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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
3gfxC2EUncharacterized protein

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3gfxC2EUncharacterized protein/1.000
3gg1C2EUncharacterized protein/0.569
3gg0C2EUncharacterized protein/0.554
3gfzC2EUncharacterized protein/0.514
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.507
3ujlA8SAbscisic acid receptor PYL2/0.505
1itzTPPTransketolase, chloroplastic2.2.1.10.504
2q7gCCLPyrrolysine--tRNA ligase/0.503
1hfpMOTDihydrofolate reductase1.5.1.30.498
2zcePYLPyrrolysine--tRNA ligase/0.498
3negPYVAbscisic acid receptor PYL1/0.497
4ds8A8SAbscisic acid receptor PYL3/0.496
4lg5A1OAbscisic acid receptor PYL2/0.496
3zvuA8SAbscisic acid receptor PYR1/0.492
3ow3SMYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.490
4m2xTMQDihydrofolate reductase1.5.1.30.486
3uudESTEstrogen receptor/0.484
2uw5GVNcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.482
1towCRZFatty acid-binding protein, adipocyte/0.481
2vo0M03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.481
1hfqMOTDihydrofolate reductase1.5.1.30.480
1nd52BFProstatic acid phosphatase3.1.3.20.480
4lgaA2OAbscisic acid receptor PYL2/0.480
3k3kA8SAbscisic acid receptor PYR1/0.479
3wv9FEGHmd co-occurring protein HcgE/0.479
4la7A1OAbscisic acid receptor PYL2/0.479
3elySAHMethyltransferase/0.478
3jrxS1AAcetyl-CoA carboxylase 2/0.478
3k47D09Dihydrofolate reductase1.5.1.30.478
3o0g3O0Cyclin-dependent-like kinase 52.7.11.10.477
3kb0A8SAbscisic acid receptor PYL2/0.476
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.476
4nj32KDCyclin-dependent kinase 22.7.11.220.476
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.475
3nxvD2FDihydrofolate reductase1.5.1.30.475
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.473
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.473
4fex0TOAminoglycoside 3'-phosphotransferase AphA1-IAB/0.473
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
1aoeGW3Dihydrofolate reductase1.5.1.30.471
3k90A8SAbscisic acid receptor PYR1/0.471
3nmhPYVAbscisic acid receptor PYL2/0.471
4kd79DRDihydrofolate reductase1.5.1.30.470
5cccDDFDihydrofolate reductase1.5.1.30.470
1x7e244Estrogen receptor/0.469
2px2SAHGenome polyprotein2.7.7.480.469
3lq2TDPPyruvate dehydrogenase E1 component1.2.4.10.469
3olsESTEstrogen receptor beta/0.469
3kdjA8SAbscisic acid receptor PYL1/0.468
4dscA8SAbscisic acid receptor PYL3/0.468
2j5sKTAAlr4455 protein/0.467
3r8zZ63Cyclin-dependent kinase 22.7.11.220.467
4bfrJ82Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform2.7.1.1530.467
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.466
2g44T3OEstrogen receptor/0.465
2yjaESTEstrogen receptor/0.464
3cseN22Uncharacterized protein/0.464
3qly55VUncharacterized protein/0.464
4k6i9RARetinoic acid receptor RXR-alpha/0.464
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.463
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
2xauADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP433.6.4.130.463
2i40BLZCyclin-dependent kinase 22.7.11.220.462
3kb3A8SAbscisic acid receptor PYL2/0.462
3njoPYVAbscisic acid receptor PYR1/0.462
3zbx6XEHepatocyte growth factor receptor2.7.10.10.462
4kak06UDihydrofolate reductase1.5.1.30.462
3emlZMAAdenosine receptor A2a/0.462
2in6839Wee1-like protein kinase2.7.10.20.461
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.461
3tnwF18Cyclin-dependent kinase 22.7.11.220.461
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.461
1bozPRDDihydrofolate reductase1.5.1.30.460
2fai459Estrogen receptor/0.460
2jdtI5ScAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.460
2nnqT4BFatty acid-binding protein, adipocyte/0.460
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.460
1synF89Thymidylate synthase/0.459
2a9z26AAdenosine kinase2.7.1.200.459
2pulACPMethylthioribose kinase2.7.1.1000.459
2wmsZYSSerine/threonine-protein kinase Chk12.7.11.10.459
3ag9A02cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
3l034OHEstrogen receptor/0.459
4a9e3PFBromodomain-containing protein 2/0.459
1dr3TAPDihydrofolate reductase1.5.1.30.458
1klkPMDDihydrofolate reductase1.5.1.30.458
1u3s797Estrogen receptor beta/0.458
1v0oINRCell division control protein 2 homolog2.7.11.220.458
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.458
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.458
2kfxWW7Troponin C, slow skeletal and cardiac muscles/0.458
4a9hTVPBromodomain-containing protein 2/0.458
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.458
1d7aAIRN5-carboxyaminoimidazole ribonucleotide mutase/0.457
1gwrESTEstrogen receptor/0.457
1sm2STUTyrosine-protein kinase ITK/TSK2.7.10.20.457
1wpgADPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.457
2mjpANPdITP/XTP pyrophosphatase3.6.1.190.457
3qaqQAQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
3qlrQLRDihydrofolate reductase1.5.1.30.457
3vjoANPEpidermal growth factor receptor2.7.10.10.457
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.457
4fjyFJYPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.457
2vnwM01cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
2vo3M04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.456
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.456
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.456
4c3yANB3-ketosteroid dehydrogenase/0.456
3uzaT4GAdenosine receptor A2a/0.456
1d7oTCLEnoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic1.3.1.90.455
1j3jCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.455
3fr5I4AFatty acid-binding protein, adipocyte/0.455
3njoP2MAbscisic acid receptor PYR1/0.455
4ap1NAPSteroid monooxygenase/0.455
4h9506UDihydrofolate reductase1.5.1.30.455
4h9753SDihydrofolate reductase1.5.1.30.455
4klaCHDFerrochelatase, mitochondrial4.99.1.10.455
1gpeFADGlucose oxidase1.1.3.40.454
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2cchATPCyclin-dependent kinase 22.7.11.220.454
2j9lATPH(+)/Cl(-) exchange transporter 5/0.454
3q95ESLEstrogen receptor/0.454
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.454
2fziDH3Dihydrofolate reductase1.5.1.30.453
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.453
3ollESTEstrogen receptor beta/0.453
3v1mHPK2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase3.7.1.80.453
4eqcXR1Serine/threonine-protein kinase PAK 12.7.11.10.453
5fsxADPUncharacterized protein/0.453
1kmvLIIDihydrofolate reductase1.5.1.30.452
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.452
2b1z17MEstrogen receptor/0.452
2b51UTPRNA editing complex protein MP57/0.452
2v95HCYCorticosteroid-binding globulin/0.452
2zbaZBATrichothecene 3-O-acetyltransferase/0.452
3v5w8PRBeta-adrenergic receptor kinase 12.7.11.150.452
4eol1ROCyclin-dependent kinase 22.7.11.220.452
4lm4JPZcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
4oicA8SBet v I allergen-like/0.452
1touB1VFatty acid-binding protein, adipocyte/0.451
2p1v5TNRetinoic acid receptor RXR-alpha/0.451
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.451
3keqNADRedox-sensing transcriptional repressor Rex/0.451
3pejBC2Endoplasmin homolog, putative/0.451
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.451
5htpANPProbable sugar kinase/0.451
5iubCLRAdenosine receptor A2a/0.451
1aq1STUCyclin-dependent kinase 22.7.11.220.450
1g50ESTEstrogen receptor/0.450
1w78PD8Dihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.450
2ab2SNLMineralocorticoid receptor/0.450
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.450
3nj0PYVAbscisic acid receptor PYL2/0.450
3pjcPJCTyrosine-protein kinase JAK32.7.10.20.450
5jtbZMAAdenosine receptor A2a/0.450
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
3m4nPA9N-acetylornithine carbamoyltransferase2.1.3.90.449
3nmvPYVAbscisic acid receptor PYL2/0.449
4eipK2CPutative FAD-monooxygenase/0.449
4h4xFADBiphenyl dioxygenase ferredoxin reductase subunit/0.449
4kfj1R0Dihydrofolate reductase1.5.1.30.449
4ocvANPAminoglycoside phosphotransferase/0.449
4ubtCOASteroid 3-ketoacyl-CoA thiolase/0.449
1dhiMTXDihydrofolate reductase1.5.1.30.448
1m78NDPDihydrofolate reductase1.5.1.30.448
1uyePU9Heat shock protein HSP 90-alpha/0.448
2qboCAMCamphor 5-monooxygenase1.14.15.10.448
2ym5YM5Serine/threonine-protein kinase Chk12.7.11.10.448
3ghvGHCDihydrofolate reductase1.5.1.30.448
4igfCHVEnoyl-acyl carrier reductase/0.448
4p6xHCYGlucocorticoid receptor/0.448
1rg9SAMS-adenosylmethionine synthase2.5.1.60.447
3a8wATPProtein kinase C iota type2.7.11.130.447
3nxrD2DDihydrofolate reductase1.5.1.30.447
3p0hFSEPutative tyrosyl-tRNA synthetase/0.447
4bgbADPPredicted molecular chaperone distantly related to HSP70-fold metalloproteases/0.447
4ixgIXGDihydrofolate reductase1.5.1.30.447
4pp6STLEstrogen receptor/0.447
5k2cZMAAdenosine receptor A2a/0.447
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
1f20FADNitric oxide synthase, brain1.14.13.390.446
1l9kSAHGenome polyprotein2.7.7.480.446
1ne4RP1cAMP-dependent protein kinase type I-alpha regulatory subunit/0.446
1td2PXLPyridoxal kinase PdxY/0.446
2ouzC3DEstrogen receptor/0.446
2p1t3TNRetinoic acid receptor RXR-alpha/0.446
2yk2YJWHeat shock protein HSP 90-alpha/0.446
3gwuSRENa(+):neurotransmitter symporter (Snf family)/0.446
4a9mP9MBromodomain-containing protein 2/0.446
4fewPP2Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.446
1cjcFADNADPH:adrenodoxin oxidoreductase, mitochondrial1.18.1.60.445
1lbbKAIGlutamate receptor 2/0.445
1txtCAAHMG-CoA synthase/0.445
1xhaR68cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
2yhdTESAndrogen receptor/0.445
3w5q3KLVitamin D3 receptor/0.445
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.445
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.445
4ddrMMVDihydrofolate reductase1.5.1.30.445
4jdaA9SAbscisic acid receptor PYL3/0.445
4kfbT27Gag-Pol polyprotein2.7.7.490.445
4l435FIRibosomal protein S6 kinase beta-12.7.11.10.445
4m0lGDPTranslation initiation factor 2 subunit gamma/0.445
4ndnSAMS-adenosylmethionine synthase isoform type-22.5.1.60.445
5k2dZMAAdenosine receptor A2a/0.445
1s3yTQTDihydrofolate reductase1.5.1.30.444
1yy44NAEstrogen receptor beta/0.444
1z2nADPInositol-tetrakisphosphate 1-kinase2.7.1.1340.444
2cjfRP43-dehydroquinate dehydratase4.2.1.100.444
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2nv7555Estrogen receptor beta/0.444
2w8yNDRProgesterone receptor/0.444
2ywvADPPhosphoribosylaminoimidazole-succinocarboxamide synthase/0.444
3dndLL2cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3v49PK0Androgen receptor/0.444
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
4gg70J8Hepatocyte growth factor receptor2.7.10.10.444
5hbsRTLRetinol-binding protein 1/0.444
5g53NECAdenosine receptor A2a/0.444
1kdkDHTSex hormone-binding globulin/0.443
1rekB8LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
1u3gTHF5-formyltetrahydrofolate cyclo-ligase6.3.3.20.443
1zky689Estrogen receptor/0.443
2op07PCEnoyl-ACP reductase/0.443
2pdaTPPPyruvate synthase/0.443
2w5bAGSSerine/threonine-protein kinase Nek22.7.11.10.443
3c1xCKKHepatocyte growth factor receptor2.7.10.10.443
3gcq1BUMitogen-activated protein kinase 14/0.443
3kdiA8SAbscisic acid receptor PYL2/0.443
3l05SN0N-acetylornithine carbamoyltransferase2.1.3.90.443
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.443
4dlxGNPGTPase HRas/0.443
4f700STCyclin-dependent kinase 82.7.11.220.443
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.442
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.442
1uydPU8Heat shock protein HSP 90-alpha/0.442
2azyCHDPhospholipase A2, major isoenzyme3.1.1.40.442
2blaCP6Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
2o2143BApoptosis regulator Bcl-2/0.442
2pklDHTAndrogen receptor/0.442
2vwv7X3Ephrin type-B receptor 42.7.10.10.442
3clbTMQBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
3qj5022Alcohol dehydrogenase class-31.1.1.10.442
3qn1A8SAbscisic acid receptor PYR1/0.442
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.442
4appN53Serine/threonine-protein kinase PAK 42.7.11.10.442
5uviZMAAdenosine receptor A2a/0.442
1jlaTNKGag-Pol polyprotein2.7.7.490.441
1l2iETCEstrogen receptor/0.441
1q66KMBQueuine tRNA-ribosyltransferase2.4.2.290.441
1u72MTXDihydrofolate reductase1.5.1.30.441
2fwzH71Heat shock protein HSP 90-alpha/0.441
2olcADPMethylthioribose kinase2.7.1.1000.441
3a7dFBNCatechol O-methyltransferase2.1.1.60.441
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
3dneLL1cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
3eem53VUncharacterized protein/0.441
3vi5M4MHematopoietic prostaglandin D synthase/0.441
3zraORBProgesterone receptor/0.441
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.441
4gueQCTRibosomal protein S6 kinase alpha-32.7.11.10.441
4kbn25UDihydrofolate reductase1.5.1.30.441
4zhiADPKinesin-like protein KIF11/0.441
5dxgESTEstrogen receptor/0.441
5hyrESTEstrogen receptor/0.441
5je2SAHMethyl transferase/0.441
1cbqRE9Cellular retinoic acid-binding protein 2/0.440
1hnvTBOGag-Pol polyprotein2.7.7.490.440
1it7GUNtRNA-guanine(15) transglycosylase2.4.2.480.440
1q65BHBQueuine tRNA-ribosyltransferase2.4.2.290.440
1s9qOHTEstrogen-related receptor gamma/0.440
2ao6R18Androgen receptor/0.440
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.440
2qkrIXMCdc2-like CDK2/CDC28 like protein kinase/0.440
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
3nxxNDPDihydrofolate reductase1.5.1.30.440
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3qdd94MHeat shock protein HSP 90-alpha/0.440
5h8tRTLRetinol-binding protein 1/0.440