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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
1u08PLPMethionine aminotransferase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
1u08PLPMethionine aminotransferase/1.000
3b1dPLSBetaC-S lyase/0.567
4w5kPLPAspartate aminotransferase, mitochondrial/0.537
1c7oPPGHemolysin/0.530
4wljIK2Kynurenine--oxoglutarate transaminase 12.6.1.70.524
2rqfJH3Hemolymph juvenile hormone binding protein/0.503
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.503
2iko7IGRenin3.4.23.150.493
4je5PLPAromatic/aminoadipate aminotransferase 12.6.1.390.490
1hfqMOTDihydrofolate reductase1.5.1.30.489
2cekN8TAcetylcholinesterase3.1.1.70.489
1r5gAO1Methionine aminopeptidase 2/0.488
3junAJDPhenazine biosynthesis protein A/B/0.486
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.484
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.484
2qimZEAClass 10 plant pathogenesis-related protein/0.483
3d8vUD1Bifunctional protein GlmU/0.483
3hl0NADMaleylacetate reductase/0.483
4yaoFMNNADPH--cytochrome P450 reductase/0.483
4eb5PLPCysteine desulfurase IscS 2/0.481
4fl0PLPAminotransferase ALD1, chloroplastic2.6.10.481
4q0kGA3Phytohormone-binding protein/0.481
1amoFMNNADPH--cytochrome P450 reductase/0.480
2rlcCHDCholoylglycine hydrolase3.5.1.240.479
4bfxZVXPantothenate kinase2.7.1.330.478
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.476
2g247IGRenin3.4.23.150.474
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.472
2il2LIXRenin3.4.23.150.472
2ea4F79Methionine aminopeptidase 2/0.470
2jh6894Prothrombin3.4.21.50.470
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
3apwDP0Alpha-1-acid glycoprotein 2/0.469
4jtrIBPAldo-keto reductase family 1 member C2/0.469
1cnfFADNitrate reductase [NADH]1.7.1.10.468
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.468
4a87NARMajor pollen allergen Bet v 1-A/0.468
1ypeUIPProthrombin3.4.21.50.467
1zgbA1EAcetylcholinesterase3.1.1.70.467
2g1y5IGRenin3.4.23.150.467
2vrjNCWBeta-glucosidase A3.2.1.210.467
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.467
3ei8PL5LL-diaminopimelate aminotransferase, chloroplastic/0.466
3elePLPAminotransferase/0.466
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.465
3pkdY10Methionine aminopeptidase 2/0.465
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.465
4eb7PLPCysteine desulfurase IscS 2/0.465
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.464
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.464
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.464
4bftZVTPantothenate kinase2.7.1.330.464
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.464
4u140HKMuscarinic acetylcholine receptor M3/0.464
1i7pFADNADH-cytochrome b5 reductase 31.6.2.20.463
1ja0FMNNADPH--cytochrome P450 reductase/0.463
2x1hX1HProstaglandin reductase 310.463
3h3t16HCollagen type IV alpha-3-binding protein/0.463
3juqAJDPhenazine biosynthesis protein A/B/0.463
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
2g1s4IGRenin3.4.23.150.462
2xujTZ5Acetylcholinesterase3.1.1.70.462
3af1GDPPantothenate kinase2.7.1.330.462
3wagTYDGlycosyltransferase/0.462
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
3hdyGDUUDP-galactopyranose mutase/0.461
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.461
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.461
4h9tHL4Phosphotriesterase/0.461
4jtrIZPAldo-keto reductase family 1 member C2/0.461
1ahgTYR_PLPAspartate aminotransferase2.6.1.10.460
1akaPLPAspartate aminotransferase, mitochondrial2.6.1.10.460
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.460
2xugTZ4Acetylcholinesterase3.1.1.70.460
4bfzZVZPantothenate kinase2.7.1.330.460
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.460
2g1r3IGRenin3.4.23.150.459
2xuoTZ4Acetylcholinesterase3.1.1.70.459
2g1n1IGRenin3.4.23.150.458
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.457
1odcA8BAcetylcholinesterase3.1.1.70.457
3af0GDPPantothenate kinase2.7.1.330.457
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.457
1ikiREYD-alanyl-D-alanine carboxypeptidase3.4.16.40.456
1mrqSTRAldo-keto reductase family 1 member C1/0.456
3c3xNAPEugenol synthase 11.1.1.3180.456
3fhxPXLPyridoxal kinase2.7.1.350.456
4bfvZVVPantothenate kinase2.7.1.330.456
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.455
1pq944BOxysterols receptor LXR-beta/0.455
1q83TZ5Acetylcholinesterase3.1.1.70.455
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.455
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.455
4u150HKMuscarinic acetylcholine receptor M3/0.455
1b8oIMHPurine nucleoside phosphorylase2.4.2.10.454
1p0pBCHCholinesterase3.1.1.80.454
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.454
3dhk23UProthrombin3.4.21.50.454
3q9bB3NAcetylpolyamine amidohydrolase/0.454
4loi1YCStimulator of interferon genes protein/0.454
4lzwTHMUridine phosphorylase/0.454
1uvsI11Prothrombin3.4.21.50.453
1vhzAPRADP compounds hydrolase NudE3.6.10.453
2c1zKMPAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.453
2c9bPUG6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.453
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.453
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.453
2ikuLIYRenin3.4.23.150.453
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.453
4a83DXCMajor pollen allergen Bet v 1-A/0.453
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.453
2g1o2IGRenin3.4.23.150.452
3ho2N323-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.452
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.452
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.452
1g63FMNEpidermin decarboxylase4.1.10.451
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.451
3p67FMNPentaerythritol tetranitrate reductase/0.451
4jt91NSNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.451
1o1t2NHProtein farnesyltransferase subunit beta2.5.1.580.450
2gmuPDGPutative pyridoxamine 5-phosphate-dependent dehydrase/0.450
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.450
2xnvVU3Soluble acetylcholine receptor/0.450
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.450
1eveE20Acetylcholinesterase3.1.1.70.449
1icqOPD12-oxophytodienoate reductase 11.3.1.420.449
2w6cBM4Acetylcholinesterase3.1.1.70.449
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.449
4rvfTYDD-mycarose 3-C-methyltransferase/0.449
4to5DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.449
1kqbFMNOxygen-insensitive NAD(P)H nitroreductase/0.448
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.448
3h3qH13Collagen type IV alpha-3-binding protein/0.448
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
3uonQNBMuscarinic acetylcholine receptor M2/0.448
1bil0IURenin3.4.23.150.447
1c5nESIProthrombin3.4.21.50.447
1fkiSB1Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.447
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1yw8A75Methionine aminopeptidase 2/0.447
2a0xDIHPurine nucleoside phosphorylase2.4.2.10.447
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.447
2jl1NAPTriphenylmethane reductase/0.447
2xuhTZ4Acetylcholinesterase3.1.1.70.447
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
3gncQQQGlutaryl-CoA dehydrogenase/0.447
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.447
4na4A1RPoly(ADP-ribose) glycohydrolase3.2.1.1430.447
1jf0CZHObelin/0.446
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.446
2w6zL21Biotin carboxylase6.3.4.140.446
2x92X92Angiotensin-converting enzyme3.4.15.10.446
3pkbY16Methionine aminopeptidase 2/0.446
4ey6GNTAcetylcholinesterase3.1.1.70.446
1gj4132Prothrombin3.4.21.50.445
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
1osvCHCBile acid receptor/0.445
2geuCOKPantothenate kinase2.7.1.330.445
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
2zshGA3Gibberellin receptor GID1A30.445
3g72A6TRenin3.4.23.150.445
3iu9T07Methionine aminopeptidase 2/0.445
4a8v2ANMajor pollen allergen Bet v 1-J/0.445
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.445
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.444
2ckmAA7Acetylcholinesterase3.1.1.70.444
2v58LZJBiotin carboxylase6.3.4.140.444
3e39FMNNitroreductase/0.444
3jq3ADPLombricine kinase/0.444
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4bb3KKAIsopenicillin N synthase1.21.3.10.444
4gv8DUPDUTPase/0.444
4lnbED5CaaX farnesyltransferase beta subunit Ram1/0.444
4xzjNADPutative NAD(+)--arginine ADP-ribosyltransferase Vis2.4.2.310.444
1r5hAO2Methionine aminopeptidase 2/0.443
1touB1VFatty acid-binding protein, adipocyte/0.443
2bjfDXCCholoylglycine hydrolase3.5.1.240.443
2g226IGRenin3.4.23.150.443
3aejAA5Methionine gamma-lyase/0.443
3aosJH2Hemolymph juvenile hormone binding protein/0.443
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
3ftxBESLeukotriene A-4 hydrolase3.3.2.60.443
4b1rITCTetracycline repressor protein class D/0.443
4bfwZVWPantothenate kinase2.7.1.330.443
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.443
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4m9aFDAAcyl-CoA dehydrogenase/0.443
4x7zZM3Mycinamicin III 3''-O-methyltransferase2.1.1.2370.443
4xo7ASDAldo-keto reductase family 1 member C2/0.443
1pqc444Oxysterols receptor LXR-beta/0.442
1w6rGNTAcetylcholinesterase3.1.1.70.442
2g8yNADHydroxycarboxylate dehydrogenase B/0.442
2zc922UProthrombin3.4.21.50.442
3vsxR32Renin3.4.23.150.442
4a86H35Major pollen allergen Bet v 1-A/0.442
4araC56Acetylcholinesterase3.1.1.70.442
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.442
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.442
1icsFMN12-oxophytodienoate reductase 11.3.1.420.441
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.441
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.441
2whqHI6Acetylcholinesterase3.1.1.70.441
2xuiTZ5Acetylcholinesterase3.1.1.70.441
3bbpGTPRas-related protein Rab-6A/0.441
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4kl1PCGPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.441
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.441
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.441
4nqgCZHMitrocomin/0.441
1e66HUXAcetylcholinesterase3.1.1.70.440
1jqdSAHHistamine N-methyltransferase2.1.1.80.440
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.440
2b58COADiamine acetyltransferase 1/0.440
2fxuBIDActin, alpha skeletal muscle/0.440
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.440
3a6qFMNFMN-binding protein/0.440
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.440
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.440
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.440
3fhxPLPPyridoxal kinase2.7.1.350.440
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.440
3vy2FMNFMN-binding protein/0.440
4gddNAIUDP-galactopyranose mutase/0.440
4j7gTRHPCZA361.3/0.440
4jbsP52Endoplasmic reticulum aminopeptidase 23.4.110.440
4jtqFLPAldo-keto reductase family 1 member C2/0.440
4xnw2IDP2Y purinoceptor 1/0.440