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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
4ubvCOASteroid 3-ketoacyl-CoA thiolase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4ubvCOASteroid 3-ketoacyl-CoA thiolase/1.000
4ubtCOASteroid 3-ketoacyl-CoA thiolase/0.509
4an4DUDPutative glycosyl transferase/0.499
1fm4DXCMajor pollen allergen Bet v 1-L/0.489
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.486
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.486
1g63FMNEpidermin decarboxylase4.1.10.485
4q71FADBifunctional protein PutA/0.485
1me6IVSPlasmepsin-23.4.23.390.484
2x7hPFNProstaglandin reductase 310.484
3h3t16HCollagen type IV alpha-3-binding protein/0.484
4a8v2ANMajor pollen allergen Bet v 1-J/0.484
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.483
4bb3KKAIsopenicillin N synthase1.21.3.10.482
5dp2NAPCurF/0.482
2iviACWIsopenicillin N synthase1.21.3.10.481
4ubuCOASteroid 3-ketoacyl-CoA thiolase/0.481
3af0GDPPantothenate kinase2.7.1.330.480
2pg0FADAcyl-CoA dehydrogenase/0.478
4oztP1AEcdysone receptor, putative/0.478
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.477
4uugPXGBranched-chain amino acid aminotransferase, putative/0.477
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.475
2ociTYCValacyclovir hydrolase3.10.475
2y60M8FIsopenicillin N synthase1.21.3.10.475
3h3sH15Collagen type IV alpha-3-binding protein/0.475
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.475
4ambDUDPutative glycosyl transferase/0.475
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.473
3gw9VNILanosterol 14-alpha-demethylase/0.472
3tdaPN0Cytochrome P450 2D6/0.472
3zkyWT4Isopenicillin N synthase1.21.3.10.471
2d29FADAcyl-CoA dehydrogenase/0.470
2jb4A14Isopenicillin N synthase1.21.3.10.470
2yyeAPCSelenide, water dikinase2.7.9.30.470
1obnASVIsopenicillin N synthase1.21.3.10.469
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.469
4irnFADAnaB/0.468
5irnADPNucleotide binding oligomerization domain containing 2/0.468
2a94AP0L-lactate dehydrogenase1.1.1.270.467
2xlrFADPutative flavin-containing monooxygenase/0.467
2yg3FADPutrescine oxidase/0.467
3lpiZ74Beta-secretase 13.4.23.460.467
3v2uATPProtein GAL3/0.467
4gl4NAIAlcohol dehydrogenase class-3/0.467
1qorNDPQuinone oxidoreductase 1/0.466
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.465
1xe55FEPlasmepsin-23.4.23.390.465
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.465
3own3OWRenin3.4.23.150.465
5f12FMNNAD(P)H dehydrogenase (quinone)/0.465
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.464
3bgxTMPThymidylate synthase/0.464
3h3r14HCollagen type IV alpha-3-binding protein/0.464
4esoNAPPutative oxidoreductase/0.464
1blzACVIsopenicillin N synthase1.21.3.10.463
1g1aNADdTDP-glucose 4,6-dehydratase/0.463
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.463
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.463
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.463
1rx0FADIsobutyryl-CoA dehydrogenase, mitochondrial1.3.990.462
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.462
2f3rG5PGuanylate kinase2.7.4.80.461
2pncCLUPrimary amine oxidase, liver isozyme/0.461
2rlcCHDCholoylglycine hydrolase3.5.1.240.461
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.461
3q44D50M1 family aminopeptidase3.4.110.461
4nieNBHNuclear receptor ROR-gamma/0.461
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.460
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.460
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.460
2pr2DG1Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
2xlsFADPutative flavin-containing monooxygenase/0.460
2y0mACOHistone acetyltransferase KAT8/0.460
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
3rueNADUDP-N-acetylglucosamine 4-epimerase/0.460
3up0D7SaceDAF-12/0.460
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.460
1mp0NADAlcohol dehydrogenase class-31.1.1.10.459
2g1r3IGRenin3.4.23.150.459
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.459
3ekuCY9Actin-5C/0.459
3f63GTXGlutathione transferase GST1-4/0.459
3gkjHC3Niemann-Pick C1 protein/0.459
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.459
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.458
1xddAAYIntegrin alpha-L/0.458
1yqzCOACoenzyme A disulfide reductase/0.458
2a9y26AAdenosine kinase2.7.1.200.458
2pswCOAN-alpha-acetyltransferase 50/0.458
3clsFADElectron transfer flavoprotein subunit alpha/0.458
3fktSIIBeta-secretase 13.4.23.460.458
1tj0FADBifunctional protein PutA1.5.5.20.457
3af1GDPPantothenate kinase2.7.1.330.457
3lqfNADGalactitol dehydrogenase/0.457
3zhoFMNNAD(P)H dehydrogenase (quinone)/0.457
4l4xNDPAmphI/0.457
1pqc444Oxysterols receptor LXR-beta/0.456
1yqdNAPSinapyl alcohol dehydrogenase/0.456
2dhfDZFDihydrofolate reductase1.5.1.30.456
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.456
3cz7ACOHistone acetyltransferase RTT1092.3.1.480.456
3ixj586Beta-secretase 13.4.23.460.456
4o1mNADEnoyl-acyl carrier reductase/0.456
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.455
1ma0NADAlcohol dehydrogenase class-31.1.1.10.455
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.455
2vbpVB1Isopenicillin N synthase1.21.3.10.455
2xhd7T9Glutamate receptor 2/0.455
3gwdNAPCyclohexanone monooxygenase/0.455
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.455
4b78KGGBeta-secretase 13.4.23.460.455
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.454
4bfzZVZPantothenate kinase2.7.1.330.454
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.454
4wriOKAOkadaic acid binding protein 2-alpha/0.454
4yerADPAntibiotic ABC transporter, ATP-binding protein, putative/0.454
1ndiCOACarnitine O-acetyltransferase2.3.1.70.453
1pd9CO4Dihydrofolate reductase1.5.1.30.453
1tysDHFThymidylate synthase/0.453
2wo7ASVIsopenicillin N synthase1.21.3.10.453
2wyaHMGHydroxymethylglutaryl-CoA synthase, mitochondrial2.3.3.100.453
2y6fM9FIsopenicillin N synthase1.21.3.10.453
3b6zCO7Enoyl reductase LovC10.453
3ixk929Beta-secretase 13.4.23.460.453
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.453
4dc0NDPPutative ketoacyl reductase1.3.10.453
4egbNADdTDP-glucose 4,6-dehydratase/0.453
4g7gVFVLanosterol 14-alpha-demethylase/0.453
1cf3FADGlucose oxidase1.1.3.40.452
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.452
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
2fvlNAPAldo-keto reductase family 1 member C41.1.1.2250.452
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.452
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3phiNDPShikimate dehydrogenase (NADP(+))/0.452
4d89BXDBeta-secretase 13.4.23.460.452
4fxfATPPyruvate kinase PKM2.7.1.400.452
4q0kGA3Phytohormone-binding protein/0.452
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.452
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.452
1hb1OCVIsopenicillin N synthase1.21.3.10.451
1nhpFADNADH peroxidase1.11.1.10.451
1ycfFMNNitric oxide reductase10.451
2c12FADNitroalkane oxidase1.7.3.10.451
2eixFADNADH-cytochrome b5 reductase/0.451
2znpK55Peroxisome proliferator-activated receptor delta/0.451
3cic316Beta-secretase 13.4.23.460.451
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.451
1gqtACPRibokinase/0.450
1qjfACSIsopenicillin N synthase1.21.3.10.450
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.450
2fhnBNIAvidin-related protein 4/5/0.450
2igoFADPyranose 2-oxidase/0.450
2ikuLIYRenin3.4.23.150.450
2x9dITCTetracycline repressor protein class D/0.450
2xx91NFGlutamate receptor 2/0.450
3jqpA2PFerredoxin--NADP reductase, apicoplast/0.450
3qbhQBHBeta-secretase 13.4.23.460.450
4bfwZVWPantothenate kinase2.7.1.330.450
4g3jVNTLanosterol 14-alpha-demethylase/0.450
4iqgNAPShort-chain dehydrogenase/reductase SDR/0.450
4z24FADPutative GMC-type oxidoreductase R13510.450
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.449
2c29NAPDihydroflavonol 4-reductase/0.449
2qujTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.449
2vkeTACTetracycline repressor protein class D/0.449
2wf1ZY1Beta-secretase 13.4.23.460.449
2zb3NDPProstaglandin reductase 21.3.1.480.449
3kgcLY7Glutamate receptor 2/0.449
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.448
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.448
2p83MR0Beta-secretase 13.4.23.460.448
2vijC44Beta-secretase 13.4.23.460.448
3l0lHC3Nuclear receptor ROR-gamma/0.448
3pm1ETHTH-type transcriptional regulator QacR/0.448
3sufSUEPolyprotein/0.448
3zoiM2WIsopenicillin N synthase1.21.3.10.448
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.447
1hb3SCVIsopenicillin N synthase1.21.3.10.447
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.447
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.447
2bu9HFVIsopenicillin N synthase1.21.3.10.447
2ea2F77Methionine aminopeptidase 2/0.447
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.447
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.447
2po7CHDFerrochelatase, mitochondrial4.99.1.10.447
2wbaFADTrypanothione reductase1.8.1.120.447
2zjuIM4Acetylcholine-binding protein/0.447
3cib314Beta-secretase 13.4.23.460.447
3kry3KRCollagenase 33.4.240.447
3q9bB3NAcetylpolyamine amidohydrolase/0.447
3qm4PN0Cytochrome P450 2D6/0.447
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.447
3vqsJT1Genome polyprotein/0.447
4dd8BATDisintegrin and metalloproteinase domain-containing protein 83.4.240.447
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.447
4rvgTYDD-mycarose 3-C-methyltransferase/0.447
4udrFAD5-(hydroxymethyl)furfural oxidase/0.447
1culFOKAdenylate cyclase type 2/0.446
1culFOKAdenylate cyclase type 5/0.446
1galFADGlucose oxidase1.1.3.40.446
1mjbACOHistone acetyltransferase ESA1/0.446
1w6hTITPlasmepsin-23.4.23.390.446
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2g1s4IGRenin3.4.23.150.446
2jj2ANPATP synthase subunit beta, mitochondrial3.6.3.140.446
2uxoTACHTH-type transcriptional regulator TtgR/0.446
3eigMTXDihydrofolate reductase1.5.1.30.446
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.446
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.446
3pm9FADPutative oxidoreductase/0.446
3ru7NADUDP-N-acetylglucosamine 4-epimerase/0.446
4px9ADPATP-dependent RNA helicase DDX3X3.6.4.130.446
4qi5FADCellobiose dehydrogenase/0.446
5k2cZMAAdenosine receptor A2a/0.446
1q23FUAChloramphenicol acetyltransferase2.3.1.280.445
2he5NDPAldo-keto reductase family 1 member C211.1.10.445
2rgoFADAlpha-Glycerophosphate Oxidase/0.445
3e2sFADBifunctional protein PutA1.5.5.20.445
3fhxPLPPyridoxal kinase2.7.1.350.445
3gwfNAPCyclohexanone monooxygenase/0.445
3lsmSFDPyranose 2-oxidase/0.445
3mddFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.445
4hb9FADUncharacterized protein/0.445
4o8aFADBifunctional protein PutA1.2.1.880.445
4q72FADBifunctional protein PutA/0.445
4rf2NAPNADPH dependent R-specific alcohol dehydrogenase/0.445
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.445
5ahsFADAcyl-CoA dehydrogenase/0.445
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1ve3SAMUncharacterized protein/0.444
2c2aADPSensor histidine kinase/0.444
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
3adaNADSubunit alpha of sarocosine oxidase/0.444
3d91REMRenin3.4.23.150.444
3k7tFAD6-hydroxy-L-nicotine oxidase/0.444
3oqfS51Renin3.4.23.150.444
4b79NADProbable short-chain dehydrogenase/0.444
4bftZVTPantothenate kinase2.7.1.330.444
4dpf0LGBeta-secretase 13.4.23.460.444
4e0u0MVCyclic dipeptide N-prenyltransferase/0.444
4jtqNAPAldo-keto reductase family 1 member C2/0.444
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
5iu86DZAdenosine receptor A2a/0.444
1cjtFOKAdenylate cyclase type 2/0.443
1cjtFOKAdenylate cyclase type 5/0.443
1f8wFADNADH peroxidase1.11.1.10.443
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
1x8lOXRRetinol dehydratase/0.443
1yqxNAPSinapyl alcohol dehydrogenase/0.443
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2rc4ACOHistone acetyltransferase KAT6A/0.443
2vkmBSDBeta-secretase 13.4.23.460.443
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.443
3lpjZ75Beta-secretase 13.4.23.460.443
3owaFADAcyl-CoA dehydrogenase/0.443
3p4tFAOPutative acyl-CoA dehydrogenase/0.443
3q43D66M1 family aminopeptidase3.4.110.443
3qe2FMNNADPH--cytochrome P450 reductase/0.443
3r7kFDAProbable acyl CoA dehydrogenase/0.443
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.443
3sglFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.443
4bfxZVXPantothenate kinase2.7.1.330.443
4do30LAFatty-acid amide hydrolase 13.5.1.990.443
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4eqsCOACoenzyme A disulfide reductase/0.443
4frs0V6Beta-secretase 13.4.23.460.443
4i0h1BLBeta-secretase 13.4.23.460.443
4rx6ATPNitrogen regulatory PII-like protein/0.443
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
5c93ACPTwo-component system histidine protein kinase/0.443
5iqiGNPBifunctional AAC/APH2.3.10.443
1q6nP90Tyrosine-protein phosphatase non-receptor type 13.1.3.480.442
1rx1NAPDihydrofolate reductase1.5.1.30.442
2b7aIZATyrosine-protein kinase JAK2/0.442
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.442
2p5uNADUDP-glucose 4-epimerase/0.442
2wu4HBPAcetylcholinesterase3.1.1.70.442
2y3rTRKTamL/0.442
2yg4FADPutrescine oxidase/0.442
3dm6757Beta-secretase 13.4.23.460.442
3l5eBDWBeta-secretase 13.4.23.460.442
3oibFDAPutative acyl-CoA dehydrogenase/0.442
3p62FMNPentaerythritol tetranitrate reductase/0.442
3u8l09QAcetylcholine-binding protein/0.442
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.442
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.442
4opgFDAConserved Archaeal protein/0.442
4xr9NADCalS8/0.442
1mvsDTMDihydrofolate reductase1.5.1.30.441
1rfuADPPyridoxal kinase2.7.1.350.441
1xe65FPPlasmepsin-23.4.23.390.441
2bf4FMNNADPH--cytochrome P450 reductase/0.441
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.441
2iko7IGRenin3.4.23.150.441
2y4gTIRTamL/0.441
3cid318Beta-secretase 13.4.23.460.441
3i5zZ48Mitogen-activated protein kinase 12.7.11.240.441
3ibdCPZCytochrome P450 2B61.14.130.441
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.441
4fse0VABeta-secretase 13.4.23.460.441
4h3j10WBeta-secretase 13.4.23.460.441
4p13FADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.441
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
5ej4TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.441
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1ot7IU5Bile acid receptor/0.440
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.440
1ycgFMNNitric oxide reductase10.440
2iqgF2IBeta-secretase 13.4.23.460.440
2pmoHMDProtein kinase 7/0.440
2trtTACTetracycline repressor protein class D/0.440
2uzfCAA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.440
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3vydVYDRenin3.4.23.150.440
4a81DXCMajor pollen allergen Bet v 1-A/0.440
4dl9NADS-(hydroxymethyl)glutathione dehydrogenase/0.440
4wudANPDNA gyrase subunit B/0.440