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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
3ko3ADPD-tyrosyl-tRNA(Tyr) deacylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3ko3ADPD-tyrosyl-tRNA(Tyr) deacylase/1.000
3ko5ADPD-tyrosyl-tRNA(Tyr) deacylase/0.609
4nbjD3YD-tyrosyl-tRNA(Tyr) deacylase/0.582
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.576
3t0kDCQSulfide-quinone reductase/0.509
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.494
1drfFOLDihydrofolate reductase1.5.1.30.493
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.491
1fvpFMANon-fluorescent flavoprotein/0.487
3lakKR1Gag-Pol polyprotein2.7.7.490.487
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.484
1xngDNDNH(3)-dependent NAD(+) synthetase6.3.1.50.482
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.479
2y035FWBeta-1 adrenergic receptor/0.477
2zevB71Geranylgeranyl pyrophosphate synthase/0.477
3hv3R49Mitogen-activated protein kinase 14/0.476
4qij1HA1,4-dihydroxy-2-naphthoyl-CoA synthase/0.476
3a1l2CCCytochrome P450/0.475
3lfeZ84Mitogen-activated protein kinase 14/0.475
3zkyWT4Isopenicillin N synthase1.21.3.10.475
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.474
3f3y4OABile salt sulfotransferase2.8.2.140.474
4dm6TTBRetinoic acid receptor beta/0.474
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.473
3aosJH2Hemolymph juvenile hormone binding protein/0.473
3njoPYVAbscisic acid receptor PYR1/0.472
5cc9DDFDihydrofolate reductase1.5.1.30.472
4qa0SHHHistone deacetylase 83.5.1.980.471
1kf6HQOFumarate reductase iron-sulfur subunit1.3.5.10.470
1kf6HQOFumarate reductase subunit C/0.470
1kf6HQOFumarate reductase subunit D/0.470
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.470
2y1w849Histone-arginine methyltransferase CARM1/0.470
3d5qT30Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.470
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.470
4hlm16STankyrase-22.4.2.300.470
1re0AFBADP-ribosylation factor 1/0.468
1re0AFBARF guanine-nucleotide exchange factor 1/0.468
1s3uTQDDihydrofolate reductase1.5.1.30.467
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.467
3ghvGHCDihydrofolate reductase1.5.1.30.467
4g95OAGDihydrofolate reductase1.5.1.30.467
4jpg1OXPyruvate kinase PKM2.7.1.400.467
4kw51W6Decaprenylphosphoryl-beta-D-ribose oxidase/0.467
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.466
1u1d181Uridine phosphorylase2.4.2.30.465
2r3xGTXGlutathione S-transferase A12.5.1.180.465
3a26MTAtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.465
3p0fBAUUridine phosphorylase 22.4.2.30.465
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.465
4u140HKMuscarinic acetylcholine receptor M3/0.465
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.464
1yhjR6CPyridoxal kinase2.7.1.350.464
4da6GA2Purine nucleoside phosphorylase DeoD-type2.4.2.10.464
4tkg09LTankyrase-22.4.2.300.464
1xdkREARetinoic acid receptor beta/0.463
3tdaPN0Cytochrome P450 2D6/0.463
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.463
4yfy0FXVioF/0.463
1jf2CZHObelin/0.462
1s9dAFBCytohesin-2/0.462
1s9dAFBADP-ribosylation factor 1/0.462
1uzwCDHIsopenicillin N synthase1.21.3.10.462
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
1frbZSTAldose reductase-related protein 2/0.461
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.461
5irnADPNucleotide binding oligomerization domain containing 2/0.461
3pblETQD(3) dopamine receptor/0.461
2r6kGTXGlutathione S-transferase A12.5.1.180.460
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.460
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.460
1dlrMXADihydrofolate reductase1.5.1.30.459
2qimZEAClass 10 plant pathogenesis-related protein/0.459
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.459
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.459
2iviACWIsopenicillin N synthase1.21.3.10.458
3arvSAUChitinase A/0.458
1gsfEAAGlutathione S-transferase A12.5.1.180.457
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.457
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.457
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.457
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.457
4boeCLRJapanin/0.457
2dhfDZFDihydrofolate reductase1.5.1.30.456
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.456
3zoiM2WIsopenicillin N synthase1.21.3.10.456
4dm8REARetinoic acid receptor beta/0.456
1ry0PG2Aldo-keto reductase family 1 member C3/0.455
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.455
2b5j3ACGag-Pol polyprotein2.7.7.490.455
2oz57XYUncharacterized protein/0.455
2psjCEIRenilla-luciferin 2-monooxygenase1.13.12.50.455
3dlaNXXGlutamine-dependent NAD(+) synthetase6.3.5.10.455
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.455
3wavDWVEctonucleotide pyrophosphatase/phosphodiesterase family member 23.1.4.390.455
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
1ycgFMNNitric oxide reductase10.454
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.454
2ipjFFAAldo-keto reductase family 1 member C2/0.454
3hbfMYCFlavonoid 3-O-glucosyltransferase2.4.10.454
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
4i9z5BAcGMP-specific 3',5'-cyclic phosphodiesterase/0.454
1p33MTXPteridine reductase 11.5.1.330.453
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.453
1x7jGENEstrogen receptor beta/0.453
2y02WHJBeta-1 adrenergic receptor/0.453
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.453
3jq9AX1Pteridine reductase, putative/0.453
3s41S41Glucokinase2.7.1.20.453
3u9y09LTankyrase-22.4.2.300.453
4n1gCEIObelin/0.453
1s0xC3SNuclear receptor ROR-alpha/0.452
1vbiNADMalate/L-lactate dehydrogenase family protein/0.452
2aotSAHHistamine N-methyltransferase2.1.1.80.452
2ycwCAUBeta-1 adrenergic receptor/0.452
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
3u8l09QAcetylcholine-binding protein/0.452
4lsaBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.452
1m9hNAD2,5-diketo-D-gluconic acid reductase A1.1.1.3460.451
1yryMSGPurine nucleoside phosphorylase2.4.2.10.451
2fzjDH3Dihydrofolate reductase1.5.1.30.451
2pd9FIDAldose reductase1.1.1.210.451
2vbpVB1Isopenicillin N synthase1.21.3.10.451
2vcgS17Histone deacetylase-like amidohydrolase3.5.10.451
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.451
4ldeP0GBeta-2 adrenergic receptor/0.451
2rd2QSIGlutamine--tRNA ligase6.1.1.180.450
2uxhQUEHTH-type transcriptional regulator TtgR/0.450
2yhuWHFPteridine reductase/0.450
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.450
4dbw511Aldo-keto reductase family 1 member C3/0.450
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.449
1ygkRRCPyridoxal kinase2.7.1.350.449
2pdlTOLAldose reductase1.1.1.210.449
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
3n39FMNProtein NrdI/0.449
3zc3FADFerredoxin--NADP reductase1.18.1.20.449
4e32DWNMethyltransferase/0.449
5c1mCLRMu-type opioid receptor/0.449
5d1bTSNHistone deacetylase 83.5.1.980.449
1pd9CO4Dihydrofolate reductase1.5.1.30.448
1x7rGENEstrogen receptor/0.448
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2lbdREARetinoic acid receptor gamma/0.448
2wo7ASVIsopenicillin N synthase1.21.3.10.448
3a25SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.448
3bzuA21Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.448
3nu03TUDihydrofolate reductase1.5.1.30.448
4at0FADPossible succinate dehydrogenase/0.448
4fc00T2Serine/threonine-protein kinase B-raf2.7.11.10.448
4mrxCZHObelin/0.448
4qa2SHHHistone deacetylase 83.5.1.980.448
4yaw2AMNADPH--cytochrome P450 reductase/0.448
1bk0ACVIsopenicillin N synthase1.21.3.10.447
1e1nFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.447
2aclREARetinoic acid receptor RXR-alpha/0.447
2aclL05Oxysterols receptor LXR-alpha/0.447
2p1t3TNRetinoic acid receptor RXR-alpha/0.447
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.447
3hggCHDCmeR/0.447
4bcsBTNAvidin-related protein 4/5/0.447
4jlj1NMDeoxycytidine kinase2.7.1.740.447
1fcx184Retinoic acid receptor gamma/0.446
1pq944BOxysterols receptor LXR-beta/0.446
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.446
1upw444Oxysterols receptor LXR-beta/0.446
1vkgCRIHistone deacetylase 83.5.1.980.446
1x7b041Estrogen receptor beta/0.446
2mm3CHOGastrotropin/0.446
2r6jNDPEugenol synthase 11.1.1.3180.446
3up3XCAaceDAF-12/0.446
4i9i1DYTankyrase-12.4.2.300.446
4n1fCZHObelin/0.446
4wx2F6FTryptophan synthase alpha chain/0.446
4wx2F6FTryptophan synthase beta chain4.2.1.200.446
1typNAPTrypanothione reductase1.8.1.120.445
1zzrH4BNitric oxide synthase, brain1.14.13.390.445
2hzqSTRApolipoprotein D/0.445
2vcmM11Isopenicillin N synthase1.21.3.10.445
3casASD3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3d2dRENReticuline oxidase1.21.3.30.445
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.445
3gcq1BUMitogen-activated protein kinase 14/0.445
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.445
3n0hTOPDihydrofolate reductase1.5.1.30.445
3nlqH4BNitric oxide synthase, brain1.14.13.390.445
4dbs0HVAldo-keto reductase family 1 member C3/0.445
4y6gF6FTryptophan synthase alpha chain/0.445
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2clfF6FTryptophan synthase alpha chain/0.444
2vqzMGTPolymerase basic protein 2/0.444
2vxkCOAGlucosamine 6-phosphate acetyltransferase, putative/0.444
4c9wVGH7,8-dihydro-8-oxoguanine triphosphatase3.6.1.550.444
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.444
4ky404JBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.444
1ejbINJ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
1tfz8694-hydroxyphenylpyruvate dioxygenase1.13.11.270.443
2ntjP1HEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
3qm4PN0Cytochrome P450 2D6/0.443
4cdmFO1Deoxyribodipyrimidine photolyase/0.443
4g1nNZTPyruvate kinase PKM2.7.1.400.443
4hyf1AKTankyrase-22.4.2.300.443
4kfo1QSNicotinamide phosphoribosyltransferase2.4.2.120.443
4li61XOTankyrase-12.4.2.300.443
4phlPILPhosphodiesterase/0.443
4yal2AMNADPH--cytochrome P450 reductase/0.443
1dgbNDPCatalase1.11.1.60.442
1hb1OCVIsopenicillin N synthase1.21.3.10.442
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.442
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
2jb4A14Isopenicillin N synthase1.21.3.10.442
2nv6ZIDEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
3fowIMHPurine nucleoside phosphorylase/0.442
3g1mRF3HTH-type transcriptional regulator EthR/0.442
3h4vDVPPteridine reductase 11.5.1.330.442
3uayADNPurine nucleoside phosphorylase DeoD-type/0.442
4at4T6EBDNF/NT-3 growth factors receptor2.7.10.10.442
4d1oH4BNitric oxide synthase, endothelial1.14.13.390.442
4ia05BBcGMP-specific 3',5'-cyclic phosphodiesterase/0.442
4n4v2GYTankyrase-12.4.2.300.442
4omaLCSMethionine gamma-lyase/0.442
4rh10TTSpore photoproduct lyase/0.442
5a4vQUEGlutathione S-transferase F22.5.1.180.442
5jqhCAUBeta-2 adrenergic receptor/0.442
1bx0FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.441
1p8dCO1Oxysterols receptor LXR-beta/0.441
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
2qe2452Polyprotein/0.441
3a783EVVitamin D3 receptor/0.441
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.441
3v94WYQPhosphodiesterase/0.441
4k5p1OSM1 family aminopeptidase3.4.110.441
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.441
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
2pnuENMAndrogen receptor/0.440
2y6fM9FIsopenicillin N synthase1.21.3.10.440
2zitNADExotoxin A2.4.2.360.440
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4f0rMTA5-methylthioadenosine/S-adenosylhomocysteine deaminase/0.440
4i2pG73Gag-Pol polyprotein2.7.7.490.440
4j6bPLOCytochrome P450 monooxygenase/0.440
4j6cSTRCytochrome P450 monooxygenase/0.440
5bt42LOBromodomain-containing protein 4/0.440