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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
1s14NOVDNA topoisomerase 4 subunit B

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1s14NOVDNA topoisomerase 4 subunit B/1.000
4nb6444Nuclear receptor ROR-gamma/0.485
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.479
4hvg19QTyrosine-protein kinase JAK32.7.10.20.479
2npxNADNADH peroxidase1.11.1.10.475
3u2xASOGlycogenin-12.4.1.1860.474
2hwrDRDPeroxisome proliferator-activated receptor gamma/0.471
2q61SF1Peroxisome proliferator-activated receptor gamma/0.471
4l6gCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.471
5cp4CAMCamphor 5-monooxygenase1.14.15.10.470
4rcvNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.468
5dr6SKEAurora kinase A2.7.11.10.468
1aj8COACitrate synthase/0.467
5e8wSTUTGF-beta receptor type-12.7.11.300.467
1c2tNHSPhosphoribosylglycinamide formyltransferase/0.466
1njsKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.466
3h0aD30Peroxisome proliferator-activated receptor gamma/0.466
3gwfFADCyclohexanone monooxygenase/0.465
4otwDB8Receptor tyrosine-protein kinase erbB-32.7.10.10.465
2znpK55Peroxisome proliferator-activated receptor delta/0.464
4l4dCAMCamphor 5-monooxygenase1.14.15.10.463
4tuvCPZCytochrome P450 1191.140.463
3cr3ADPPTS-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.462
1s3uTQDDihydrofolate reductase1.5.1.30.461
1xddAAYIntegrin alpha-L/0.461
4xumIMNPeroxisome proliferator-activated receptor gamma/0.461
1dajMOTDihydrofolate reductase1.5.1.30.460
1iwiCAMCamphor 5-monooxygenase1.14.15.10.460
3cppCAMCamphor 5-monooxygenase1.14.15.10.460
3wrjCAMCamphor 5-monooxygenase1.14.15.10.460
3wv9FEGHmd co-occurring protein HcgE/0.460
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.460
1gpdNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.459
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.459
1rbqKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.459
2a1nCAMCamphor 5-monooxygenase1.14.15.10.459
2eleSAHDiphthine synthase/0.459
3ajrNADNDP-sugar epimerase/0.459
3nmpPYVAbscisic acid receptor PYL2/0.459
3pe6ZYHMonoglyceride lipase/0.459
4ejmNAPPutative zinc-binding dehydrogenase/0.459
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.458
3zsi52PMitogen-activated protein kinase 14/0.458
4q72FADBifunctional protein PutA/0.458
4u9aSTUInterleukin-1 receptor-associated kinase 42.7.11.10.458
4uyf73BBromodomain-containing protein 2/0.458
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.457
2huvSAHDiphthine synthase/0.457
2rhgIGPTryptophan synthase alpha chain/0.457
3ocpCMPcGMP-dependent protein kinase 12.7.11.120.457
3qlsNDPDihydrofolate reductase1.5.1.30.457
6cp4CAMCamphor 5-monooxygenase1.14.15.10.457
1a59COA2-methylcitrate synthase/0.456
1esvLARActin, alpha skeletal muscle/0.456
3nu3478Gag-Pol polyprotein3.4.23.160.456
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.456
3zoiM2WIsopenicillin N synthase1.21.3.10.456
4kkyCAMCamphor 5-monooxygenase1.14.15.10.456
1c2tGARPhosphoribosylglycinamide formyltransferase/0.455
1rrmAPRLactaldehyde reductase1.1.1.770.455
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.455
2p6iSAHDiphthine synthase/0.455
2pckSAHDiphthine synthase/0.455
2qbnCAMCamphor 5-monooxygenase1.14.15.10.455
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
1qvnFRIInterleukin-2/0.454
1v9aSAHUncharacterized protein/0.454
2ek2SAHDiphthine synthase/0.454
2excJNKMitogen-activated protein kinase 102.7.11.240.454
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.454
3bv3P39Mitogen-activated protein kinase 14/0.454
3nwq2NCGag-Pol polyprotein3.4.23.160.454
3sqq99ZCyclin-dependent kinase 22.7.11.220.454
3t1tGDPProbable gliding protein mglA/0.454
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
5dhgDGVNociceptin receptor/0.454
1sxjADPReplication factor C subunit 5/0.453
1vikBAYGag-Pol polyprotein/0.453
2gr1FADFerredoxin reductase/0.453
3wrmCAMCamphor 5-monooxygenase1.14.15.10.453
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.453
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.453
2eh4SAHDiphthine synthase/0.452
2q8sL92Peroxisome proliferator-activated receptor gamma/0.452
3v9v21LPeroxisome proliferator-activated receptor gamma/0.452
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.452
4jin1L7RIO-type serine/threonine-protein kinase Rio12.7.11.10.452
4q73FADBifunctional protein PutA/0.452
1adcPADAlcohol dehydrogenase E chain1.1.1.10.451
1c3eNHRPhosphoribosylglycinamide formyltransferase/0.451
1dz4CAMCamphor 5-monooxygenase1.14.15.10.451
1q0qNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.451
1t87CAMCamphor 5-monooxygenase1.14.15.10.451
2dv3SAHDiphthine synthase/0.451
2huqSAHDiphthine synthase/0.451
2po7CHDFerrochelatase, mitochondrial4.99.1.10.451
2w06FRVCyclin-dependent kinase 22.7.11.220.451
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.451
3cktYDPGag-Pol polyprotein3.4.23.160.451
3flzFLZMitogen-activated protein kinase 14/0.451
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.451
4o2bLOCTubulin beta-2B chain/0.451
2owkSAHDiphthine synthase/0.450
3da1FADGlycerol-3-phosphate dehydrogenase/0.450
4dfg0JVGag-Pol polyprotein3.4.23.160.450
4pleCPSNuclear receptor subfamily 5 group A member 2/0.450
1c3eGARPhosphoribosylglycinamide formyltransferase/0.449
1xny191Propionyl-CoA carboxylase complex B subunit/0.449
1yrcCAMCamphor 5-monooxygenase1.14.15.10.449
2dwpACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.449
2ien017Gag-Pol polyprotein3.4.23.160.449
2m56CAMCamphor 5-monooxygenase1.14.15.10.449
2qd4CHDFerrochelatase, mitochondrial4.99.1.10.449
2zawCAMCamphor 5-monooxygenase1.14.15.10.449
3l63CAMCamphor 5-monooxygenase1.14.15.10.449
3lqfNADGalactitol dehydrogenase/0.449
4an2EUIDual specificity mitogen-activated protein kinase kinase 12.7.12.20.449
4cp4CAMCamphor 5-monooxygenase1.14.15.10.449
4k5p1OSM1 family aminopeptidase3.4.110.449
4qmtH1NSerine/threonine-protein kinase 242.7.11.10.449
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.449
1pd9CO4Dihydrofolate reductase1.5.1.30.448
2a1mCAMCamphor 5-monooxygenase1.14.15.10.448
2e16SAHDiphthine synthase/0.448
2hog710Serine/threonine-protein kinase Chk12.7.11.10.448
2ym1FADPhenylacetone monooxygenase1.14.13.920.448
2z97CAMCamphor 5-monooxygenase1.14.15.10.448
2zaxCAMCamphor 5-monooxygenase1.14.15.10.448
3c4xATPRhodopsin kinase/0.448
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.448
3fwiCAMCamphor 5-monooxygenase1.14.15.10.448
3s1dZIRCytokinin dehydrogenase 11.5.99.120.448
4gmy0X5Tyrosine-protein kinase JAK2/0.448
4i8vBHFCytochrome P450 1A11.14.14.10.448
5cpbNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
1ai9NDPDihydrofolate reductase1.5.1.30.447
1m13HYFNuclear receptor subfamily 1 group I member 2/0.447
1nooCAHCamphor 5-monooxygenase1.14.15.10.447
1z1rHBHGag-Pol polyprotein3.4.23.160.447
2aqhNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2e8rSAHDiphthine synthase/0.447
2i1vADP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 32.7.1.1050.447
3mxdK53Gag-Pol polyprotein3.4.23.160.447
3oxv478Gag-Pol polyprotein3.4.23.160.447
3qlrNDPDihydrofolate reductase1.5.1.30.447
3sls77DDual specificity mitogen-activated protein kinase kinase 12.7.12.20.447
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.447
4d0l093Phosphatidylinositol 4-kinase beta2.7.1.670.447
4fr4STUSerine/threonine-protein kinase 32A2.7.11.10.447
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
4pd6URINucleoside permease/0.447
4xldBRLPeroxisome proliferator-activated receptor gamma/0.447
1dssNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.446
1iwjCAMCamphor 5-monooxygenase1.14.15.10.446
2izrBRKCasein kinase I isoform gamma-32.7.11.10.446
2uuvFADAlkyldihydroxyacetonephosphate synthase2.5.1.260.446
2znnS44Peroxisome proliferator-activated receptor alpha/0.446
3d78NBBPheromone-binding protein ASP1/0.446
3friSAH16S rRNA methylase/0.446
3vjhJ35Peroxisome proliferator-activated receptor gamma/0.446
4e4qRRHPeroxisome proliferator-activated receptor gamma/0.446
4l4bCAMCamphor 5-monooxygenase1.14.15.10.446
1g38NEAModification methylase TaqI2.1.1.720.445
1phgMYTCamphor 5-monooxygenase1.14.15.10.445
1yrdCAMCamphor 5-monooxygenase1.14.15.10.445
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.445
2feuCAMCamphor 5-monooxygenase1.14.15.10.445
2q5g1FAPeroxisome proliferator-activated receptor delta/0.445
2qbmCAMCamphor 5-monooxygenase1.14.15.10.445
2y60M8FIsopenicillin N synthase1.21.3.10.445
2ylzFADPhenylacetone monooxygenase1.14.13.920.445
2zuiCAMCamphor 5-monooxygenase1.14.15.10.445
3cjfSAVVascular endothelial growth factor receptor 22.7.10.10.445
3gep24HHypoxanthine-guanine phosphoribosyltransferase2.4.2.80.445
3oqfS51Renin3.4.23.150.445
4ew2DXYTrifunctional purine biosynthetic protein adenosine-32.1.2.20.445
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.445
1t85CAMCamphor 5-monooxygenase1.14.15.10.444
1uyuCAMCamphor 5-monooxygenase1.14.15.10.444
2he5NDPAldo-keto reductase family 1 member C211.1.10.444
2hy81STSerine/threonine-protein kinase PAK 12.7.11.10.444
2iviACWIsopenicillin N synthase1.21.3.10.444
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.444
2qd9LGFMitogen-activated protein kinase 14/0.444
3tjsD0RCytochrome P450 3A4/0.444
4l4aCAMCamphor 5-monooxygenase1.14.15.10.444
4lhtCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.444
4nfhPFBAlcohol dehydrogenase E chain1.1.1.10.444
4z9rNADOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.444
1b3rNADAdenosylhomocysteinase3.3.1.10.443
1hvhQ82Gag-Pol polyprotein3.4.23.160.443
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.443
1ouy094Mitogen-activated protein kinase 14/0.443
1v59FADDihydrolipoyl dehydrogenase, mitochondrial1.8.1.40.443
2ozuACOHistone acetyltransferase KAT6A/0.443
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.443
2p9dSAHDiphthine synthase/0.443
2y6o1N1Ephrin type-A receptor 42.7.10.10.443
2znq401Peroxisome proliferator-activated receptor delta/0.443
3fwfCAMCamphor 5-monooxygenase1.14.15.10.443
3iqfE4MF420-dependent methylenetetrahydromethanopterin dehydrogenase1.5.98.10.443
3qa2XNAKetohexokinase/0.443
3wrlCAMCamphor 5-monooxygenase1.14.15.10.443
3zkyWT4Isopenicillin N synthase1.21.3.10.443
4fko20KCyclin-dependent kinase 22.7.11.220.443
4g2rH1LProbable propionyl-CoA carboxylase beta chain 66.4.1.30.443
4hxyNDPPlm1/0.443
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.443
1cdeGARPhosphoribosylglycinamide formyltransferase/0.442
1gebCAMCamphor 5-monooxygenase1.14.15.10.442
1i7gAZ2Peroxisome proliferator-activated receptor alpha/0.442
1iyzNDPProbable quinone oxidoreductase/0.442
1j39UPGDNA beta-glucosyltransferase/0.442
1mvtDTMDihydrofolate reductase1.5.1.30.442
1npvL27Gag-Pol polyprotein3.4.23.160.442
1pnvTYDdTDP-epi-vancosaminyltransferase2.4.1.3110.442
1rc0KT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.442
2b60RITPol polyprotein/0.442
2drcMTXDihydrofolate reductase1.5.1.30.442
2i4uDJRProtease/0.442
2ittAEEEpidermal growth factor receptor2.7.10.10.442
2j3kNAPNADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.442
2j5xGSPADP-ribosylation factor 6/0.442
2q6sPLBPeroxisome proliferator-activated receptor gamma/0.442
2yjxYJXHeat shock protein HSP 90-alpha/0.442
3fwjCAMCamphor 5-monooxygenase1.14.15.10.442
3h1vTK1Glucokinase2.7.1.20.442
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
3pm0BHFCytochrome P450 1B1/0.442
3tkh07SSerine/threonine-protein kinase Chk12.7.11.10.442
3zdu38RCyclin-dependent kinase-like 32.7.11.220.442
4a81DXCMajor pollen allergen Bet v 1-A/0.442
4b99R4LMitogen-activated protein kinase 72.7.11.240.442
4bdhWVISerine/threonine-protein kinase Chk22.7.11.10.442
4fklCK2Cyclin-dependent kinase 22.7.11.220.442
4ft5H2KSerine/threonine-protein kinase Chk12.7.11.10.442
4z34ON7Lysophosphatidic acid receptor 1/0.442
1dz6CAMCamphor 5-monooxygenase1.14.15.10.441
1w2xRCPAcetyl-CoA carboxylase/0.441
2w17I19Cyclin-dependent kinase 22.7.11.220.441
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.441
3ekwDR7Gag-Pol polyprotein3.4.23.160.441
3em3478Gag-Pol polyprotein3.4.23.160.441
3i2l2NCProtease/0.441
3lxiCAMCytochrome P450/0.441
3lzs017Gag-Pol polyprotein3.4.23.160.441
3pwrROCGag-Pol polyprotein3.4.23.160.441
4dfrMTXDihydrofolate reductase1.5.1.30.441
4emaBRLPeroxisome proliferator-activated receptor gamma/0.441
4enhFVXCholesterol 24-hydroxylase/0.441
4g6nEK0Mitogen-activated protein kinase 12.7.11.240.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.441
4ktc1X3Genome polyprotein3.4.21.980.441
4m6jNDPDihydrofolate reductase1.5.1.30.441
4nka2K7Fibroblast growth factor receptor 1/0.441
4pl4ADPSerine/threonine-protein kinase/endoribonuclease IRE12.7.11.10.441
4q71FADBifunctional protein PutA/0.441
5bmvVLBTubulin alpha-1B chain/0.441
5bmvVLBTubulin beta chain/0.441
1k6pXN3Gag-Pol polyprotein3.4.23.160.440
1sh9RITGag-Pol polyprotein3.4.23.160.440
2a94AP0L-lactate dehydrogenase1.1.1.270.440
2ath3EAPeroxisome proliferator-activated receptor gamma/0.440
2cppCAMCamphor 5-monooxygenase1.14.15.10.440
2e8hSAHDiphthine synthase/0.440
2ih2NEAModification methylase TaqI2.1.1.720.440
2qblCAMCamphor 5-monooxygenase1.14.15.10.440
2xf3J01Uncharacterized protein/0.440
3djkG55Gag-Pol polyprotein3.4.23.160.440
3dtwA96Vascular endothelial growth factor receptor 22.7.10.10.440
3gdsVAL_TYR_TYR_PHESerine endoprotease DegS3.4.21.1070.440
3ieuGDPGTPase Era/0.440
3mjeNDPAmphB/0.440
3pwm017Gag-Pol polyprotein3.4.23.160.440
3tucFPWTyrosine-protein kinase SYK2.7.10.20.440
4a9e3PFBromodomain-containing protein 2/0.440
4c9pCAMCytochrome P450/0.440
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.440
4f650S9Fibroblast growth factor receptor 1/0.440
4fxfATPPyruvate kinase PKM2.7.1.400.440
4o4eATPKinase/0.440
4rvnCOAPhenylacetate-coenzyme A ligase/0.440