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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
4jbxSK7Thymidine kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4jbxSK7Thymidine kinase/1.000
1e2jTHMThymidine kinase/0.611
1e2nRCAThymidine kinase/0.604
4ivrN50Thymidine kinase/0.584
4ivqI43Thymidine kinase/0.579
1e2lTMCThymidine kinase/0.559
1p72THMThymidine kinase/0.518
2acwUPGGlycosyltransferase/0.506
3fr4F8AFatty acid-binding protein, adipocyte/0.502
1ay0TPPTransketolase 12.2.1.10.501
2zf051UProthrombin3.4.21.50.493
4bamMM9Prothrombin3.4.21.50.491
4jq2SUZAldo-keto reductase family 1 member C2/0.491
2r59PH0Leukotriene A-4 hydrolase3.3.2.60.485
2xf3J01Uncharacterized protein/0.481
2vqsBVDDeoxynucleoside kinase/0.479
4nv0MG77-methylguanosine phosphate-specific 5'-nucleotidase/0.477
3vri1KXHLA class I histocompatibility antigen, B-57 alpha chain/0.476
3emlZMAAdenosine receptor A2a/0.476
2bxqIMNSerum albumin/0.475
2jj8AZZDeoxynucleoside kinase/0.475
1tojHCIAspartate aminotransferase2.6.1.10.474
2ab8MTPAdenosine kinase2.7.1.200.474
1e2kTMCThymidine kinase/0.473
1rftPXMPyridoxal kinase2.7.1.350.473
2r8pT6FTransketolase 1/0.472
3ldoANP78 kDa glucose-regulated protein/0.472
4emdC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.472
4yao2AMNADPH--cytochrome P450 reductase/0.472
1clqGDPDNA-directed DNA polymerase/0.471
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.471
2pamTYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.470
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.470
4g090VDHistidinol dehydrogenase/0.470
2r8oT5XTransketolase 1/0.469
2c97JCL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.468
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
3hcrCHDFerrochelatase, mitochondrial4.99.1.10.467
3ogkOGKCoronatine-insensitive protein 1/0.467
4bfvZVVPantothenate kinase2.7.1.330.466
4ixd1HVIntegrin alpha-L/0.466
5epeSAHUncharacterized protein/0.466
3lq2TDPPyruvate dehydrogenase E1 component1.2.4.10.465
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.464
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
2y882ERPhosphoribosyl isomerase A5.3.1.160.464
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.464
1touB1VFatty acid-binding protein, adipocyte/0.463
3tm5SFGUncharacterized protein/0.463
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.463
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.463
4m9aFDAAcyl-CoA dehydrogenase/0.463
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.462
2zhe13UProthrombin3.4.21.50.462
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.462
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.462
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.462
4f700STCyclin-dependent kinase 82.7.11.220.462
4gncASORegucalcin3.1.1.170.462
4j3mAJ8Tankyrase-22.4.2.300.462
4jln18VDeoxycytidine kinase2.7.1.740.462
1ih7GMPDNA-directed DNA polymerase/0.461
1u1f183Uridine phosphorylase2.4.2.30.461
1i5cADPChemotaxis protein CheA2.7.13.30.460
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.460
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.459
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.459
1xxjUNCUricase1.7.3.30.459
1zgaHMKIsoflavone 4'-O-methyltransferase/0.459
2v2qNVG4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.459
3dcsMZMCarbonic anhydrase 24.2.1.10.459
3rdqDTBStreptavidin/0.459
3tydXHPDihydropteroate synthase/0.459
4bfuZVUPantothenate kinase2.7.1.330.459
1txtCAAHMG-CoA synthase/0.458
1xmmM7Gm7GpppX diphosphatase3.6.1.590.458
3juqAKDPhenazine biosynthesis protein A/B/0.458
3qh23NMThiazole tautomerase/0.458
4bqyFNTEgl nine homolog 1/0.458
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.457
2x06NADL-sulfolactate dehydrogenase/0.457
3akm11DFatty acid-binding protein, intestinal/0.457
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.456
1qinGIPLactoylglutathione lyase4.4.1.50.456
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.456
2wp5FADTrypanothione reductase/0.456
2xlrFADPutative flavin-containing monooxygenase/0.456
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.456
3vtdTKDVitamin D3 receptor/0.456
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.456
5k2dZMAAdenosine receptor A2a/0.456
2ptfFMNUncharacterized protein MTH_863/0.455
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3r1rATPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.455
4uy6SAHHistidine N-alpha-methyltransferase/0.455
5d3fFSC14-3-3 protein zeta/delta/0.455
5k2bZMAAdenosine receptor A2a/0.455
1kyzFERCaffeic acid 3-O-methyltransferase2.1.1.680.454
1mdrAPGMandelate racemase/0.454
1vkgCRIHistone deacetylase 83.5.1.980.454
1vrqFMNSubunit alpha of sarocosine oxidase/0.454
1vrqFMNSubunit beta of sarcosine oxidase/0.454
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2o12FMNChorismate synthase/0.454
4egbNADdTDP-glucose 4,6-dehydratase/0.454
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.454
2v8pCDP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.453
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
3nxyD2HDihydrofolate reductase1.5.1.30.453
4ju41O3Genome polyprotein2.7.7.480.453
5cnsDATRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.453
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.452
1stdBFSScytalone dehydratase4.2.1.940.452
1uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
1zg32HIIsoflavone 4'-O-methyltransferase/0.452
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.452
2y67N21UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.452
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.452
4l1xSTRAldo-keto reductase family 1 member C2/0.452
1hlk113Metallo-beta-lactamase type 2/0.451
1lcwSHMStreptavidin/0.451
2j3qTFLAcetylcholinesterase3.1.1.70.451
2zgx29UProthrombin3.4.21.50.451
3mytEQUSteroid Delta-isomerase5.3.3.10.451
3wyqBTNStreptavidin/0.451
4yau2AMNADPH--cytochrome P450 reductase/0.451
1orrCDPCDP-paratose 2-epimerase/0.450
1rd4L08Integrin alpha-L/0.450
2c9dPHR6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.450
3cavCI23-oxo-5-beta-steroid 4-dehydrogenase/0.450
3eq02TSProthrombin3.4.21.50.450
3hkuTORCarbonic anhydrase 24.2.1.10.450
3nxrD2DDihydrofolate reductase1.5.1.30.450
3wtkTH4Acetylcholine-binding protein/0.450
4bfwZVWPantothenate kinase2.7.1.330.450
4jlm1NNDeoxycytidine kinase2.7.1.740.450
4p9dTMPDeoxycytidylate deaminase/0.450
4pnrG18Tankyrase-22.4.2.300.450
5fd8A5APutative carboxypeptidase yocD/0.450
1cqp803Integrin alpha-L/0.449
1gpeFADGlucose oxidase1.1.3.40.449
1pkfEPDEpothilone C/D epoxidase1.140.449
1pq944BOxysterols receptor LXR-beta/0.449
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.449
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
4bfyZVYPantothenate kinase2.7.1.330.449
4k39SAMAnaerobic sulfatase-maturating enzyme1.8.980.449
4l5b1UXDeoxycytidine kinase2.7.1.740.449
4xz3COAAcyl-CoA synthetase (NDP forming)/0.449
5c1mCLRMu-type opioid receptor/0.449
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.449
5stdUNNScytalone dehydratase4.2.1.940.449
1d6w00RProthrombin3.4.21.50.448
1suiFRECaffeoyl-CoA O-methyltransferase2.1.1.1040.448
1uofPNNDeacetoxycephalosporin C synthase1.14.20.10.448
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3i6rJ5ZDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.448
3o9pMHIPeriplasmic murein peptide-binding protein/0.448
4hlg20BTankyrase-22.4.2.300.448
4zwpM44Xaa-Pro dipeptidase3.4.13.90.448
3d4sTIMBeta-2 adrenergic receptor/0.448
2ea4F79Methionine aminopeptidase 2/0.447
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
2pakTYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.447
2zgb21UProthrombin3.4.21.50.447
3mflDHYProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.447
3mflDHYProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.447
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.447
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.447
3zncBZ1Carbonic anhydrase 44.2.1.10.447
4dxlC5P4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.447
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.447
5k2aZMAAdenosine receptor A2a/0.447
1nc1MTH5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase3.2.2.90.446
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
1sreHABStreptavidin/0.446
1wnz2VAIsoleucine--tRNA ligase6.1.1.50.446
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.446
2hveADPNucleoside diphosphate kinase A2.7.4.60.446
2nnqT4BFatty acid-binding protein, adipocyte/0.446
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.446
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.446
3to3ATPPetrobactin biosynthesis protein AsbB/0.446
4bqwQNMEgl nine homolog 1/0.446
4hkiFLNTankyrase-22.4.2.300.446
4mzuTYDWxcM-like protein/0.446
4ntcFADThioredoxin reductase gliT/0.446
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.446
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
1mewXMPInosine-5'-monophosphate dehydrogenase/0.445
2g226IGRenin3.4.23.150.445
2izhBTNStreptavidin/0.445
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3qeoLLTDeoxycytidine kinase2.7.1.740.445
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.445
5jtbZMAAdenosine receptor A2a/0.445
1g8oU5PN-acetyllactosaminide alpha-1,3-galactosyltransferase/0.444
1kt3RTLRetinol-binding protein 4/0.444
1so2666cGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.444
1xh6R94cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.444
4eiyZMAAdenosine receptor A2a/0.444
4hy6FJ1Heat shock protein HSP 90-alpha/0.444
4qa2SHHHistone deacetylase 83.5.1.980.444
5fm7ADPRuvB-like helicase/0.444
1njjORXOrnithine decarboxylase/0.443
1pr0NOSPurine nucleoside phosphorylase DeoD-type/0.443
1qiqACCIsopenicillin N synthase1.21.3.10.443
2c92TP66,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
2v34CTN4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.443
3cr0809Wee1-like protein kinase2.7.10.20.443
3epsATPIsocitrate dehydrogenase kinase/phosphatase/0.443
3ix8TX3Transcriptional activator protein LasR/0.443
3juhANPCasein kinase II subunit alpha2.7.11.10.443
3zm62GNUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.443
4bz8J38Histone deacetylase/0.443
4dmgSAMUncharacterized protein/0.443
4l9q9TPSerum albumin/0.443
4lgaA2OAbscisic acid receptor PYL2/0.443
4zu44TGWxcM-like protein/0.443
5dv2C5PCCR4-NOT transcription complex subunit 6-like3.1.13.40.443
4ug2NGIAdenosine receptor A2a/0.443
1l8qADPChromosomal replication initiator protein DnaA/0.442
1mc0PCGcGMP-dependent 3',5'-cyclic phosphodiesterase/0.442
1nbiSAMGlycine N-methyltransferase2.1.1.200.442
1wxjIPLTryptophan synthase alpha chain/0.442
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
1zgv501Prothrombin3.4.21.50.442
2dvlFADAcyl-CoA dehydrogenase/0.442
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.442
2qc8ADPGlutamine synthetase6.3.1.20.442
2rgxAP5Adenylate kinase/0.442
2xvv9DNSerum albumin/0.442
3b9lAZZSerum albumin/0.442
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4b68NAPL-ornithine N(5)-monooxygenase/0.442
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4ffrATPUncharacterized protein/0.442
4jhz1KVBeta-glucuronidase3.2.1.310.442
4kq1U5PGlycogen [starch] synthase/0.442
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.442
1kceCB3Thymidylate synthase/0.441
1r58AO5Methionine aminopeptidase 2/0.441
1rfuPLPPyridoxal kinase2.7.1.350.441
2a9y26AAdenosine kinase2.7.1.200.441
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.441
2vq7FADPutative flavin-containing monooxygenase/0.441
2xegCI9Glutamate carboxypeptidase 23.4.17.210.441
2zhw12UProthrombin3.4.21.50.441
3fr5I4AFatty acid-binding protein, adipocyte/0.441
3h3qH13Collagen type IV alpha-3-binding protein/0.441
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.441
3nxoD2BDihydrofolate reductase1.5.1.30.441
4dbc3QPAspartate aminotransferase2.6.1.10.441
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.441
4jzr4JREgl nine homolog 1/0.441
4mryCEIObelin/0.441
3p0gP0GBeta-2 adrenergic receptor/0.441
1cjtFOKAdenylate cyclase type 2/0.440
1cjtFOKAdenylate cyclase type 5/0.440
1i5bANPChemotaxis protein CheA2.7.13.30.440
1ivrCBAAspartate aminotransferase, mitochondrial2.6.1.10.440
1ngsTPPTransketolase 12.2.1.10.440
1pl6572Sorbitol dehydrogenase1.1.1.140.440
1q63AIQQueuine tRNA-ribosyltransferase2.4.2.290.440
1qy2IPZMajor urinary protein 1/0.440
1rzuADPGlycogen synthase 12.4.1.210.440
2f2sCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.440
2g72F21Phenylethanolamine N-methyltransferase2.1.1.280.440
2qimZEAClass 10 plant pathogenesis-related protein/0.440
2v59LZKBiotin carboxylase6.3.4.140.440
2v95HCYCorticosteroid-binding globulin/0.440
2zdv37UProthrombin3.4.21.50.440
3aezGDPPantothenate kinase2.7.1.330.440
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.440
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.440
4b64NAPL-ornithine N(5)-monooxygenase/0.440
4bahMELProthrombin3.4.21.50.440
4dlcUMPDeoxyuridine triphosphatase, putative/0.440
4fwjFADLysine-specific histone demethylase 1B10.440
4p5fAR6Inosine-uridine nucleoside N-ribohydrolase/0.440
4xmxBESAminopeptidase N3.4.11.20.440