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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
1olsTDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.4

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1olsTDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.41.000
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.512
2vcmM11Isopenicillin N synthase1.21.3.10.505
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.501
1pdhFASp-hydroxybenzoate hydroxylase/0.494
4c7xTPPTransketolase/0.490
3tm5SFGUncharacterized protein/0.487
4fhd0TTSpore photoproduct lyase/0.486
2ihvTPPN(2)-(2-carboxyethyl)arginine synthase/0.484
4zz7NADMethylmalonate-semialdehyde dehydrogenase/0.484
2nnqT4BFatty acid-binding protein, adipocyte/0.482
2vbdV10Isopenicillin N synthase1.21.3.10.482
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.481
3aezGDPPantothenate kinase2.7.1.330.479
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.479
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.479
1v11TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.478
2xvv9DNSerum albumin/0.478
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.478
3ddw055Glycogen phosphorylase, liver form2.4.1.10.477
3h03UBPGlutamate receptor 2/0.477
4isuIKMGlutamate receptor 2/0.477
1rr6IMHPurine nucleoside phosphorylase2.4.2.10.476
2bjaNAD1-pyrroline-5-carboxylate dehydrogenase/0.476
3h4vDVPPteridine reductase 11.5.1.330.476
4dpy2P0Mevalonate diphosphate decarboxylase/0.476
4tleAGSCircadian clock protein kinase KaiC2.7.11.10.476
2j4kU5PUridylate kinase2.7.4.220.475
2ehqNAP1-pyrroline-5-carboxylate dehydrogenase/0.474
3m0eATPTranscriptional regulator (NtrC family)/0.474
2z4sADPChromosomal replication initiator protein DnaA/0.473
4ffrATPUncharacterized protein/0.473
1aj22PHDihydropteroate synthase/0.472
1lb9DNQGlutamate receptor 2/0.472
1qxoFMNChorismate synthase/0.472
3zhvTDWMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.472
5c80URIUridine phosphorylase/0.472
3mnrSD1Heat shock protein HSP 90-alpha/0.471
5aqzSGVHeat shock 70 kDa protein 1A/0.471
2zsaADPPantothenate kinase2.7.1.330.470
2qxxTTPdCTP deaminase3.5.4.130.469
4cukNAID-lactate dehydrogenase/0.469
1rzuADPGlycogen synthase 12.4.1.210.468
2i1m5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.468
2yk2YJWHeat shock protein HSP 90-alpha/0.468
3aheTHDProbable phosphoketolase/0.468
3ahjTPPProbable phosphoketolase/0.468
4dymIYZActivin receptor type-12.7.11.300.468
2pbzATPUncharacterized protein/0.467
2i0v6C3Macrophage colony-stimulating factor 1 receptor2.7.10.10.466
2iorADPChaperone protein HtpG/0.466
5iotUMPFlavin-dependent thymidylate synthase2.1.1.1480.466
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.465
1i5cADPChemotaxis protein CheA2.7.13.30.465
2yeiXQIHeat shock protein HSP 90-alpha/0.465
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.465
3beaIXHMacrophage colony-stimulating factor 1 receptor2.7.10.10.465
4b78KGGBeta-secretase 13.4.23.460.465
4f3gKAIGlutamate receptor 3/0.465
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
2bxmIMNSerum albumin/0.464
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.464
3ahiHTLProbable phosphoketolase/0.464
3ghh2NFCD38 molecule/0.464
4tldAGSCircadian clock protein kinase KaiC2.7.11.10.464
4pt3NDPAldehyde dehydrogenase/0.463
1fmjRTLRetinol dehydratase/0.462
1z5aADPType 2 DNA topoisomerase 6 subunit B/0.462
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.462
2ojg19AMitogen-activated protein kinase 12.7.11.240.462
2ylwNAPPhenylacetone monooxygenase1.14.13.920.462
3qiyQI1Botulinum neurotoxin type A3.4.24.690.462
4ycoFMNtRNA-dihydrouridine(16) synthase/0.462
1dqaCOA3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.461
3otwCOAPhosphopantetheine adenylyltransferase/0.461
4em3FADCoenzyme A disulfide reductase/0.461
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.459
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
2b8jADNClass B acid phosphatase3.1.3.20.459
2bxqIMNSerum albumin/0.459
2jfz003Glutamate racemase/0.459
2x1eX1EAcyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form2.3.1.1640.459
3junAJDPhenazine biosynthesis protein A/B/0.459
3o6o94MHeat shock protein 83/0.459
4bfvZVVPantothenate kinase2.7.1.330.459
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.459
4qa0SHHHistone deacetylase 83.5.1.980.459
1e94ANPATP-dependent protease ATPase subunit HslU/0.458
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.458
1krhFADBenzoate 1,2-dioxygenase electron transfer component1.18.1.30.458
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.458
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.458
4bb6HD1Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.458
4bfzZVZPantothenate kinase2.7.1.330.458
1i5bANPChemotaxis protein CheA2.7.13.30.457
3h65I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.457
2fhnBNIAvidin-related protein 4/5/0.456
2qc8ADPGlutamine synthetase6.3.1.20.456
2ylrNAPPhenylacetone monooxygenase1.14.13.920.456
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.456
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.455
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.455
2xf3J01Uncharacterized protein/0.455
3hz142CHeat shock protein HSP 90-alpha/0.455
4yaf2AMNADPH--cytochrome P450 reductase/0.455
1blzACVIsopenicillin N synthase1.21.3.10.454
1qm5PLPMaltodextrin phosphorylase2.4.1.10.454
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.454
2b56UTPRNA editing complex protein MP57/0.454
2cmoM1LGlutamate receptor 2/0.454
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.454
2y6o1N1Ephrin type-A receptor 42.7.10.10.454
3cehAVEGlycogen phosphorylase, liver form2.4.1.10.454
3fmz2T1Retinol-binding protein 4/0.454
3qvrFADGlucose oxidase1.1.3.40.454
3znsNU7Histone deacetylase 73.5.1.980.454
4eftEFTHeat shock protein HSP 90-alpha/0.454
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
1oc1ASVIsopenicillin N synthase1.21.3.10.453
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.453
2j40NAD1-pyrroline-5-carboxylate dehydrogenase/0.453
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
2wo7ASVIsopenicillin N synthase1.21.3.10.453
3b9lAZZSerum albumin/0.453
3dds26BGlycogen phosphorylase, liver form2.4.1.10.453
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.453
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.453
3nf8CDQGag-Pol polyprotein/0.453
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4oviN01Phenylacetone monooxygenase1.14.13.920.453
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.453
4yx6FMNOmega-3 polyunsaturated fatty acid synthase subunit PfaD/0.453
1odnAPVIsopenicillin N synthase1.21.3.10.452
2eitNAD1-pyrroline-5-carboxylate dehydrogenase/0.452
2vbpVB1Isopenicillin N synthase1.21.3.10.452
2wi72KLHeat shock protein HSP 90-alpha/0.452
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.452
3qizQI2Botulinum neurotoxin type A3.4.24.690.452
1ay0TPPTransketolase 12.2.1.10.451
1crbRTLRetinol-binding protein 1/0.451
1ri1GTGmRNA cap guanine-N7 methyltransferase2.1.1.560.451
2bfaCB3Pteridine reductase 11.5.1.330.451
2ejzSAHDiphthine synthase/0.451
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.451
2zs8ADPPantothenate kinase2.7.1.330.451
3e23SAMUncharacterized protein/0.451
3f47I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.451
3imgBZ2Pantothenate synthetase6.3.2.10.451
4jdcNADProbable pyrroline-5-carboxylate dehydrogenase RocA/0.451
4l04NAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.451
1i5aACPChemotaxis protein CheA2.7.13.30.450
1r2jFADFkbI/0.450
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.450
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.450
2xlsNAPPutative flavin-containing monooxygenase/0.450
2yejXQKHeat shock protein HSP 90-alpha/0.450
3gtsD3MDdmC/0.450
3il4ACO3-oxoacyl-[acyl-carrier-protein] synthase 3/0.450
3lnmNAPVoltage-gated potassium channel subunit beta-2/0.450
3o0iP54Heat shock protein HSP 90-alpha/0.450
4awo99BHeat shock protein HSP 90-alpha/0.450
4blcNDPCatalase1.11.1.60.450
4h6pFMNChromate reductase/0.450
4nh82LCHeat shock protein HSP 90-alpha/0.450
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.450
1g41ADPATP-dependent protease ATPase subunit HslU/0.449
2puiADPMethylthioribose kinase2.7.1.1000.449
2xgoZKDUncharacterized protein/0.449
2yejZZ3Heat shock protein HSP 90-alpha/0.449
3adaNADSubunit alpha of sarocosine oxidase/0.449
3c9sACPThiamine-monophosphate kinase/0.449
3ipkPMSSurface protein adhesin/0.449
3ojiPYVAbscisic acid receptor PYL3/0.449
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.449
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.449
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.449
4gi40EXQueuine tRNA-ribosyltransferase2.4.2.290.449
5dstSAHProtein arginine N-methyltransferase 82.1.10.449
1kmyBPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.448
2b82ADNClass B acid phosphatase3.1.3.20.448
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.448
2fjeFADAdenylylsulfate reductase, subunit A (AprA)/0.448
2qo9ANPEphrin type-A receptor 32.7.10.10.448
2yee2ECHeat shock protein HSP 90-alpha/0.448
2zs9ADPPantothenate kinase2.7.1.330.448
3i0pNADMalate dehydrogenase, putative/0.448
3ia4MTXDihydrofolate reductase/0.448
3qdd94MHeat shock protein HSP 90-alpha/0.448
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.448
4dbw511Aldo-keto reductase family 1 member C3/0.448
4uz6SCRPalmitoleoyl-protein carboxylesterase NOTUM/0.448
5dozNDPJamJ/0.448
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.447
2fpcSCGStrictosidine synthase4.3.3.20.447
2gesCOKPantothenate kinase2.7.1.330.447
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
4yekTHMThymidine phosphorylase/0.447
1ftlDNQGlutamate receptor 2/0.446
1i58ACPChemotaxis protein CheA2.7.13.30.446
1kqgMGDFormate dehydrogenase, nitrate-inducible, major subunit1.1.5.60.446
1ykdCMPAdenylate cyclase/0.446
2bu9HFVIsopenicillin N synthase1.21.3.10.446
2cibCM6Lanosterol 14-alpha demethylase1.14.13.700.446
2y6fM9FIsopenicillin N synthase1.21.3.10.446
2yk2YJXHeat shock protein HSP 90-alpha/0.446
3cr0809Wee1-like protein kinase2.7.10.20.446
3elePLPAminotransferase/0.446
3hdqGDUUDP-galactopyranose mutase/0.446
3l9nL9NcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.446
4dptAGSMevalonate diphosphate decarboxylase/0.446
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.446
4y6nUPGGlucosyl-3-phosphoglycerate synthase2.4.1.2660.446
1e92HBIPteridine reductase 11.5.1.330.445
1fwmCB3Thymidylate synthase/0.445
1i59ADPChemotaxis protein CheA2.7.13.30.445
3dd125DGlycogen phosphorylase, liver form2.4.1.10.445
3hkoANPCalcium/calmodulin-dependent protein kinase with a kinase domain and 2 calmodulin-like EF hands/0.445
4qa2SHHHistone deacetylase 83.5.1.980.445
5gcnCOAHAT A1/0.445
1kekHTLPyruvate synthase/0.444
1ypkCCRProthrombin3.4.21.50.444
2fk8SAMHydroxymycolate synthase MmaA42.1.10.444
2gjnFMNNitronate monooxygenase1.13.12.160.444
2o7pNAPRiboflavin biosynthesis protein RibD/0.444
2v3wTPPBenzoylformate decarboxylase4.1.1.70.444
2w6pOA4Biotin carboxylase6.3.4.140.444
3gueUPGUTP-glucose-1-phosphate uridylyltransferase 2, putative/0.444
3k8q22APurine nucleoside phosphorylase2.4.2.10.444
3o9pMHIPeriplasmic murein peptide-binding protein/0.444
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4a2aATPCell division protein FtsA/0.444
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.444
4n8iCOAPutative 4-hydroxybutyrate coenzyme A transferase/0.444
1f9aATPNicotinamide-nucleotide adenylyltransferase/0.443
1i59ANPChemotaxis protein CheA2.7.13.30.443
1towCRZFatty acid-binding protein, adipocyte/0.443
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.443
1u9iATPCircadian clock protein kinase KaiC2.7.11.10.443
1vyrFMNPentaerythritol tetranitrate reductase/0.443
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2ehuNAD1-pyrroline-5-carboxylate dehydrogenase/0.443
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2iluNDPLactaldehyde dehydrogenase1.2.1.220.443
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.443
4ixd1HVIntegrin alpha-L/0.443
4u0mGTPCyclic GMP-AMP synthase/0.443
1b87ACOAac(6')-Ii protein/0.442
1d6w00RProthrombin3.4.21.50.442
1efaNPFLactose operon repressor/0.442
1o02NADAldehyde dehydrogenase, mitochondrial1.2.1.30.442
2p6lSAHDiphthine synthase/0.442
3evbSAHGenome polyprotein2.1.1.560.442
3hdyGDUUDP-galactopyranose mutase/0.442
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
4fflADPUncharacterized protein/0.442
4fh5UTPTerminal uridylyltransferase cid1/0.442
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4ri1ACOUDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase2.3.1.2020.442
1enpNADEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.441
1tf7ATPCircadian clock protein kinase KaiC2.7.11.10.441
1xzqFONtRNA modification GTPase MnmE3.6.50.441
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
2xvw9NRSerum albumin/0.441
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
2zzaFOLDihydrofolate reductase/0.441
3arvSAUChitinase A/0.441
3gwfFADCyclohexanone monooxygenase/0.441
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.441
4a33PS8Glycylpeptide N-tetradecanoyltransferase/0.441
4bb3KKAIsopenicillin N synthase1.21.3.10.441
4eqrFADCoenzyme A disulfide reductase/0.441
4ihiNADProbable pyrroline-5-carboxylate dehydrogenase RocA/0.441
4mv1ADPBiotin carboxylase6.3.4.140.441
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.441
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.440
1fxvPNNPenicillin G acylase3.5.1.110.440
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.440
1ja1FADNADPH--cytochrome P450 reductase/0.440
1qzfCB3Bifunctional dihydrofolate reductase-thymidylate synthase/0.440
1x8b824Wee1-like protein kinase2.7.10.20.440
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.440
1yqj6NPMitogen-activated protein kinase 14/0.440
1z6tADPApoptotic protease-activating factor 1/0.440
2ag0TPPBenzaldehyde lyase/0.440
2v5aLZLBiotin carboxylase6.3.4.140.440
3keqNADRedox-sensing transcriptional repressor Rex/0.440
3rl35GPMetallophosphoesterase MPPED23.10.440
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.440
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.440
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.440
4utkFNRXenobiotic reductase/0.440
4uugPXGBranched-chain amino acid aminotransferase, putative/0.440
5c1d12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.440