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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
5ioqDURFlavin-dependent thymidylate synthase2.1.1.148

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
5ioqDURFlavin-dependent thymidylate synthase2.1.1.1481.000
5iotUMPFlavin-dependent thymidylate synthase2.1.1.1480.512
2oapANPType II secretion system protein (GspE-2)/0.490
4qms1N1Serine/threonine-protein kinase 242.7.11.10.490
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.489
2itwITQEpidermal growth factor receptor2.7.10.10.486
1i59ADPChemotaxis protein CheA2.7.13.30.483
2zazGK1Mitogen-activated protein kinase 14/0.483
2qo9ANPEphrin type-A receptor 32.7.10.10.482
3vjoANPEpidermal growth factor receptor2.7.10.10.481
3kc02T5Fructose-1,6-bisphosphatase 13.1.3.110.479
2y6o1N1Ephrin type-A receptor 42.7.10.10.476
1cf2NAPGlyceraldehyde-3-phosphate dehydrogenase/0.475
1cqp803Integrin alpha-L/0.474
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.474
2ituITQEpidermal growth factor receptor2.7.10.10.474
2rlcCHDCholoylglycine hydrolase3.5.1.240.474
2zybKSLTyrosine-protein kinase Lck2.7.10.20.474
2vwx7X4Ephrin type-B receptor 42.7.10.10.473
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.473
3ac5KZMTyrosine-protein kinase Lck2.7.10.20.473
1m17AQ4Epidermal growth factor receptor2.7.10.10.472
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.470
2zm4KSMTyrosine-protein kinase Lck2.7.10.20.470
3apwDP0Alpha-1-acid glycoprotein 2/0.470
4hjoAQ4Epidermal growth factor receptor2.7.10.10.470
1il0NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.469
2z4sADPChromosomal replication initiator protein DnaA/0.469
2zm1KSFTyrosine-protein kinase Lck2.7.10.20.469
2pe15173-phosphoinositide-dependent protein kinase 12.7.11.10.468
4eqcXR1Serine/threonine-protein kinase PAK 12.7.11.10.468
4i231C9Epidermal growth factor receptor2.7.10.10.468
2ohvNHLGlutamate racemase/0.467
4mxoDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.467
2itvANPEpidermal growth factor receptor2.7.10.10.466
3p82FMNPentaerythritol tetranitrate reductase/0.466
3p0jTYEPutative tyrosyl-tRNA synthetase/0.465
4ie0PD2Alpha-ketoglutarate-dependent dioxygenase FTO/0.465
1xnjADPBifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 12.7.1.250.464
1z5aADPType 2 DNA topoisomerase 6 subunit B/0.464
3s1dZIRCytokinin dehydrogenase 11.5.99.120.464
1di9MSQMitogen-activated protein kinase 14/0.463
2nnqT4BFatty acid-binding protein, adipocyte/0.463
2q46NAPUncharacterized protein At5g02240/0.463
3h06VBPGlutamate receptor 2/0.463
3op5REBSerine/threonine-protein kinase VRK12.7.11.10.463
4dieC5PCytidylate kinase/0.463
4tmcFMNOld yellow enzyme/0.463
1p9wANPType II secretion system protein E/0.462
2itxANPEpidermal growth factor receptor2.7.10.10.462
3mvm39PMitogen-activated protein kinase 14/0.462
3q5dGDPAtlastin-13.6.50.462
4fkg4CKCyclin-dependent kinase 22.7.11.220.462
2itqITQEpidermal growth factor receptor2.7.10.10.461
2vwqNAPGlucose 1-dehydrogenase/0.461
4hiaFMNLOV protein/0.461
1fpqSAMIsoliquiritigenin 2'-O-methyltransferase/0.460
1m75CAAHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.460
2of4979Tyrosine-protein kinase Lck2.7.10.20.460
2olrATPPhosphoenolpyruvate carboxykinase (ATP)/0.460
2qg4NADUDP-glucose 6-dehydrogenase1.1.1.220.460
2v51LABActin, alpha skeletal muscle/0.460
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.460
3kjiADPCO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC/0.460
4dpuAGSMevalonate diphosphate decarboxylase/0.460
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.460
1nzfUPGDNA beta-glucosyltransferase/0.459
1szmBI4cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.459
2rghFADAlpha-Glycerophosphate Oxidase/0.459
2zva1N1Tyrosine-protein kinase Lyn2.7.10.20.459
4dan2FAPurine nucleoside phosphorylase DeoD-type2.4.2.10.459
4jrvKJVEpidermal growth factor receptor2.7.10.10.459
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.458
1vi2NADQuinate/shikimate dehydrogenase/0.458
2nr4FMNConserved protein/0.458
2tpsTPSThiamine-phosphate synthase/0.458
3ac2KSETyrosine-protein kinase Lck2.7.10.20.458
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3gbuATPUncharacterized sugar kinase PH14592.7.10.458
3t50FMNBlue-light-activated histidine kinase2.7.13.30.458
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.458
1g9cBABBotulinum neurotoxin type B3.4.24.690.457
1rfuADPPyridoxal kinase2.7.1.350.457
3kr4BESM17 leucyl aminopeptidase/0.457
4c02TAKActivin receptor type-12.7.11.300.457
4z875GPInosine-5'-monophosphate dehydrogenase/0.457
1eioGCHGastrotropin/0.456
1lhwESMSex hormone-binding globulin/0.456
1wkhPPE[LysW]-aminoadipate semialdehyde transaminase/0.456
2gr0FADFerredoxin reductase/0.456
2zbaZBATrichothecene 3-O-acetyltransferase/0.456
3cgcCOACoenzyme A disulfide reductase/0.456
3ns2PYVAbscisic acid receptor PYL2/0.456
4jloADPAdenylate kinase/0.456
4tv3ML9Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.456
1x2hLPALipoate-protein ligase A6.3.1.200.455
3kr5BEYM17 leucyl aminopeptidase/0.455
3pcfFHBProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.455
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
2ds11CDCyclin-dependent kinase 22.7.11.220.454
2f3rG5PGuanylate kinase2.7.4.80.454
2j9gADPBiotin carboxylase6.3.4.140.454
2rkiTT1Gag-Pol polyprotein2.7.7.490.454
2ylrNAPPhenylacetone monooxygenase1.14.13.920.454
3qs817DAnthranilate phosphoribosyltransferase/0.454
4m11MXMProstaglandin G/H synthase 21.14.99.10.454
1vyrFMNPentaerythritol tetranitrate reductase/0.453
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.453
2py7ATPPhosphoenolpyruvate carboxykinase (ATP)/0.453
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.453
2ym5YM5Serine/threonine-protein kinase Chk12.7.11.10.453
3a14NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.453
3p62FMNPentaerythritol tetranitrate reductase/0.453
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.453
4eftEFTHeat shock protein HSP 90-alpha/0.453
1gii1PUCyclin-dependent kinase 22.7.11.220.452
1h6vNDPThioredoxin reductase 1, cytoplasmic1.8.1.90.452
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.452
3b2eADPATPase GET3/0.452
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.452
3mpt1GKMitogen-activated protein kinase 14/0.452
4dpy2P0Mevalonate diphosphate decarboxylase/0.452
4fxy0W2Neurolysin, mitochondrial3.4.24.160.452
4kiq1RAMitogen-activated protein kinase 14/0.452
4y9qC2EUncharacterized protein/0.452
4z17PEPEnolase/0.452
5kgpACOPredicted acetyltransferase/0.452
1f3pNADFerredoxin reductase/0.451
1fp6ADPNitrogenase iron protein 11.18.6.10.451
2dbzNAPGlyoxylate reductase1.1.1.260.451
2of2547Tyrosine-protein kinase Lck2.7.10.20.451
3ormAGSSerine/threonine protein kinase/0.451
4ct1ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.451
4g95OAGDihydrofolate reductase1.5.1.30.451
1i58ADPChemotaxis protein CheA2.7.13.30.450
1i5cADPChemotaxis protein CheA2.7.13.30.450
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.450
2cy0NAPShikimate dehydrogenase (NADP(+))/0.450
2xf3J01Uncharacterized protein/0.450
3otwCOAPhosphopantetheine adenylyltransferase/0.450
3r1rATPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.450
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.450
4c3f7KWTyrosine-protein kinase Lck2.7.10.20.450
4dreNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
4m55NADUDP-glucuronic acid decarboxylase 14.1.1.350.450
4qmxH8HSerine/threonine-protein kinase 242.7.11.10.450
4rqvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.450
4uyf73BBromodomain-containing protein 2/0.450
4xx9ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.450
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.449
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
1tqf32PBeta-secretase 13.4.23.460.449
2vcmM11Isopenicillin N synthase1.21.3.10.449
2ww4ADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.449
3cgdFADCoenzyme A disulfide reductase/0.449
3fr5I4AFatty acid-binding protein, adipocyte/0.449
4ejmNAPPutative zinc-binding dehydrogenase/0.449
4jq7KJQEpidermal growth factor receptor2.7.10.10.449
4k5sPM0Oxygenase/0.449
4l425FIRibosomal protein S6 kinase beta-12.7.11.10.449
1bwlFMNNADPH dehydrogenase 11.6.99.10.448
1t2cNAIL-lactate dehydrogenase1.1.1.270.448
2balPQAMitogen-activated protein kinase 14/0.448
2bdjHETProto-oncogene tyrosine-protein kinase Src2.7.10.20.448
2itpAEEEpidermal growth factor receptor2.7.10.10.448
2rhrEMOPutative ketoacyl reductase1.3.10.448
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.448
3ac3KSHTyrosine-protein kinase Lck2.7.10.20.448
3ag9A02cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.448
1bxoPP7Penicillopepsin-13.4.23.200.447
1dz8CAMCamphor 5-monooxygenase1.14.15.10.447
1i58ACPChemotaxis protein CheA2.7.13.30.447
1qpePP2Tyrosine-protein kinase Lck2.7.10.20.447
2d8aNADL-threonine 3-dehydrogenase/0.447
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.447
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.447
2w9hTOPDihydrofolate reductase1.5.1.30.447
2y3sTIRTamL/0.447
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.447
3fr8NDPKetol-acid reductoisomerase, chloroplastic1.1.1.860.447
3tnlNADShikimate dehydrogenase (NADP(+))/0.447
4m69ANPReceptor-interacting serine/threonine-protein kinase 32.7.11.10.447
4xli1N1Abelson tyrosine-protein kinase 22.7.10.20.447
1xddAAYIntegrin alpha-L/0.446
2cmoM1LGlutamate receptor 2/0.446
2ojg19AMitogen-activated protein kinase 12.7.11.240.446
2ym3YM3Serine/threonine-protein kinase Chk12.7.11.10.446
3c50ADPRhodopsin kinase/0.446
3h3t16HCollagen type IV alpha-3-binding protein/0.446
3ntaCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.446
3ortAGSSerine/threonine protein kinase/0.446
4fd2ADPChaperone protein ClpB/0.446
4otpADPSerine/threonine-protein kinase RIO12.7.11.10.446
4r2lATPUniversal stress protein F/0.446
4wudANPDNA gyrase subunit B/0.446
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.446
1diuBDMDihydrofolate reductase1.5.1.30.445
1j39UPGDNA beta-glucosyltransferase/0.445
1pl8NADSorbitol dehydrogenase1.1.1.140.445
1rbyKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.445
2b53D23Cyclin-dependent kinase 22.7.11.220.445
2briANPUridylate kinase2.7.4.220.445
2l84J28CREB-binding protein/0.445
2uyyNA7Putative oxidoreductase GLYR110.445
3ac1KZITyrosine-protein kinase Lck2.7.10.20.445
3fwyADPLight-independent protochlorophyllide reductase iron-sulfur ATP-binding protein/0.445
3nl6TPSUncharacterized protein/0.445
3ntdCOAFAD-dependent pyridine nucleotide-disulphide oxidoreductase/0.445
3svj4LIPeptide deformylase/0.445
4d81ADPAAA ATPase, central domain protein/0.445
4fv7E94Mitogen-activated protein kinase 12.7.11.240.445
4hjfC2EGGDEF family protein/0.445
4jqlVJ6Heat shock protein HSP 90-alpha/0.445
1a8pFADFerredoxin--NADP reductase/0.444
1i5aACPChemotaxis protein CheA2.7.13.30.444
1mqwADVMutT/nudix family protein/0.444
1zarADPRIO-type serine/threonine-protein kinase Rio22.7.11.10.444
2a7r5GPGMP reductase 2/0.444
2bjfDXCCholoylglycine hydrolase3.5.1.240.444
2breKJ2ATP-dependent molecular chaperone HSP82/0.444
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.444
2qtvGNPSmall COPII coat GTPase SAR13.6.50.444
2ydxSTLMethionine adenosyltransferase 2 subunit beta/0.444
3a4vNADNDP-sugar epimerase/0.444
3evbSAHGenome polyprotein2.1.1.560.444
3m2uCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.444
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.444
4lj9ACPChaperone protein ClpB/0.444
4xhgADPUncharacterized protein/0.444
5f0a1FBcGMP-dependent protein kinase, putative/0.444
1f20NAPNitric oxide synthase, brain1.14.13.390.443
1h1wATP3-phosphoinositide-dependent protein kinase 12.7.11.10.443
1txtCAAHMG-CoA synthase/0.443
2ay3MPPAromatic-amino-acid aminotransferase2.6.1.570.443
2b9yFADPutative aminooxidase/0.443
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.443
3mtfA3FActivin receptor type-12.7.11.300.443
3opxU5PSuppressor of disruption of TFIIS/0.443
3t8wDGZM17 leucyl aminopeptidase/0.443
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.443
3vs6VSHTyrosine-protein kinase HCK2.7.10.20.443
3w8rACPUridine kinase/0.443
4du82P0Mevalonate diphosphate decarboxylase/0.443
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.443
4wq5ATPtRNA N6-adenosine threonylcarbamoyltransferase/0.443
1dj3GDPAdenylosuccinate synthetase, chloroplastic/0.442
1g4tFTPThiamine-phosphate synthase/0.442
1jm6ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.442
1mf0GDPAdenylosuccinate synthetase isozyme 1/0.442
1touB1VFatty acid-binding protein, adipocyte/0.442
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.442
1zp9ATPRIO-type serine/threonine-protein kinase Rio12.7.11.10.442
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.442
2p4iMR9Angiopoietin-1 receptor2.7.10.10.442
2qdxFADFerredoxin--NADP+ reductase/0.442
2rh9IGPTryptophan synthase alpha chain/0.442
2xyuQ9GEphrin type-A receptor 42.7.10.10.442
3acjKSSTyrosine-protein kinase Lck2.7.10.20.442
3ahiHTLProbable phosphoketolase/0.442
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3p67FMNPentaerythritol tetranitrate reductase/0.442
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.442
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
4jrnANPRhoptry kinase family protein/0.442
4lg5A1OAbscisic acid receptor PYL2/0.442
5bsgNAPPyrroline-5-carboxylate reductase/0.442
5eg3ACPFibroblast growth factor receptor 2/0.442
1bxqPP8Penicillopepsin-13.4.23.200.441
1sn5T3Transthyretin/0.441
2acxANPG protein-coupled receptor kinase 62.7.11.160.441
2bdf24AProto-oncogene tyrosine-protein kinase Src2.7.10.20.441
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.441
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.441
2iviACWIsopenicillin N synthase1.21.3.10.441
2iyfERYOleandomycin glycosyltransferase2.4.10.441
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.441
2xjxXJXHeat shock protein HSP 90-alpha/0.441
3b2sB2STrichothecene 3-O-acetyltransferase/0.441
3m2vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.441
3nyrMLCPutative fatty acid synthase/0.441
3ocgOCGMitogen-activated protein kinase 14/0.441
3p8jFMNPentaerythritol tetranitrate reductase/0.441
3pj8404Cyclin-dependent kinase 22.7.11.220.441
3w0pADPHygromycin-B 4-O-kinase2.7.1.1630.441
4an4DUDPutative glycosyl transferase/0.441
4fyhTR52'-deoxynucleoside 5'-phosphate N-hydrolase 1/0.441
4hj6FMNLOV protein/0.441
4ie6UN9Alpha-ketoglutarate-dependent dioxygenase FTO/0.441
4nbwNADShort-chain dehydrogenase/reductase SDR/0.441
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.441
1fmjRTLRetinol dehydratase/0.440
1hkuNADC-terminal-binding protein 11.1.10.440
1joaFADNADH peroxidase1.11.1.10.440
1wvgAPRCDP-glucose 4,6-dehydratase4.2.1.450.440
2bueCOAAAC(6')-Ib/0.440
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.440
2i5bADPPyridoxine kinase/0.440
2ociTYCValacyclovir hydrolase3.10.440
2rkvZBATrichothecene 3-O-acetyltransferase/0.440
2xkaGSPCell division protein FtsZ/0.440
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
3el8PD5Proto-oncogene tyrosine-protein kinase Src2.7.10.20.440
3f8kCOAUncharacterized protein/0.440
3kh5ADPUncharacterized protein MJ1225/0.440
3oafOAGDihydrofolate reductase1.5.1.30.440
3r6c17NAnthranilate phosphoribosyltransferase/0.440
3tdwGDPGentamicin resistance protein/0.440
3ub5ATPActin, cytoplasmic 1/0.440
4c57FEFCyclin-G-associated kinase2.7.11.10.440
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4gapFADRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial1.6.5.90.440
4i6gFADCryptochrome-2/0.440
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440