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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
4e8yIHAD-beta-D-heptose 7-phosphate kinase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4e8yIHAD-beta-D-heptose 7-phosphate kinase/1.000
2aa0MTPAdenosine kinase2.7.1.200.567
4e8wIHAD-beta-D-heptose 7-phosphate kinase/0.554
5c3zACPRibokinase/0.537
1likADNAdenosine kinase2.7.1.200.528
1d4jMSCGag-Pol polyprotein3.4.23.160.509
1gqtACPRibokinase/0.508
3gbuATPUncharacterized sugar kinase PH14592.7.10.507
2i5bADPPyridoxine kinase/0.505
5c3yAN2Ribokinase/0.500
1mrwK57Gag-Pol polyprotein3.4.23.160.499
5c41ACPRibokinase/0.499
1d4hBEHGag-Pol polyprotein3.4.23.160.498
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.491
1npa3NHGag-Pol polyprotein3.4.23.160.488
1npwLGZGag-Pol polyprotein3.4.23.160.488
1msmJE2Gag-Pol polyprotein3.4.23.160.485
2r43G3GGag-Pol polyprotein3.4.23.160.484
1p31EPUUDP-N-acetylmuramate--L-alanine ligase6.3.2.80.478
2znpK55Peroxisome proliferator-activated receptor delta/0.478
3iaeD7KBenzaldehyde lyase/0.478
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.477
3vfa031Gag-Pol polyprotein3.4.23.160.477
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.476
4a6cQG9Gag-Pol polyprotein3.4.23.160.475
4pd6URINucleoside permease/0.475
3lkiATPFructokinase/0.472
2znq401Peroxisome proliferator-activated receptor delta/0.471
4du82P0Mevalonate diphosphate decarboxylase/0.471
1kzkJE2Gag-Pol polyprotein3.4.23.160.469
2givACOHistone acetyltransferase KAT8/0.469
3bgbLJGGag-Pol polyprotein3.4.23.160.469
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.468
2i4uDJRProtease/0.468
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.468
4dfg0JVGag-Pol polyprotein3.4.23.160.468
1bv9XV6Gag-Pol polyprotein3.4.23.160.467
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.467
1hiiC20Gag-Pol polyprotein/0.466
3q92XNBKetohexokinase/0.466
2ou2ACOHistone acetyltransferase KAT5/0.465
3b6zCO7Enoyl reductase LovC10.465
4ge70K5Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.465
1jpaANPEphrin type-B receptor 22.7.10.10.464
1kboFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.464
1sguMK1Gag-Pol polyprotein3.4.23.160.464
3bgcLJHGag-Pol polyprotein3.4.23.160.464
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.464
4kwi1TJReductase homolog/0.464
1c6yMK1Protease/0.463
1ppjANYCytochrome b/0.463
3t2kFADSulfide-quinone reductase/0.463
4gh5NADShort-chain dehydrogenase/reductase SDR/0.463
1dhjMTXDihydrofolate reductase1.5.1.30.462
1kkq471Peroxisome proliferator-activated receptor alpha/0.462
1p0hACOMycothiol acetyltransferase2.3.1.1890.462
3i7eDJRGag-Pol polyprotein/0.462
3s54017Protease/0.462
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.462
1msnJE2Gag-Pol polyprotein3.4.23.160.461
3i6oGR6Gag-Pol polyprotein3.4.23.160.461
1esvLARActin, alpha skeletal muscle/0.460
1qr6NADNAD-dependent malic enzyme, mitochondrial1.1.1.380.460
3l0lHC3Nuclear receptor ROR-gamma/0.460
3lqfNADGalactitol dehydrogenase/0.460
4hy6FJ1Heat shock protein HSP 90-alpha/0.460
4ipw1G7Mycocyclosin synthase1.14.21.90.460
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.459
2p83MR0Beta-secretase 13.4.23.460.459
3o6o94MHeat shock protein 83/0.459
1rfvADPPyridoxal kinase2.7.1.350.458
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.458
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.458
4r1lADPPhenylacetate-coenzyme A ligase/0.458
1wbk568Pol protein/0.457
3mnrSD1Heat shock protein HSP 90-alpha/0.457
3oxv478Gag-Pol polyprotein3.4.23.160.457
3w8qAGSDual specificity mitogen-activated protein kinase kinase 12.7.12.20.457
4a99FADTetX family tetracycline inactivation enzyme/0.457
1uy8PU5Heat shock protein HSP 90-alpha/0.456
1y5rC0RCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.456
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.456
2iqgF2IBeta-secretase 13.4.23.460.456
2j9lATPH(+)/Cl(-) exchange transporter 5/0.456
3nu3478Gag-Pol polyprotein3.4.23.160.456
3sp9IL2Peroxisome proliferator-activated receptor delta/0.456
4z9rNADOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.456
1mj9COAHistone acetyltransferase ESA1/0.455
1r2jFADFkbI/0.455
1tdrMTXDihydrofolate reductase1.5.1.30.455
2bi4NADLactaldehyde reductase1.1.1.770.455
2h55DZ8Heat shock protein HSP 90-alpha/0.455
2y0mACOHistone acetyltransferase KAT8/0.455
3i0pNADMalate dehydrogenase, putative/0.455
3otxAP5Adenosine kinase, putative/0.455
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.454
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.454
1nvtNAPShikimate dehydrogenase (NADP(+))/0.454
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.454
3dk1G05Gag-Pol polyprotein3.4.23.160.454
3ft8MOJHeat shock protein HSP 90-alpha/0.454
3lpjZ75Beta-secretase 13.4.23.460.454
3qaiXNNKetohexokinase/0.454
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.454
3vt7VDXVitamin D3 receptor/0.454
3zpuM8BGag-Pol polyprotein3.4.23.160.454
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
1c70L75Protease/0.453
1h69FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
3cyw017Gag-Pol polyprotein3.4.23.160.453
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.453
3o9hK2EGag-Pol polyprotein/0.453
3p62FMNPentaerythritol tetranitrate reductase/0.453
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.453
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.453
1k6pXN3Gag-Pol polyprotein3.4.23.160.452
1t7kBH0Gag-Pol polyprotein3.4.23.160.452
2bpw1INGag-Pol polyprotein3.4.23.160.452
2ctsCOACitrate synthase, mitochondrial2.3.3.10.452
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
3nbvANPKetohexokinase/0.452
4tuvCPZCytochrome P450 1191.140.452
1ajvNMBGag-Pol polyprotein3.4.23.160.451
1hsgMK1Gag-Pol polyprotein/0.451
2pwrG4GGag-Pol polyprotein3.4.23.160.451
2qhcAB1Protease/0.451
3inmNDPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.451
3k4nFADPyranose 2-oxidase/0.451
3t3c017Gag-Pol polyprotein3.4.23.160.451
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4lj6ACPChaperone protein ClpB/0.451
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.451
1a9yUPGUDP-glucose 4-epimerase5.1.3.20.450
1b16NAQAlcohol dehydrogenase1.1.1.10.450
1ec3MS3Gag-Pol polyprotein3.4.23.160.450
1nzdUPGDNA beta-glucosyltransferase/0.450
2bpv1INGag-Pol polyprotein3.4.23.160.450
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.450
2ozuACOHistone acetyltransferase KAT6A/0.450
2wf4ZY4Beta-secretase 13.4.23.460.450
5cwa0GAAnthranilate synthase component 14.1.3.270.450
1q3qANPThermosome subunit alpha/0.449
2avvMK1Gag-Pol polyprotein3.4.23.160.449
2bb9AKCGag-Pol polyprotein3.4.23.160.449
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.449
2yyyNAPGlyceraldehyde-3-phosphate dehydrogenase1.2.1.590.449
3bxrDRRGag-Pol polyprotein3.4.23.160.449
3cid318Beta-secretase 13.4.23.460.449
3nu4478Gag-Pol polyprotein3.4.23.160.449
5a3cNADSIR2 family protein/0.449
1b15NAEAlcohol dehydrogenase1.1.1.10.448
1npvL27Gag-Pol polyprotein3.4.23.160.448
2hs2017Protease/0.448
2qnqQN3Gag-Pol polyprotein3.4.23.160.448
2yyuC5POrotidine 5'-phosphate decarboxylase/0.448
3drcMTXDihydrofolate reductase1.5.1.30.448
3ecg065Gag-Pol polyprotein3.4.23.470.448
3gwfFADCyclohexanone monooxygenase/0.448
3ieuGDPGTPase Era/0.448
3kfr3TLGag-Pol polyprotein/0.448
3livE16Protease/0.448
3qa2XNAKetohexokinase/0.448
4a6bQG8Gag-Pol polyprotein3.4.23.160.448
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.448
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.448
1e1kFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.447
1guyNADMalate dehydrogenase/0.447
1mjbACOHistone acetyltransferase ESA1/0.447
1rx8NAPDihydrofolate reductase1.5.1.30.447
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.447
1w5vBE3Gag-Pol polyprotein3.4.23.160.447
1yb5NAPQuinone oxidoreductase1.6.5.50.447
2hydADPPutative multidrug export ATP-binding/permease protein SAV18663.6.30.447
2ykeYKEHeat shock protein HSP 90-alpha/0.447
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.447
3nc9TR3Ketohexokinase/0.447
3so9017Pol protein/0.447
3zuyTCHTransporter/0.447
4iteTEYVitamin D3 receptor/0.447
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1kevNDPNADP-dependent isopropanol dehydrogenase1.1.1.800.446
2f8g017Gag-Pol polyprotein3.4.23.160.446
2hs1017Protease/0.446
2i4xKGQProtease/0.446
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.446
3bvb017Gag-Pol polyprotein3.4.23.160.446
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.446
3ekp478Gag-Pol polyprotein3.4.23.160.446
3gobHXXDdmC/0.446
3gqvNAPEnoyl reductase LovC10.446
3gwfNAPCyclohexanone monooxygenase/0.446
3kddJZQGag-Pol polyprotein3.4.23.160.446
3qaaG04Gag-Pol polyprotein3.4.23.160.446
3qw4U5POrotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative/0.446
3t2zFADSulfide-quinone reductase/0.446
3zuxTCHTransporter/0.446
4fidGDPG protein alpha subunit, putative/0.446
4nh82LCHeat shock protein HSP 90-alpha/0.446
4wsoNADProbable nicotinate-nucleotide adenylyltransferase/0.446
4y93746Tyrosine-protein kinase/0.446
4yryFADGlutamate synthase, beta subunit/0.446
1nzfUPGDNA beta-glucosyltransferase/0.445
1qcjAPTAntiviral protein I3.2.2.220.445
1uxkNADMalate dehydrogenase/0.445
2c29NAPDihydroflavonol 4-reductase/0.445
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.445
3gvhNADMalate dehydrogenase/0.445
3hx4ANPCalmodulin-domain protein kinase 1/0.445
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.445
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.445
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.445
4dc0NDPPutative ketoacyl reductase1.3.10.445
4fg8ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.445
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.445
5kjcPFBAlcohol dehydrogenase E chain1.1.1.10.445
1fmjRTLRetinol dehydratase/0.444
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1uyfPU1Heat shock protein HSP 90-alpha/0.444
2bqvA1AProtease/0.444
2gjnFMNNitronate monooxygenase1.13.12.160.444
2p9gNAID-3-phosphoglycerate dehydrogenase1.1.1.950.444
3a2oKNJGag-Pol polyprotein3.4.23.160.444
3b70NAPEnoyl reductase LovC10.444
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.444
3ekv478Gag-Pol polyprotein3.4.23.160.444
3mdvCL6Cholesterol 24-hydroxylase/0.444
3pe2E1BCasein kinase II subunit alpha2.7.11.10.444
3qlsNDPDihydrofolate reductase1.5.1.30.444
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.444
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.444
1hpxKNIGag-Pol polyprotein/0.443
1k6tXN1Gag-Pol polyprotein3.4.23.160.443
1uyhPU0Heat shock protein HSP 90-alpha/0.443
2ifaFMNUncharacterized protein/0.443
2pwcG3GGag-Pol polyprotein3.4.23.160.443
2r3wG3GGag-Pol polyprotein3.4.23.160.443
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.443
2wl05AHGag-Pol polyprotein/0.443
2xw7NDPDihydrofolate reductase/0.443
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.443
3slkNDPPolyketide synthase extender module 2/0.443
3wmxNADNAD dependent epimerase/dehydratase/0.443
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.443
4lj9ACPChaperone protein ClpB/0.443
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.443
1ebyBEBGag-Pol polyprotein3.4.23.160.442
1jioDEB6-deoxyerythronolide B hydroxylase/0.442
1jolFFODihydrofolate reductase1.5.1.30.442
1odw0E8Gag-Pol polyprotein3.4.23.160.442
1psa0ZLPepsin A3.4.23.10.442
2ohvNHLGlutamate racemase/0.442
2vn0TDZCytochrome P450 2C8/0.442
2y4gTIRTamL/0.442
3in1ADPUncharacterized sugar kinase YdjH2.7.10.442
3ogqAB1Pol polyprotein/0.442
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
4iwyADPRibosomal protein S6--L-glutamate ligase/0.442
5fm7ADPRuvB-like helicase/0.442
1bdrIM1Gag-Pol polyprotein3.4.23.160.441
1n49RITGag-Pol polyprotein3.4.23.160.441
1ryiFADGlycine oxidase1.4.3.190.441
1uymPU3Heat shock protein HSP 90-beta/0.441
1w5xBE5Gag-Pol polyprotein3.4.23.160.441
2a4fAAUV-1 protease/0.441
2dteNAIGlucose 1-dehydrogenase related protein/0.441
2fzwNADAlcohol dehydrogenase class-31.1.1.10.441
2gjlFMNNitronate monooxygenase1.13.12.160.441
2gr1FADFerredoxin reductase/0.441
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.441
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.441
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.441
3nu9478Gag-Pol polyprotein3.4.23.160.441
3qlrNDPDihydrofolate reductase1.5.1.30.441
3rbqGLY_ALA_GLY_DAOProtein unc-119 homolog A/0.441
3tl9ROCGag-Pol polyprotein3.4.23.160.441
3vt9YI4Vitamin D3 receptor/0.441
4dqh017Gag-Pol polyprotein/0.441
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.441
4itfTFYVitamin D3 receptor/0.441
1bwb146Gag-Pol polyprotein3.4.23.160.440
1gegNADDiacetyl reductase [(S)-acetoin forming]1.1.1.3040.440
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1izhQ50Protease/0.440
1j21ATPArgininosuccinate synthase/0.440
1xdpATPPolyphosphate kinase/0.440
2a94AP0L-lactate dehydrogenase1.1.1.270.440
2cduFADNADH oxidase/0.440
2eglSAHDiphthine synthase/0.440
2i4wKGQProtease/0.440
2q641UNGag-Pol polyprotein3.4.23.160.440
3ekx1UNGag-Pol polyprotein3.4.23.160.440
3kfs3TLGag-Pol polyprotein/0.440
3n6uTSUHTH-type transcriptional regulator TsaR/0.440
3qihFG7Gag-Pol polyprotein3.4.23.160.440
3vtdTKDVitamin D3 receptor/0.440
3wbbNAPMeso-diaminopimelate D-dehydrogenase/0.440
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.440
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.440
4l4xNDPAmphI/0.440
4u03GTPCyclic GMP-AMP synthase/0.440
5cvfATPCasein kinase II subunit alpha2.7.11.10.440
5jlaNADPutative short-chain dehydrogenase/reductase/0.440