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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
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.98

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.981.000
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.520
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.506
1kyyINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.499
1x8lOXRRetinol dehydratase/0.498
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.490
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.488
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.485
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.484
3arvSAUChitinase A/0.483
1fmlRTLRetinol dehydratase/0.482
2getCOKPantothenate kinase2.7.1.330.482
2w3mFOLDihydrofolate reductase1.5.1.30.481
2zsdCOAPantothenate kinase2.7.1.330.481
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.481
4uugPXGBranched-chain amino acid aminotransferase, putative/0.480
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.478
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.478
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.477
3nmpPYVAbscisic acid receptor PYL2/0.477
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.475
4a312CBGlycylpeptide N-tetradecanoyltransferase/0.475
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.475
4rvfTYDD-mycarose 3-C-methyltransferase/0.475
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.474
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.474
2g1a5HGClass B acid phosphatase3.1.3.20.474
3fhxPLPPyridoxal kinase2.7.1.350.473
4bftZVTPantothenate kinase2.7.1.330.473
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.471
1nsgRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.470
1nsgRADSerine/threonine-protein kinase mTOR2.7.11.10.470
1ygjRMCPyridoxal kinase2.7.1.350.470
2xysSY9Soluble acetylcholine receptor/0.470
2geuCOKPantothenate kinase2.7.1.330.469
4dbs0HVAldo-keto reductase family 1 member C3/0.469
3c1kT15Prothrombin3.4.21.50.468
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.468
4c2z646Glycylpeptide N-tetradecanoyltransferase 1/0.467
4q0kGA3Phytohormone-binding protein/0.466
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.466
2po3T4K4-dehydrase/0.465
2xviFADPutative flavin-containing monooxygenase/0.465
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.465
1pqc444Oxysterols receptor LXR-beta/0.464
2gesCOKPantothenate kinase2.7.1.330.464
2pncCLUPrimary amine oxidase, liver isozyme/0.464
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.464
1tcoFK5Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.463
1tcoFK5Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform3.1.3.160.463
3gwfFADCyclohexanone monooxygenase/0.463
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.462
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.462
2vqbNAPPutative flavin-containing monooxygenase/0.461
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.461
3wagTYDGlycosyltransferase/0.461
4bfxZVXPantothenate kinase2.7.1.330.461
4e2yJHZMethyltransferase/0.461
4bb3KKAIsopenicillin N synthase1.21.3.10.460
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.460
1ex75GPGuanylate kinase2.7.4.80.459
1qiqACCIsopenicillin N synthase1.21.3.10.459
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
3arpDEQChitinase A/0.459
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.459
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.458
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.458
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.458
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.458
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.458
3uzxAOM3-oxo-5-beta-steroid 4-dehydrogenase/0.458
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.458
4fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.458
4fapARDSerine/threonine-protein kinase mTOR2.7.11.10.458
5fd8A5APutative carboxypeptidase yocD/0.457
1b9iPXG3-amino-5-hydroxybenzoate synthase4.2.1.1440.456
2wo7ASVIsopenicillin N synthase1.21.3.10.456
3h3sH15Collagen type IV alpha-3-binding protein/0.456
3qe2FMNNADPH--cytochrome P450 reductase/0.456
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.456
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.456
4usrFADMonooxygenase/0.456
1lnmDTXBilin-binding protein/0.455
1t4cCOAFormyl-CoA:oxalate CoA-transferase/0.455
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.455
3biz61EWee1-like protein kinase2.7.10.20.455
2g8yNADHydroxycarboxylate dehydrogenase B/0.454
3cr0809Wee1-like protein kinase2.7.10.20.454
4b68FADL-ornithine N(5)-monooxygenase/0.454
1vf3GDNGlutathione S-transferase 32.5.1.180.453
2ym1NAPPhenylacetone monooxygenase1.14.13.920.453
3pm1ETHTH-type transcriptional regulator QacR/0.453
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.452
1obnASVIsopenicillin N synthase1.21.3.10.452
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.452
4bfwZVWPantothenate kinase2.7.1.330.452
4bubADPUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase/0.452
1fw0KAIGlutamate receptor 2/0.451
1qtiGNTAcetylcholinesterase3.1.1.70.451
1ry8RUTAldo-keto reductase family 1 member C3/0.451
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.451
3fr5I4AFatty acid-binding protein, adipocyte/0.451
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.451
4r81FMNPredicted NADH dehydrogenase/0.451
1mrqSTRAldo-keto reductase family 1 member C1/0.450
1ycfFMNNitric oxide reductase10.450
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.450
2vkeTACTetracycline repressor protein class D/0.450
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.450
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.450
3v2uATPProtein GAL3/0.450
4cdmFO1Deoxyribodipyrimidine photolyase/0.450
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.449
3c1oNAPEugenol synthase/0.449
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.449
3ufl508Beta-secretase 13.4.23.460.449
3zkuHCVIsopenicillin N synthase1.21.3.10.449
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.449
4rvgTYDD-mycarose 3-C-methyltransferase/0.449
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.448
1ygkRRCPyridoxal kinase2.7.1.350.448
2xlpNAPPutative flavin-containing monooxygenase/0.448
2zevIPEGeranylgeranyl pyrophosphate synthase/0.448
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.448
3v0o4GWHisto-blood group ABO system transferase/0.448
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.448
1lc3NADBiliverdin reductase A1.3.1.240.447
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
1pd9CO4Dihydrofolate reductase1.5.1.30.447
1x8b824Wee1-like protein kinase2.7.10.20.447
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.447
2lbaCHOFatty acid binding protein 6/0.447
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.447
2wu4HBPAcetylcholinesterase3.1.1.70.447
2xytTC9Soluble acetylcholine receptor/0.447
3rufNADUDP-N-acetylglucosamine 4-epimerase/0.447
4q71FADBifunctional protein PutA/0.447
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
2c20NADUDP-glucose 4-epimerase/0.446
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.446
3nnz59WNitric oxide synthase, brain1.14.13.390.446
3s5wFADL-ornithine N(5)-monooxygenase/0.446
3zkyWT4Isopenicillin N synthase1.21.3.10.446
4xxvNAD3-isopropylmalate dehydrogenase/0.446
1oc1ASVIsopenicillin N synthase1.21.3.10.445
1r2jFADFkbI/0.445
1w76GNTAcetylcholinesterase3.1.1.70.445
2cekN8TAcetylcholinesterase3.1.1.70.445
2gevCOKPantothenate kinase2.7.1.330.445
2v5uFMNFlavodoxin/0.445
3q9bB3NAcetylpolyamine amidohydrolase/0.445
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.445
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.445
4jq3ZOMAldo-keto reductase family 1 member C2/0.445
5esdTDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.445
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.444
1yplRA8Prothrombin3.4.21.50.444
2vcmM11Isopenicillin N synthase1.21.3.10.444
3h0bB35Beta-secretase 13.4.23.460.444
3h3r14HCollagen type IV alpha-3-binding protein/0.444
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.444
3sfy3FYUncharacterized protein/0.444
4a86H35Major pollen allergen Bet v 1-A/0.444
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.444
4gki0JNAminoglycoside 3'-phosphotransferase AphA1-IAB/0.444
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1esmCOAPantothenate kinase2.7.1.330.443
1icqOPD12-oxophytodienoate reductase 11.3.1.420.443
1nm6L86Prothrombin3.4.21.50.443
2ptfFMNUncharacterized protein MTH_863/0.443
2xveFADPutative flavin-containing monooxygenase/0.443
4tvj09LPoly [ADP-ribose] polymerase 22.4.2.300.443
2zs9ADPPantothenate kinase2.7.1.330.442
3ndjJHZMethyltransferase/0.442
1cf3FADGlucose oxidase1.1.3.40.441
1krrACOGalactoside O-acetyltransferase2.3.1.180.441
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.441
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.441
2vt4P32Beta-1 adrenergic receptor/0.441
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.441
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.441
4bfsZVSPantothenate kinase2.7.1.330.441
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.441
1yhjR6CPyridoxal kinase2.7.1.350.440
2in6839Wee1-like protein kinase2.7.10.20.440
3dv0TPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.440
3dv0TPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.440
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3q7fED2Uncharacterized protein/0.440
3rtnRTNBeta-secretase 13.4.23.460.440
3v0p4GWHisto-blood group ABO system transferase/0.440
3zc3FADFerredoxin--NADP reductase1.18.1.20.440
4c49HCYCorticosteroid-binding globulin/0.440
4qg1DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4rn615UProthrombin3.4.21.50.440
4rxsTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.440