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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
2xtoGDPGTPase IMAP family member 2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2xtoGDPGTPase IMAP family member 2/1.000
2vbpVB1Isopenicillin N synthase1.21.3.10.490
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.486
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.484
3bb3GDPTranslocase of chloroplast 33, chloroplastic3.6.50.479
3oibFDAPutative acyl-CoA dehydrogenase/0.478
2gjnFMNNitronate monooxygenase1.13.12.160.476
2xtnGTPGTPase IMAP family member 2/0.473
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.472
1aj22PHDihydropteroate synthase/0.471
1rbyGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.470
4fc7NAPPeroxisomal 2,4-dienoyl-CoA reductase1.3.1.340.470
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.470
2y60M8FIsopenicillin N synthase1.21.3.10.469
3g45988cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.469
2p5uNADUDP-glucose 4-epimerase/0.468
1rbzKT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.467
3e8xNAPBH1520 protein/0.467
2bu9HFVIsopenicillin N synthase1.21.3.10.466
2vcmM11Isopenicillin N synthase1.21.3.10.466
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
1cg6MTAS-methyl-5'-thioadenosine phosphorylase/0.465
3t4nADP5'-AMP-activated protein kinase subunit gamma/0.465
1a4iNDPC-1-tetrahydrofolate synthase, cytoplasmic1.5.1.50.464
2gmhFADElectron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial1.5.5.10.464
2r26CMCCitrate synthase2.3.3.160.464
2ed3SAHDiphthine synthase/0.463
2givACOHistone acetyltransferase KAT8/0.463
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
1menGARTrifunctional purine biosynthetic protein adenosine-32.1.2.20.462
2fznFADBifunctional protein PutA1.5.5.20.462
4z63ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.462
3uwlFOZThymidylate synthase/0.461
4z24FADPutative GMC-type oxidoreductase R13510.461
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.460
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.459
1njsKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.459
1z7yAA5Cysteine synthase 12.5.1.470.459
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.459
2a1mCAMCamphor 5-monooxygenase1.14.15.10.458
2cahNDPCatalase1.11.1.60.458
3g1oRF1HTH-type transcriptional regulator EthR/0.458
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.458
3q3cNADNAD-dependent L-serine dehydrogenase/0.458
1eh4IC1Casein kinase I homolog 12.7.11.10.457
2bglNAJSecoisolariciresinol dehydrogenase1.1.1.3310.457
2iviACWIsopenicillin N synthase1.21.3.10.457
3aw9NADNAD-dependent epimerase/dehydratase/0.457
4q73FADBifunctional protein PutA/0.457
5dozNDPJamJ/0.457
1txzAPRProbable ADP-ribose 1''-phosphate phosphatase YML087W3.1.3.840.456
1yb5NAPQuinone oxidoreductase1.6.5.50.456
2aa0MTPAdenosine kinase2.7.1.200.456
4rgqNDPGlycerol-1-phosphate dehydrogenase [NAD(P)+]/0.456
4u0mGTPCyclic GMP-AMP synthase/0.456
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.455
1qrpHH0Pepsin A-43.4.23.10.455
1tl7ONMAdenylate cyclase type 2/0.455
1tl7ONMAdenylate cyclase type 5/0.455
1vsvNADGlyceraldehyde-3-phosphate dehydrogenase/0.455
2ftoCB3Thymidylate synthase/0.455
3w8fNAD3-hydroxybutyrate dehydrogenase/0.455
3zkyWT4Isopenicillin N synthase1.21.3.10.455
4jqh1MFAlr2278 protein/0.455
5a3bAPRSIR2 family protein/0.455
1osvCHCBile acid receptor/0.454
1pmv537Mitogen-activated protein kinase 102.7.11.240.454
3a1nNADNDP-sugar epimerase/0.454
4yaiNAIC alpha-dehydrogenase/0.454
1bk0ACVIsopenicillin N synthase1.21.3.10.453
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.453
2hq9FADMll6688 protein/0.453
2xvw9NRSerum albumin/0.453
3mgdACOPredicted acetyltransferase/0.453
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.453
5fm7ADPRuvB-like helicase/0.453
1lsjNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
1obnASVIsopenicillin N synthase1.21.3.10.452
1uzwCDHIsopenicillin N synthase1.21.3.10.452
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.452
3ad9NADSubunit alpha of sarocosine oxidase/0.452
3anmSYD1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.452
3btsNADGalactose/lactose metabolism regulatory protein GAL80/0.452
3pqbVGPPutative oxidoreductase/0.452
4qaiFMNNADPH dehydrogenase/0.452
1o76CAMCamphor 5-monooxygenase1.14.15.10.451
2hqpNDPDihydrofolate reductase1.5.1.30.451
2jb4A14Isopenicillin N synthase1.21.3.10.451
3h5sH5SGenome polyprotein2.7.7.480.451
3zu2NAIEnoyl-[acyl-carrier-protein] reductase [NADH]/0.451
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.451
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.450
1pr9NAPL-xylulose reductase1.1.1.100.450
1tj0FADBifunctional protein PutA1.5.5.20.450
1z6tADPApoptotic protease-activating factor 1/0.450
2ylzFADPhenylacetone monooxygenase1.14.13.920.450
4knzCB3Thymidylate synthase/0.450
4l4aCAMCamphor 5-monooxygenase1.14.15.10.450
4l4bCAMCamphor 5-monooxygenase1.14.15.10.450
1a59COA2-methylcitrate synthase/0.449
1ae1NAPTropinone reductase 1/0.449
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.449
1ju9NADAlcohol dehydrogenase E chain1.1.1.10.449
1me6IVSPlasmepsin-23.4.23.390.449
1psa0ZLPepsin A3.4.23.10.449
1qjfACSIsopenicillin N synthase1.21.3.10.449
2c59NADGDP-mannose 3,5-epimerase5.1.3.180.449
2feuCAMCamphor 5-monooxygenase1.14.15.10.449
2j3jHC4NADPH-dependent oxidoreductase 2-alkenal reductase1.3.1.740.449
2rehFADNitroalkane oxidase1.7.3.10.449
3r9uFADThioredoxin reductase/0.449
3rsrN5PRibonucleoside-diphosphate reductase large chain 11.17.4.10.449
4gs4ACOAlpha-tubulin N-acetyltransferase 1/0.449
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.449
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.449
1b16NAQAlcohol dehydrogenase1.1.1.10.448
1kquBR4Phospholipase A2, membrane associated/0.448
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.448
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.448
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.448
3kpkFADSulfide-quinone reductase/0.448
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
3wv9FEGHmd co-occurring protein HcgE/0.448
4boyNADGlyceraldehyde-3-phosphate dehydrogenase/0.448
4fj0NAP17beta-hydroxysteroid dehydrogenase/0.448
4if5ACOAlpha-tubulin N-acetyltransferase 1/0.448
4qysPLRTryptophan synthase beta chain 24.2.1.200.448
4rvnCOAPhenylacetate-coenzyme A ligase/0.448
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.447
1jnzFADAdenylylsulfate reductase, subunit A (AprA)/0.447
1pq944BOxysterols receptor LXR-beta/0.447
1rszDIHPurine nucleoside phosphorylase2.4.2.10.447
1u4oNDDL-lactate dehydrogenase1.1.1.270.447
1vi0DCCFatty acid metabolism regulator protein/0.447
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.447
2gjlFMNNitronate monooxygenase1.13.12.160.447
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.447
3ds6A17Mitogen-activated protein kinase 14/0.447
3g0eB49Mast/stem cell growth factor receptor Kit2.7.10.10.447
3o3jBB4Peptide deformylase 1B, chloroplastic/mitochondrial3.5.1.880.447
3qfaFADThioredoxin reductase 1, cytoplasmic1.8.1.90.447
4aw1ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.447
4ienCOAPutative acyl-CoA hydrolase/0.447
4l8u9AZSerum albumin/0.447
1mjaCOAHistone acetyltransferase ESA1/0.446
1qiqACCIsopenicillin N synthase1.21.3.10.446
1ykfNAPNADP-dependent isopropanol dehydrogenase1.1.1.800.446
2a0wDIHPurine nucleoside phosphorylase2.4.2.10.446
2in6839Wee1-like protein kinase2.7.10.20.446
2xvv9DNSerum albumin/0.446
3bbtFMMReceptor tyrosine-protein kinase erbB-42.7.10.10.446
3ggoNAIPrephenate dehydrogenase/0.446
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.446
3l0lHC3Nuclear receptor ROR-gamma/0.446
3p62FMNPentaerythritol tetranitrate reductase/0.446
4b4w9L9Bifunctional protein FolD/0.446
4fhd0TTSpore photoproduct lyase/0.446
4i02CMPcAMP-activated global transcriptional regulator CRP/0.446
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.446
1dbvNADGlyceraldehyde-3-phosphate dehydrogenase/0.445
1knrFADL-aspartate oxidase1.4.3.160.445
1rbqKEUTrifunctional purine biosynthetic protein adenosine-32.1.2.20.445
1rc0KT5Trifunctional purine biosynthetic protein adenosine-32.1.2.20.445
1rx5DDFDihydrofolate reductase1.5.1.30.445
1t88CAMCamphor 5-monooxygenase1.14.15.10.445
2fjdSFDAdenylylsulfate reductase, subunit A (AprA)/0.445
3bnkFMNFlavoredoxin/0.445
3e2sFADBifunctional protein PutA1.5.5.20.445
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.445
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.445
4l4xNDPAmphI/0.445
5kgjACOPredicted acetyltransferase/0.445
1dz6CAMCamphor 5-monooxygenase1.14.15.10.444
2dwbANPAurora kinase A2.7.11.10.444
2oj9BMIInsulin-like growth factor 1 receptor2.7.10.10.444
2vmyFFOSerine hydroxymethyltransferase/0.444
2y6fM9FIsopenicillin N synthase1.21.3.10.444
3frqERYErythromycin resistance repressor protein/0.444
3fznD7KBenzoylformate decarboxylase4.1.1.70.444
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.444
3upf0BUPolyprotein/0.444
3vt7VDXVitamin D3 receptor/0.444
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.444
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.444
1ib6NADMalate dehydrogenase/0.443
1iwiCAMCamphor 5-monooxygenase1.14.15.10.443
1mewXMPInosine-5'-monophosphate dehydrogenase/0.443
1xq6NAPUncharacterized protein At5g02240/0.443
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.443
2o23NAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.443
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.443
2y0mACOHistone acetyltransferase KAT8/0.443
3a20FMNFMN-binding protein/0.443
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.443
3mjhGTPRas-related protein Rab-5A/0.443
3nmpPYVAbscisic acid receptor PYL2/0.443
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.443
3vdqNAD3-hydroxybutyrate dehydrogenase/0.443
4g2fC07Ephrin type-A receptor 32.7.10.10.443
4g3rCAMCamphor 5-monooxygenase1.14.15.10.443
4iah1DXAlr2278 protein/0.443
4l17DNQGlutamate receptor 2/0.443
1blzACVIsopenicillin N synthase1.21.3.10.442
1mg5NAIAlcohol dehydrogenase1.1.1.10.442
1ygjRMCPyridoxal kinase2.7.1.350.442
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
2hr8SAHDiphthine synthase/0.442
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.442
2yphQQY2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3eluSAMMethyltransferase/0.442
3gncQQQGlutaryl-CoA dehydrogenase/0.442
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.442
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
3sdkP3NProteasome subunit beta type-53.4.25.10.442
3sdkP3NProteasome subunit beta type-63.4.25.10.442
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.442
4aotGW8Serine/threonine-protein kinase 102.7.11.10.442
4dh60KNBeta-secretase 13.4.23.460.442
4fmxCNL1,8-cineole 2-endo-monooxygenase1.14.13.1560.442
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.442
4opiFDAConserved Archaeal protein/0.442
4xvqGNPGTPase HRas/0.442
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.442
5lc1NADL-threonine 3-dehydrogenase/0.442
1e5qNDPSaccharopine dehydrogenase [NADP(+), L-glutamate-forming]1.5.1.100.441
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.441
1ja0NAPNADPH--cytochrome P450 reductase/0.441
1n5dNDPCarbonyl reductase [NADPH] 1/0.441
1xelUPGUDP-glucose 4-epimerase5.1.3.20.441
2b7aIZATyrosine-protein kinase JAK2/0.441
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.441
2ew5Y12Peptide deformylase/0.441
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.441
3w0gW07Vitamin D3 receptor/0.441
3zoiM2WIsopenicillin N synthase1.21.3.10.441
4b3aTACTetracycline repressor protein class D/0.441
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.441
4hjoAQ4Epidermal growth factor receptor2.7.10.10.441
4y35F90Endothiapepsin3.4.23.220.441
4zj8SUVOrexin receptor type 1/0.441
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.440
1flmFMNFMN-binding protein/0.440
1iwjCAMCamphor 5-monooxygenase1.14.15.10.440
1u80C5PCoenzyme A biosynthesis bifunctional protein CoaBC6.3.2.50.440
1yjqNAP2-dehydropantoate 2-reductase1.1.1.1690.440
2fzmFADBifunctional protein PutA1.5.5.20.440
2w9hTOPDihydrofolate reductase1.5.1.30.440
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.440
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.440
3eigMTXDihydrofolate reductase1.5.1.30.440
3i59N6SCRP-like cAMP-activated global transcriptional regulator/0.440
3nxxNDPDihydrofolate reductase1.5.1.30.440
3oquA8SAbscisic acid receptor PYL9/0.440
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.440
4dc0NDPPutative ketoacyl reductase1.3.10.440
4do30LAFatty-acid amide hydrolase 13.5.1.990.440
4ubvCOASteroid 3-ketoacyl-CoA thiolase/0.440