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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
1xxjUNCUricase1.7.3.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1xxjUNCUricase1.7.3.31.000
3fhyATPPyridoxal kinase2.7.1.350.498
1jedADPSulfate adenylyltransferase/0.490
1xjqADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.490
4twnB96Ephrin type-A receptor 32.7.10.10.489
2x06NADL-sulfolactate dehydrogenase/0.487
1dgfNDPCatalase1.11.1.60.485
1x1bSAHC-20 methyltransferase/0.483
4bqyFNTEgl nine homolog 1/0.477
1dfoPLGSerine hydroxymethyltransferase2.1.2.10.476
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.476
3v0o4GWHisto-blood group ABO system transferase/0.475
3fktSIIBeta-secretase 13.4.23.460.473
1kqwRTLCellular retinol-binding protein type II/0.472
2zs9ADPPantothenate kinase2.7.1.330.472
4qak2AMRNA 2',3'-cyclic phosphodiesterase/0.472
4dyp0MSNucleoprotein/0.470
1ay0TPPTransketolase 12.2.1.10.469
1x1dSAHC-20 methyltransferase/0.469
2ejzSAHDiphthine synthase/0.469
3af1GDPPantothenate kinase2.7.1.330.469
3tjzGNPADP-ribosylation factor 1/0.469
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.469
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.469
4hmvWUBPhenazine biosynthesis protein PhzG1.40.469
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.468
1qpl587Peptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.468
1x28PGUAspartate aminotransferase2.6.1.10.468
2pamTYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.467
4dvi2IWTankyrase-12.4.2.300.467
2tplHPPTyrosine phenol-lyase4.1.99.20.466
3aw9GDUNAD-dependent epimerase/dehydratase/0.466
1muuGDXGDP-mannose 6-dehydrogenase1.1.1.1320.465
1stdBFSScytalone dehydratase4.2.1.940.465
2r7pANPNon-structural protein 23.6.40.465
2zs8ADPPantothenate kinase2.7.1.330.465
4gd40WSLysine-specific demethylase 4A1.14.110.465
1xmmM7Gm7GpppX diphosphatase3.6.1.590.464
2cekN8TAcetylcholinesterase3.1.1.70.464
2wwjY28Lysine-specific demethylase 4A/0.464
2ffqGSPRas-related protein Rab-6B/0.463
2qs4LY5Glutamate receptor ionotropic, kainate 1/0.463
3qfaFADThioredoxin reductase 1, cytoplasmic1.8.1.90.463
4yp05IQHistidyl-tRNA synthetase, putative/0.463
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.462
1jf0CZHObelin/0.462
1n2gAPCPantothenate synthetase6.3.2.10.462
1s07PLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.462
2eudGCQRibonucleoside-diphosphate reductase large chain 11.17.4.10.462
2h2aDNDProbable nicotinate-nucleotide adenylyltransferase/0.462
3uzzASD3-oxo-5-beta-steroid 4-dehydrogenase/0.462
1u1gBBBUridine phosphorylase2.4.2.30.461
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.461
1h6cNDPGlucose--fructose oxidoreductase1.1.99.280.460
1z48FMNNADPH dehydrogenase/0.460
2e1zB4PPropionate kinase/0.460
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.460
3fr5I4AFatty acid-binding protein, adipocyte/0.460
3zoiM2WIsopenicillin N synthase1.21.3.10.460
4ffrATPUncharacterized protein/0.460
4fhd0TTSpore photoproduct lyase/0.460
1orrCDPCDP-paratose 2-epimerase/0.459
1z0dGDPRas-related protein Rab-5C/0.459
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.459
4rpgGDUUDP-galactopyranose mutase5.4.99.90.459
1gotGDPGuanine nucleotide-binding protein G(t) subunit alpha-1/0.458
1q84TZ4Acetylcholinesterase3.1.1.70.458
1rftPXMPyridoxal kinase2.7.1.350.458
2iu8UD1UDP-3-O-acylglucosamine N-acyltransferase2.3.10.458
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.458
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3h3r14HCollagen type IV alpha-3-binding protein/0.458
3p0fBAUUridine phosphorylase 22.4.2.30.458
4bqzGNPEctonucleoside triphosphate diphosphohydrolase 2/0.458
4itxIN5Cystathionine beta-lyase MetC4.4.1.80.458
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.457
3qe2FMNNADPH--cytochrome P450 reductase/0.457
3w8rACPUridine kinase/0.457
4h9tHL4Phosphotriesterase/0.457
1ci0FMNPyridoxamine 5'-phosphate oxidase1.4.3.50.456
1cnfFADNitrate reductase [NADH]1.7.1.10.456
1argPPDAspartate aminotransferase2.6.1.10.455
2vkvTDCTetracycline repressor protein class D/0.455
3af4GCPPantothenate kinase2.7.1.330.455
3keuATPPyridoxal kinase2.7.1.350.455
3ufgATPGlycine--tRNA ligase alpha subunit/0.455
4dbc3QPAspartate aminotransferase2.6.1.10.455
4e2dFMNDehydrogenase/0.455
4nesUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.455
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.454
3pm1ETHTH-type transcriptional regulator QacR/0.454
4kbyC2EStimulator of interferon genes protein/0.454
4n4v2GYTankyrase-12.4.2.300.454
2ea2F77Methionine aminopeptidase 2/0.453
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.453
4en4ATPPyridoxal kinase2.7.1.350.453
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.453
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.452
1dgbNDPCatalase1.11.1.60.452
2cjfRP43-dehydroquinate dehydratase4.2.1.100.452
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.452
2g1n1IGRenin3.4.23.150.452
3af0GDPPantothenate kinase2.7.1.330.452
3rvhHQ2Lysine-specific demethylase 4A1.14.110.452
4a802ANMajor pollen allergen Bet v 1-A/0.452
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.452
4dptAGSMevalonate diphosphate decarboxylase/0.452
4f6w0SSCyclin-dependent kinase 82.7.11.220.452
4hjfC2EGGDEF family protein/0.452
1i7lATPSynapsin-2/0.451
2hfuMEVMevalonate kinase/0.451
3ekuCY9Actin-5C/0.451
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.451
4dya0MFNucleoprotein/0.451
4jicFMNGTN Reductase/0.451
4q0kGA3Phytohormone-binding protein/0.451
1jdtMTAPurine nucleoside phosphorylase/0.450
2ea4F79Methionine aminopeptidase 2/0.450
2vcxD26Hematopoietic prostaglandin D synthase/0.450
2whqHI6Acetylcholinesterase3.1.1.70.450
3junAJDPhenazine biosynthesis protein A/B/0.450
3ndjJHZMethyltransferase/0.450
4mvcCDCCholine-phosphate cytidylyltransferase A/0.450
1og4NAIT-cell ecto-ADP-ribosyltransferase 2/0.449
1yw8A75Methionine aminopeptidase 2/0.449
3hdyGDUUDP-galactopyranose mutase/0.449
3o153NMThiamine-phosphate synthase/0.449
4aoaIK2Beta-phenylalanine transaminase2.6.10.449
4jc51K5Stimulator of interferon genes protein/0.449
4rx6ATPNitrogen regulatory PII-like protein/0.449
1n2eAPCPantothenate synthetase6.3.2.10.448
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.448
2rqfJH3Hemolymph juvenile hormone binding protein/0.448
3c3xNAPEugenol synthase 11.1.1.3180.448
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.448
1dghNDPCatalase1.11.1.60.447
1icsFMN12-oxophytodienoate reductase 11.3.1.420.447
1je1GMPPurine nucleoside phosphorylase/0.447
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.447
2f3rG5PGuanylate kinase2.7.4.80.447
2zcvNDPQuinone oxidoreductase 21.6.5.20.447
3nt2NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.447
4b3aTACTetracycline repressor protein class D/0.447
4bfzZVZPantothenate kinase2.7.1.330.447
4kp5E1FCarbonic anhydrase 124.2.1.10.447
1kvtUPGUDP-glucose 4-epimerase5.1.3.20.446
2re8GSUGlutamine--tRNA ligase6.1.1.180.446
3e39FMNNitroreductase/0.446
3gwfFADCyclohexanone monooxygenase/0.446
4jtqFLPAldo-keto reductase family 1 member C2/0.446
4uovAZMCarbonate dehydratase/0.446
1hb3SCVIsopenicillin N synthase1.21.3.10.445
1mfzGDXGDP-mannose 6-dehydrogenase1.1.1.1320.445
1u1iNADMyo-inositol-1-phosphate synthase (Ino1)/0.445
2cftPLPPyridoxal phosphate phosphatase/0.445
2hp2KE4Glutamate-1-semialdehyde 2,1-aminomutase5.4.3.80.445
2xrlDXTTetracycline repressor protein class D/0.445
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.445
4fkzUD1UDP-N-acetylglucosamine 2-epimerase5.1.3.140.445
4l0oPLPCystathionine gamma-synthase2.5.1.480.445
4psbGA3Cytokinin-specific binding protein/0.445
4xzjNADPutative NAD(+)--arginine ADP-ribosyltransferase Vis2.4.2.310.445
4ycoFMNtRNA-dihydrouridine(16) synthase/0.445
4xnw2IDP2Y purinoceptor 1/0.445
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.444
1njjORXOrnithine decarboxylase/0.444
1qtqQSIGlutamine--tRNA ligase6.1.1.180.444
1szgFNSCytochrome b2, mitochondrial1.1.2.30.444
2iko7IGRenin3.4.23.150.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2oapANPType II secretion system protein (GspE-2)/0.444
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
2v58LZJBiotin carboxylase6.3.4.140.444
3gvhNADMalate dehydrogenase/0.444
3zgz84TLeucine--tRNA ligase/0.444
5c3aURMHisto-blood group ABO system transferase/0.444
1ex75GPGuanylate kinase2.7.4.80.443
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.443
1mv8GDXGDP-mannose 6-dehydrogenase1.1.1.1320.443
1o01NADAldehyde dehydrogenase, mitochondrial1.2.1.30.443
1wxyFRKAdenosine deaminase3.5.4.40.443
1yqzCOACoenzyme A disulfide reductase/0.443
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.443
2stdCRPScytalone dehydratase4.2.1.940.443
4bfvZVVPantothenate kinase2.7.1.330.443
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.443
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.443
4lutDCSAlanine racemase/0.443
4zgsNADPutative D-lactate dehydrogenase/0.443
1obnASVIsopenicillin N synthase1.21.3.10.442
2g78REACellular retinoic acid-binding protein 2/0.442
2q3rFMN12-oxophytodienoate reductase 11.3.1.420.442
3phiNDPShikimate dehydrogenase (NADP(+))/0.442
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.442
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.442
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.442
4pzsACOHistone acetyltransferase p300/0.442
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.442
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
1el4CTZObelin/0.441
1f20NAPNitric oxide synthase, brain1.14.13.390.441
1lnmDTXBilin-binding protein/0.441
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.441
1qv0CZHObelin/0.441
1s4pGDPGlycolipid 2-alpha-mannosyltransferase/0.441
2vaxCSCAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.441
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
3b6pTMPThree-prime repair exonuclease 13.1.11.20.441
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.441
5l3rGCPCell division protein FtsY homolog, chloroplastic/0.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
1dx6GNTAcetylcholinesterase3.1.1.70.440
1gpnHUBAcetylcholinesterase3.1.1.70.440
1r58AO5Methionine aminopeptidase 2/0.440
2bf4FMNNADPH--cytochrome P450 reductase/0.440
2vczVC3Hematopoietic prostaglandin D synthase/0.440
2yxuATPPyridoxal kinase2.7.1.350.440
2z4sADPChromosomal replication initiator protein DnaA/0.440
3dzkNMNADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.440
3opxU5PSuppressor of disruption of TFIIS/0.440
3sfh1DIHistone deacetylase 83.5.1.980.440
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.440
4dyb0MHNucleoprotein/0.440
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.440
5fkoTDCTetracycline repressor protein class D/0.440