Prothrombin3.4.21.50.461
3k4nFADPyranose 2-oxidase/0.461
4a81DXCMajor pollen allergen Bet v 1-A/0.461
4at0FADPossible succinate dehydrogenase/0.461
1c4uIH1Prothrombin3.4.21.50.460
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.460
2zfr46UProthrombin3.4.21.50.460
3biu10UProthrombin3.4.21.50.460
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
4awo99BHeat shock protein HSP 90-alpha/0.460
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.460
4rn615UProthrombin3.4.21.50.460
5fm7ADPRuvB-like helicase/0.460
1d6w00RProthrombin3.4.21.50.459
1dr3HBIDihydrofolate reductase1.5.1.30.459
2bvs2CEProthrombin3.4.21.50.459
1kzjCB3Thymidylate synthase/0.458
1sb1165Prothrombin3.4.21.50.458
2fwyH64Heat shock protein HSP 90-alpha/0.458
1oytFSNProthrombin3.4.21.50.457
1yplRA8Prothrombin3.4.21.50.457
2rlcCHDCholoylglycine hydrolase3.5.1.240.457
2v3hI25Prothrombin3.4.21.50.457
3v2uATPProtein GAL3/0.457
4d03FADPhenylacetone monooxygenase1.14.13.920.457
1u1f183Uridine phosphorylase2.4.2.30.456
1zgv501Prothrombin3.4.21.50.456
1zrb062Prothrombin3.4.21.50.456
2pksG44Prothrombin3.4.21.50.456
3zeiAWHO-acetylserine sulfhydrylase/0.456
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.456
4bamMM9Prothrombin3.4.21.50.456
1rfuADPPyridoxal kinase2.7.1.350.455
1ypkCCRProthrombin3.4.21.50.455
2hkoFADLysine-specific histone demethylase 1A10.455
3inwJZBHeat shock protein HSP 90-alpha/0.455
3q43D66M1 family aminopeptidase3.4.110.455
3wleNAD(R)-specific carbonyl reductase/0.455
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.455
4g95OAGDihydrofolate reductase1.5.1.30.455
2xytTC9Soluble acetylcholine receptor/0.454
3ctyFADProbable thioredoxin reductase/0.454
3hyg099A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.454
4az29MUProthrombin3.4.21.50.454
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.454
5fd8A5APutative carboxypeptidase yocD/0.454
5kgpACOPredicted acetyltransferase/0.454
1t2cNAIL-lactate dehydrogenase1.1.1.270.453
1uy9PU6Heat shock protein HSP 90-alpha/0.453
1x1cSAHC-20 methyltransferase/0.453
1ypgUIRProthrombin3.4.21.50.453
2a94AP0L-lactate dehydrogenase1.1.1.270.453
2v3oI26Prothrombin3.4.21.50.453
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.453
4bfzZVZPantothenate kinase2.7.1.330.453
4dvi2IWTankyrase-12.4.2.300.453
4i8vBHFCytochrome P450 1A11.14.14.10.453
4isk1JYThymidylate synthase/0.453
4n3l2FNProthrombin3.4.21.50.453
2iyaZIOOleandomycin glycosyltransferase/0.452
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.452
3iaeD7KBenzaldehyde lyase/0.452
3tw6ADPPyruvate carboxylase/0.452
4l9kEHFSerum albumin/0.452
1k21IGNProthrombin3.4.21.50.451
1nqw5YL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.451
1tduCB3Thymidylate synthase/0.451
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.451
3c35KAIGlutamate receptor ionotropic, kainate 1/0.451
3mlaJJZProbable nicotinate-nucleotide adenylyltransferase/0.451
3qlrNDPDihydrofolate reductase1.5.1.30.451
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA23.6.30.451
4zirANPEnergy-coupling factor transporter ATP-binding protein EcfA1/0.451
1mu6CDAProthrombin3.4.21.50.450
1rx1NAPDihydrofolate reductase1.5.1.30.450
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
2zff53UProthrombin3.4.21.50.450
3drcMTXDihydrofolate reductase1.5.1.30.450
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.450
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.450
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.450
3v94WYQPhosphodiesterase/0.450
4fv7E94Mitogen-activated protein kinase 12.7.11.240.450
1d3dBZTProthrombin3.4.21.50.449
1k22MELProthrombin3.4.21.50.449
1towCRZFatty acid-binding protein, adipocyte/0.449
1xe65FPPlasmepsin-23.4.23.390.449
2fr0NDP6-deoxyerythronolide-B synthase EryA1, modules 1 and 2/0.449
2jh6894Prothrombin3.4.21.50.449
2y98MIVMycinamicin IV hydroxylase/epoxidase/0.449
3ox1695Ribosyldihydronicotinamide dehydrogenase [quinone]/0.449
3ppkFNISerine/threonine-protein kinase B-raf2.7.11.10.449
4bftZVTPantothenate kinase2.7.1.330.449
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.449
4oztP1AEcdysone receptor, putative/0.449
1bk0ACVIsopenicillin N synthase1.21.3.10.448
1f8gNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.448
1pq944BOxysterols receptor LXR-beta/0.448
1vzqSHYProthrombin3.4.21.50.448
1ypjUIBProthrombin3.4.21.50.448
2ftoCB3Thymidylate synthase/0.448
2geuCOKPantothenate kinase2.7.1.330.448
2nq8ZIDEnoyl-ACP reductase/0.448
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.448
2xpuTDCTetracycline repressor protein class D/0.448
2xvfFADPutative flavin-containing monooxygenase/0.448
2xvv9DNSerum albumin/0.448
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.448
3nd1SAHPrecorrin-6A synthase (Deacetylating)/0.448
4awp99AHeat shock protein HSP 90-alpha/0.448
4iji99TGlutathione S-transferase-like protein YibF/0.448
4lb2DM5Serum albumin/0.448
1ae8AZLProthrombin3.4.21.50.447
1r2jFADFkbI/0.447
2igoFADPyranose 2-oxidase/0.447
2o7pNAPRiboflavin biosynthesis protein RibD/0.447
2uuk897Prothrombin3.4.21.50.447
2xveFADPutative flavin-containing monooxygenase/0.447
3cr0809Wee1-like protein kinase2.7.10.20.447
4gxs0YSGlutamate receptor 2/0.447
4ho6UTPGlucose-1-phosphate thymidylyltransferase/0.447
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.446
1uykPUXHeat shock protein HSP 90-alpha/0.446
1xm1GAHProthrombin3.4.21.50.446
1xs7MMIBeta-secretase 13.4.23.460.446
2cf8ESHProthrombin3.4.21.50.446
2f3mGTDGlutathione S-transferase Mu 12.5.1.180.446
2jfhLK1UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.446
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.446
3i2834NBifunctional epoxide hydrolase 23.3.2.100.446
4awq592Heat shock protein HSP 90-alpha/0.446
4xbfFADLysine-specific histone demethylase 1A10.446
5bp9SAHPutative methyltransferase protein/0.446
5dg3U21Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase/0.446
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.445
2v5aLZLBiotin carboxylase6.3.4.140.445
2xviFADPutative flavin-containing monooxygenase/0.445
2z4sADPChromosomal replication initiator protein DnaA/0.445
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.445
3vqsJT1Genome polyprotein/0.445
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.445
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.445
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.445
4kl9NDPDihydrofolate reductase1.5.1.30.445
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.445
1d4pBPPProthrombin3.4.21.50.444
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.444
1yhjR6CPyridoxal kinase2.7.1.350.444
2ay95PVAromatic-amino-acid aminotransferase2.6.1.570.444
2r9vATPATP synthase subunit alpha/0.444
2vq7FADPutative flavin-containing monooxygenase/0.444
2xlpFADPutative flavin-containing monooxygenase/0.444
2yeiXQIHeat shock protein HSP 90-alpha/0.444
2zhf49UProthrombin3.4.21.50.444
3bgxMEFThymidylate synthase/0.444
4ez8DHFThymidylate synthase2.1.1.450.444
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.444
7kmeACE_0BN_CHG_PRRProthrombin3.4.21.50.444
1d9i00PProthrombin3.4.21.50.443
1t4u81AProthrombin3.4.21.50.443
1u1cBAUUridine phosphorylase2.4.2.30.443
1upw444Oxysterols receptor LXR-beta/0.443
2c12FADNitroalkane oxidase1.7.3.10.443
2p83MR0Beta-secretase 13.4.23.460.443
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.443
3a9wNADNDP-sugar epimerase/0.443
3bi2FADPolyamine oxidase FMS1/0.443
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.443
3qiyQI1Botulinum neurotoxin type A3.4.24.690.443
3qwc98PProthrombin3.4.21.50.443
3to3ATPPetrobactin biosynthesis protein AsbB/0.443
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
4a83DXCMajor pollen allergen Bet v 1-A/0.443
4bfvZVVPantothenate kinase2.7.1.330.443
5dp2NAPCurF/0.443
1eioGCHGastrotropin/0.442
1pw1HELD-alanyl-D-alanine carboxypeptidase3.4.16.40.442
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.442
2w9hTOPDihydrofolate reductase1.5.1.30.442
2x9dITCTetracycline repressor protein class D/0.442
2yj5ATPCopper-transporting ATPase/0.442
3bg7FADPyranose 2-oxidase/0.442
3bhlTHGThymidylate synthase/0.442
3hatGLY_VAL_ARG_RNGProthrombin3.4.21.50.442
3p1799PProthrombin3.4.21.50.442
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.442
3pqbVGPPutative oxidoreductase/0.442
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.442
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.442
5eccNAPDehydrofolate reductase type I/0.442
5iosFADFlavin-dependent thymidylate synthase2.1.1.1480.442
1f20FADNitric oxide synthase, brain1.14.13.390.441
1fvpFMANon-fluorescent flavoprotein/0.441
1fwmCB3Thymidylate synthase/0.441
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
1twwHH2Dihydropteroate synthase/0.441
2rqfJH3Hemolymph juvenile hormone binding protein/0.441
2vqbFADPutative flavin-containing monooxygenase/0.441
2zdv37UProthrombin3.4.21.50.441
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.441
3k2hLYABifunctional dihydrofolate reductase-thymidylate synthase/0.441
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.441
4h6pFMNChromate reductase/0.441
4jx1CAHCamphor 5-monooxygenase1.14.15.10.441
1axwMTXThymidylate synthase/0.440
1bwlFMNNADPH dehydrogenase 11.6.99.10.440
1bxsNADRetinal dehydrogenase 11.2.1.360.440
1fm4DXCMajor pollen allergen Bet v 1-L/0.440
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1jwtBLIProthrombin3.4.21.50.440
1kceCB3Thymidylate synthase/0.440
1phgMYTCamphor 5-monooxygenase1.14.15.10.440
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.440
2e94364Geranylgeranyl pyrophosphate synthase/0.440
2gjlFMNNitronate monooxygenase1.13.12.160.440
2vaxCSCAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.440
2wi72KLHeat shock protein HSP 90-alpha/0.440
3a783EVVitamin D3 receptor/0.440
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3ju8NADN-succinylglutamate 5-semialdehyde dehydrogenase1.2.1.710.440
3mdmFJZCholesterol 24-hydroxylase/0.440
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.440
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.440
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.440
4b7754MBeta-secretase 13.4.23.460.440
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.440
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.440