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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
4nh92LCEndoplasmin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4nh92LCEndoplasmin/1.000
3hz5Z64Heat shock protein HSP 90-alpha/0.548
1uy6PU3Heat shock protein HSP 90-alpha/0.534
3mnrSD1Heat shock protein HSP 90-alpha/0.531
1uymPU3Heat shock protein HSP 90-beta/0.524
2ykcYKCHeat shock protein HSP 90-alpha/0.524
2fwyH64Heat shock protein HSP 90-alpha/0.523
3o6o94MHeat shock protein 83/0.523
2yk2YJXHeat shock protein HSP 90-alpha/0.521
2ykjYKJHeat shock protein HSP 90-alpha/0.518
2ykiYKIHeat shock protein HSP 90-alpha/0.517
1uydPU8Heat shock protein HSP 90-alpha/0.516
2ykbYKBHeat shock protein HSP 90-alpha/0.516
2yjxYJXHeat shock protein HSP 90-alpha/0.514
4hy6FJ1Heat shock protein HSP 90-alpha/0.514
2ykeYKEHeat shock protein HSP 90-alpha/0.513
2yeiXQIHeat shock protein HSP 90-alpha/0.512
4z1fH71Heat shock protein 75 kDa, mitochondrial/0.512
4efuEFUHeat shock protein HSP 90-alpha/0.506
2qg2A91Heat shock protein HSP 90-alpha/0.503
4eftEFTHeat shock protein HSP 90-alpha/0.502
1xddAAYIntegrin alpha-L/0.501
2h55DZ8Heat shock protein HSP 90-alpha/0.501
1dkfBMSRetinoic acid receptor alpha/0.496
2yk2YJWHeat shock protein HSP 90-alpha/0.494
3inxJZCHeat shock protein HSP 90-alpha/0.494
2fwzH71Heat shock protein HSP 90-alpha/0.491
2yee2ECHeat shock protein HSP 90-alpha/0.491
2yejZZ3Heat shock protein HSP 90-alpha/0.491
1uy8PU5Heat shock protein HSP 90-alpha/0.490
1uyfPU1Heat shock protein HSP 90-alpha/0.490
4iarERM5-hydroxytryptamine receptor 1B/0.490
1uykPUXHeat shock protein HSP 90-alpha/0.489
1uyePU9Heat shock protein HSP 90-alpha/0.487
2wi4ZZ4Heat shock protein HSP 90-alpha/0.486
3o0iP54Heat shock protein HSP 90-alpha/0.486
4l8u9AZSerum albumin/0.485
1uycPU7Heat shock protein HSP 90-alpha/0.484
1uyhPU0Heat shock protein HSP 90-alpha/0.482
3hz142CHeat shock protein HSP 90-alpha/0.482
1uy9PU6Heat shock protein HSP 90-alpha/0.481
2wi72KLHeat shock protein HSP 90-alpha/0.481
4j6bPLOCytochrome P450 monooxygenase/0.481
4p9dTMPDeoxycytidylate deaminase/0.481
3inwJZBHeat shock protein HSP 90-alpha/0.480
3qdd94MHeat shock protein HSP 90-alpha/0.479
3hz137DHeat shock protein HSP 90-alpha/0.477
4nh82LCHeat shock protein HSP 90-alpha/0.477
1og5SWFCytochrome P450 2C9/0.475
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.475
2zevB71Geranylgeranyl pyrophosphate synthase/0.475
3ft8MOJHeat shock protein HSP 90-alpha/0.474
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.474
4bqg50QHeat shock protein HSP 90-alpha/0.473
4j6dTESCytochrome P450 monooxygenase/0.473
4nb6444Nuclear receptor ROR-gamma/0.473
4oztP1AEcdysone receptor, putative/0.473
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.472
4c717RD3-oxoacyl-ACP synthase/0.472
5bp9SAHPutative methyltransferase protein/0.471
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.470
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.470
3cxhSMACytochrome b/0.469
3eel53TUncharacterized protein/0.469
4i8vBHFCytochrome P450 1A11.14.14.10.469
4itmATPTetraacyldisaccharide 4'-kinase/0.469
1diuBDMDihydrofolate reductase1.5.1.30.468
3bfa9ODOdorant binding protein ASP1/0.468
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.468
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.468
4j6cSTRCytochrome P450 monooxygenase/0.468
1kyoSMACytochrome b/0.467
3t37FADPyridoxine 4-oxidase/0.467
1disBDMDihydrofolate reductase1.5.1.30.466
3ar6TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.466
3q0gBCOProbable enoyl-CoA hydratase echA84.2.1.170.466
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.466
4y8wSTRSteroid 21-hydroxylase/0.466
3junAKDPhenazine biosynthesis protein A/B/0.465
2uxoTACHTH-type transcriptional regulator TtgR/0.463
3bfb9ODPheromone-binding protein ASP1/0.463
3fhxPXLPyridoxal kinase2.7.1.350.463
3sa27DRDihydrofolate reductase/0.463
1q5dEPBEpothilone C/D epoxidase1.140.462
2bu9HFVIsopenicillin N synthase1.21.3.10.462
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.462
4ktl1CQCytochrome P450/0.462
1ml6GBXGlutathione S-transferase A22.5.1.180.461
2o7pNAPRiboflavin biosynthesis protein RibD/0.461
2opsHBQGag-Pol polyprotein2.7.7.490.461
2yiuSMACytochrome b/0.461
4bb5HD2Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.461
4bgiI4IEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.461
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.461
4ele31IDihydrofolate reductase/0.461
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.460
1fm4DXCMajor pollen allergen Bet v 1-L/0.459
3cseN22Uncharacterized protein/0.459
3cx5SMACytochrome b/0.459
3d75NBBPheromone-binding protein ASP1/0.459
3p9tTCLRepressor/0.459
3qrwNDPPutative ketoacyl reductase1.3.10.459
1pkfEPDEpothilone C/D epoxidase1.140.458
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.458
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.458
1zgaHMKIsoflavone 4'-O-methyltransferase/0.457
3lu8IQXSerum albumin/0.457
3vt65YIVitamin D3 receptor/0.457
3vtbTKAVitamin D3 receptor/0.457
4lt63ATPoly(A) polymerase gamma2.7.7.190.457
1uyiPUZHeat shock protein HSP 90-alpha/0.456
1x8lOXRRetinol dehydratase/0.456
1xuoLA1Integrin alpha-L/0.456
1zw9H64ATP-dependent molecular chaperone HSP82/0.456
1w4zNAPPutative ketoacyl reductase1.3.10.455
2ejvNADL-threonine 3-dehydrogenase/0.455
3bxxQUEDihydroflavonol 4-reductase1.1.1.2190.455
3c3dFO12-phospho-L-lactate transferase/0.455
3dxjNE6DNA-directed RNA polymerase subunit beta/0.455
3dxjNE6DNA-directed RNA polymerase subunit beta'/0.455
3uwlFOZThymidylate synthase/0.455
4g48PZBMycocyclosin synthase1.14.21.90.455
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.454
3r4nFU5Heat shock protein HSP 90-alpha/0.454
4l9q9TPSerum albumin/0.454
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.453
1pqc444Oxysterols receptor LXR-beta/0.453
1s9pDESEstrogen-related receptor gamma/0.453
3p6nDSOCamphor 5-monooxygenase1.14.15.10.453
3s1cZIRCytokinin dehydrogenase 11.5.99.120.453
3w5p4OAVitamin D3 receptor/0.453
4awp99AHeat shock protein HSP 90-alpha/0.453
4elb34RDihydrofolate reductase/0.453
4g34924Eukaryotic translation initiation factor 2-alpha kinase 32.7.11.10.453
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.453
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1bk0ACVIsopenicillin N synthase1.21.3.10.452
1ci7UMPThymidylate synthase2.1.1.450.452
1enzNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.452
2iwuNP5ATP-dependent molecular chaperone HSP82/0.452
3h3r14HCollagen type IV alpha-3-binding protein/0.452
3invNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
3irn1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.452
3pehIBDEndoplasmin homolog, putative/0.452
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.452
4em9TCEPeroxisome proliferator-activated receptor gamma/0.452
4iaq2GM5-hydroxytryptamine receptor 1B/0.452
4kwhNAPReductase homolog/0.452
1enyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
2hm9TRRDihydrofolate reductase1.5.1.30.451
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.451
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.451
3glmCOOGlutaconyl-CoA decarboxylase alpha subunit/0.451
3tkyN7I(Iso)eugenol O-methyltransferase2.1.1.1460.451
3wv9FEGHmd co-occurring protein HcgE/0.451
4dsbA8SAbscisic acid receptor PYL3/0.451
3gwfNAPCyclohexanone monooxygenase/0.450
3vt5YI2Vitamin D3 receptor/0.450
3wfjNAD2-dehydropantoate 2-reductase/0.450
4as94QSATP-dependent molecular chaperone HSP82/0.450
4g1z0VPVitamin D3 receptor A/0.450
4nmbFADBifunctional protein PutA/0.450
4rh10TTSpore photoproduct lyase/0.450
1towCRZFatty acid-binding protein, adipocyte/0.449
2e9dB76Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.449
2iviACWIsopenicillin N synthase1.21.3.10.449
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.449
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.449
3h18PMSEsterase/lipase/0.449
3r9dX6BCyclin-dependent kinase 22.7.11.220.449
4boeCLRJapanin/0.449
4fehFADDecaprenylphosphoryl-beta-D-ribose oxidase/0.449
4ia1BIVVitamin D3 receptor A/0.449
4ldkFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.449
4xuhSFIPeroxisome proliferator-activated receptor gamma/0.449
1bvrTHTEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
1tg56454-hydroxyphenylpyruvate dioxygenase1.13.11.270.448
2h9iEADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
3cppCAMCamphor 5-monooxygenase1.14.15.10.448
3tguWF3Cytochrome b/0.448
4eoi1ROCyclin-dependent kinase 22.7.11.220.448
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.448
5uviZMAAdenosine receptor A2a/0.448
3pwhZMAAdenosine receptor A2a/0.448
3rfmCFFAdenosine receptor A2a/0.448
1fmjRTLRetinol dehydratase/0.447
1re9DSOCamphor 5-monooxygenase1.14.15.10.447
2zl9VDAVitamin D3 receptor/0.447
3mg3ECHOrange carotenoid-binding protein/0.447
3w0hW12Vitamin D3 receptor/0.447
4a83DXCMajor pollen allergen Bet v 1-A/0.447
4a84DXCMajor pollen allergen Bet v 1-A/0.447
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4elg52JDihydrofolate reductase/0.447
4ktf1TMCytochrome P450/0.447
5dhgDGVNociceptin receptor/0.447
1pq944BOxysterols receptor LXR-beta/0.446
1y4sADPChaperone protein HtpG/0.446
2zb8IMNProstaglandin reductase 21.3.1.480.446
3eek53SUncharacterized protein/0.446
3oezSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.446
3tm5SFGUncharacterized protein/0.446
4asg814ATP-dependent molecular chaperone HSP82/0.446
4bfuZVUPantothenate kinase2.7.1.330.446
4bgiNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
4dscA8SAbscisic acid receptor PYL3/0.446
4g95OAGDihydrofolate reductase1.5.1.30.446
4gncASORegucalcin3.1.1.170.446
4iq71G9Mycocyclosin synthase1.14.21.90.446
4jaqCOAAlpha-pyrone synthesis polyketide synthase-like Pks112.3.10.446
4je5PLPAromatic/aminoadipate aminotransferase 12.6.1.390.446
4qo9627Serine/threonine-protein kinase 242.7.11.10.446
5cp8TCUEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
1hb1OCVIsopenicillin N synthase1.21.3.10.445
1sozVAL_TYR_GLN_PHESerine endoprotease DegS3.4.21.1070.445
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.445
3crzFADFerredoxin--NADP+ reductase/0.445
3g70A5TRenin3.4.23.150.445
3nr4PYVAbscisic acid receptor PYL2/0.445
3q3cNADNAD-dependent L-serine dehydrogenase/0.445
4cax646Glycylpeptide N-tetradecanoyltransferase2.3.1.970.445
4j4vSVRNucleocapsid protein/0.445
4tzt468Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.444
2ev9NAPShikimate dehydrogenase (NADP(+))/0.444
2jb4A14Isopenicillin N synthase1.21.3.10.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3bheBZNGag-Pol polyprotein3.4.23.160.444
3vnt0JAVascular endothelial growth factor receptor 22.7.10.10.444
4g47TZFMycocyclosin synthase1.14.21.90.444
4jlj1NMDeoxycytidine kinase2.7.1.740.444
3reyXACAdenosine receptor A2a/0.444
3uzaT4GAdenosine receptor A2a/0.444
1dhjMTXDihydrofolate reductase1.5.1.30.443
1ek2CDUBifunctional epoxide hydrolase 2/0.443
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.443
1fmlRTLRetinol dehydratase/0.443
1n4hREANuclear receptor ROR-beta/0.443
1uumAFIDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.443
1uzwCDHIsopenicillin N synthase1.21.3.10.443
3eigMTXDihydrofolate reductase1.5.1.30.443
3l0lHC3Nuclear receptor ROR-gamma/0.443
3nglNAPBifunctional protein FolD/0.443
3njoPYVAbscisic acid receptor PYR1/0.443
3p6mDSOCamphor 5-monooxygenase1.14.15.10.443
3reoEUG(Iso)eugenol O-methyltransferase2.1.1.1460.443
3stv3HOMethylketone synthase I/0.443
4awo99BHeat shock protein HSP 90-alpha/0.443
1ai9NDPDihydrofolate reductase1.5.1.30.442
1bzfTMQDihydrofolate reductase1.5.1.30.442
1p7tACOMalate synthase G/0.442
1sm2STUTyrosine-protein kinase ITK/TSK2.7.10.20.442
2bx8AZQSerum albumin/0.442
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.442
2qjySMACytochrome b/0.442
2rqfJH3Hemolymph juvenile hormone binding protein/0.442
2vn0TDZCytochrome P450 2C8/0.442
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.442
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.442
4fhf0TTSpore photoproduct lyase/0.442
4qysPLRTryptophan synthase beta chain 24.2.1.200.442
1ep4S11Gag-Pol polyprotein2.7.7.490.441
1n83CLRNuclear receptor ROR-alpha/0.441
1sr7MOFProgesterone receptor/0.441
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.441
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.441
2hw2RFPRifampin ADP-ribosyl transferase/0.441
2jblSMAReaction center protein L chain/0.441
2po7CHDFerrochelatase, mitochondrial4.99.1.10.441
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.441
2vcmM11Isopenicillin N synthase1.21.3.10.441
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.441
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.441
3td8D2RDihydrofolate reductase1.5.1.30.441
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.441
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
4l0qNADAlcohol dehydrogenase class-3/0.441
4o7uTHFThymidylate synthase/0.441
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
5dp2NAPCurF/0.441
5jsfNAD17-beta-hydroxysteroid dehydrogenase 141.1.10.441
1crbRTLRetinol-binding protein 1/0.440
1o5rFR9Adenosine deaminase3.5.4.40.440
1oqcFADFAD-linked sulfhydryl oxidase ALR1.8.3.20.440
1rftPXMPyridoxal kinase2.7.1.350.440
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.440
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.440
2wpwACOOrf14/0.440
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.440
3dhoB2MStreptogramin A acetyltransferase2.3.10.440
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
3fwjCAMCamphor 5-monooxygenase1.14.15.10.440
3nguADPNucleoside diphosphate kinase/0.440
4dhyS41Glucokinase2.7.1.20.440
4iui1GQEstrogen receptor/0.440
4q0a4OAVitamin D3 receptor A/0.440
5ahkTPPAcetolactate synthase II, large subunit/0.440