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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
3nl1GTQGentisate 1,2-dioxygenase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3nl1GTQGentisate 1,2-dioxygenase/1.000
3nw4GTQGentisate 1,2-dioxygenase/0.673
3nkt1HNGentisate 1,2-dioxygenase/0.644
4fagGTQGentisate 1,2-dioxygenase/0.529
3c14FOKAdenylate cyclase type 2/0.509
3c14FOKAdenylate cyclase type 5/0.509
4lgaA2OAbscisic acid receptor PYL2/0.496
3nxrD2DDihydrofolate reductase1.5.1.30.493
3kb0A8SAbscisic acid receptor PYL2/0.491
1w78PD8Dihydrofolate synthase/folylpolyglutamate synthase6.3.2.120.487
1m2xMCOMetallo-beta-lactamase type 2/0.486
2v58LZJBiotin carboxylase6.3.4.140.486
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.485
1opbRETRetinol-binding protein 2/0.484
4emyPLPAminotransferase class I and II/0.482
3tr9PT1Dihydropteroate synthase/0.480
4c9wVGH7,8-dihydro-8-oxoguanine triphosphatase3.6.1.550.480
1j3kWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.477
1ly4COQDihydrofolate reductase1.5.1.30.477
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.477
1qy2IPZMajor urinary protein 1/0.476
1dr4HBIDihydrofolate reductase1.5.1.30.475
3pn1IVHDNA ligase/0.475
3nxvD2FDihydrofolate reductase1.5.1.30.474
1cjvFOKAdenylate cyclase type 2/0.473
1cjvFOKAdenylate cyclase type 5/0.473
3zkuHCVIsopenicillin N synthase1.21.3.10.473
1ddtAPUDiphtheria toxin/0.472
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.472
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.472
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.471
2bfmTOPPteridine reductase 11.5.1.330.471
3ghvGHCDihydrofolate reductase1.5.1.30.471
3zvuA8SAbscisic acid receptor PYR1/0.470
4jdaA9SAbscisic acid receptor PYL3/0.470
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.469
3ntz3TZDihydrofolate reductase1.5.1.30.469
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.469
1mvsDTMDihydrofolate reductase1.5.1.30.468
1xj7DHTAndrogen receptor/0.467
3k3kA8SAbscisic acid receptor PYR1/0.467
1cs4FOKAdenylate cyclase type 2/0.466
1cs4FOKAdenylate cyclase type 5/0.466
1cjtFOKAdenylate cyclase type 2/0.465
1cjtFOKAdenylate cyclase type 5/0.465
1mvcBM6Retinoic acid receptor RXR-alpha/0.465
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
3kdiA8SAbscisic acid receptor PYL2/0.465
3nxyD2HDihydrofolate reductase1.5.1.30.465
4kfjFOLDihydrofolate reductase1.5.1.30.465
4mv3ACPBiotin carboxylase6.3.4.140.465
1pd8CO4Dihydrofolate reductase1.5.1.30.464
3kb3A8SAbscisic acid receptor PYL2/0.464
3pd4A3GThreonine--tRNA ligase6.1.1.30.463
3sa27DRDihydrofolate reductase/0.462
3zrbOR8Progesterone receptor/0.462
1tl7FOKAdenylate cyclase type 2/0.461
1tl7FOKAdenylate cyclase type 5/0.461
2od7A1RNAD-dependent protein deacetylase HST23.5.10.461
2vqsBVDDeoxynucleoside kinase/0.461
4jufTPPBenzoylformate decarboxylase4.1.1.70.461
4n1gCEIObelin/0.461
1crbRTLRetinol-binding protein 1/0.460
4kak06UDihydrofolate reductase1.5.1.30.460
4mv1ADPBiotin carboxylase6.3.4.140.460
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.459
3hxeBD8Geranylgeranyl transferase type-2 subunit beta2.5.1.600.459
3q9bB3NAcetylpolyamine amidohydrolase/0.459
1tg2H2BPhenylalanine-4-hydroxylase1.14.16.10.458
2ipjFFAAldo-keto reductase family 1 member C2/0.458
4m6l21VDihydrofolate reductase1.5.1.30.458
5kf1ACOPredicted acetyltransferase/0.458
1sr7MOFProgesterone receptor/0.457
2fziDH3Dihydrofolate reductase1.5.1.30.457
2gvdFKPAdenylate cyclase type 2/0.457
2gvdFKPAdenylate cyclase type 5/0.457
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.457
3junAKDPhenazine biosynthesis protein A/B/0.456
3r336MEDihydrofolate reductase1.5.1.30.456
4jq2SUZAldo-keto reductase family 1 member C2/0.456
5h8tRTLRetinol-binding protein 1/0.456
1wxyFRKAdenosine deaminase3.5.4.40.455
2adaHPRAdenosine deaminase3.5.4.40.455
2cfcKPC2-(R)-hydroxypropyl-CoM dehydrogenase1.1.1.2680.455
2fzjDH3Dihydrofolate reductase1.5.1.30.455
2p1u4TNRetinoic acid receptor RXR-alpha/0.455
2vczVC3Hematopoietic prostaglandin D synthase/0.455
3ujlA8SAbscisic acid receptor PYL2/0.455
4hfnCIY2-alkenal reductase (NADP(+)-dependent)/0.455
4jlt8PRCytochrome P450 2B41.14.14.10.455
4l7vSAHProtein-L-isoaspartate O-methyltransferase/0.455
1trgCB3Thymidylate synthase/0.454
1zrb062Prothrombin3.4.21.50.454
2v3hI25Prothrombin3.4.21.50.454
3qpg3QPAspartate aminotransferase2.6.1.10.454
4kko1REGag-Pol polyprotein2.7.7.490.454
4l1xSTRAldo-keto reductase family 1 member C2/0.454
1ihiIU5Aldo-keto reductase family 1 member C2/0.453
1synF89Thymidylate synthase/0.453
3lalKRVGag-Pol polyprotein2.7.7.490.453
3qlxQLRUncharacterized protein/0.453
4zn7DESEstrogen receptor/0.453
1culFOKAdenylate cyclase type 2/0.452
1culFOKAdenylate cyclase type 5/0.452
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.452
2pixDHTAndrogen receptor/0.452
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3vg9ZMAAdenosine receptor A2a/0.452
4jbxSK7Thymidine kinase/0.452
5ai5BSUBifunctional epoxide hydrolase 23.1.3.760.452
1e3kR18Progesterone receptor/0.451
2w6oOA3Biotin carboxylase6.3.4.140.451
2w71L23Biotin carboxylase6.3.4.140.451
3zecANPAdenosine monophosphate-protein transferase SoFic2.7.7.n10.451
4jvlESTEstrogen sulfotransferase2.8.2.40.451
4jxzATPGlutamine--tRNA ligase6.1.1.180.451
1x2hLPALipoate-protein ligase A6.3.1.200.450
3d75NBBPheromone-binding protein ASP1/0.450
3fhxPLPPyridoxal kinase2.7.1.350.450
3k47D09Dihydrofolate reductase1.5.1.30.450
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
3kdjA8SAbscisic acid receptor PYL1/0.450
3p8iFMNPentaerythritol tetranitrate reductase/0.450
3tydXHPDihydropteroate synthase/0.450
4g8cC6LAlpha/beta hydrolase fold protein/0.450
1al7HSTPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.449
1dhiMTXDihydrofolate reductase1.5.1.30.449
1kmsLIHDihydrofolate reductase1.5.1.30.449
1y2e5DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
1y56FMNUncharacterized protein/0.449
1y56FMN382aa long hypothetical sarcosine oxidase/0.449
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
2pdfZSTAldose reductase1.1.1.210.449
2yatEEUEstrogen receptor/0.449
3erdDESEstrogen receptor/0.449
3zrbORCProgesterone receptor/0.449
4jq4IMNAldo-keto reductase family 1 member C2/0.449
1cjkFOKAdenylate cyclase type 2/0.448
1cjkFOKAdenylate cyclase type 5/0.448
1klkPMDDihydrofolate reductase1.5.1.30.448
1mvtDTMDihydrofolate reductase1.5.1.30.448
1rx5DDFDihydrofolate reductase1.5.1.30.448
2bbqPFGThymidylate synthase/0.448
2iejS48Protein farnesyltransferase subunit beta2.5.1.580.448
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.448
3i1y33NBifunctional epoxide hydrolase 23.3.2.100.448
1s3yTQTDihydrofolate reductase1.5.1.30.447
2fzhDH1Dihydrofolate reductase1.5.1.30.447
2ix5CAAAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.447
2v3wTPPBenzoylformate decarboxylase4.1.1.70.447
2vdyHCYCorticosteroid-binding globulin/0.447
3nj0PYVAbscisic acid receptor PYL2/0.447
3o9pMHIPeriplasmic murein peptide-binding protein/0.447
3sai9DRDihydrofolate reductase/0.447
3zraORBProgesterone receptor/0.447
4jtrIBPAldo-keto reductase family 1 member C2/0.447
4yswNAIXanthine dehydrogenase/oxidase/0.447
1odnAPVIsopenicillin N synthase1.21.3.10.446
1vzqSHYProthrombin3.4.21.50.446
2zbaZBATrichothecene 3-O-acetyltransferase/0.446
3aosJH2Hemolymph juvenile hormone binding protein/0.446
3fnu006HAP protein/0.446
3vv8B02Beta-secretase 13.4.23.460.446
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.446
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.446
4iyg1HUStrictosidine synthase4.3.3.20.446
4kbn25UDihydrofolate reductase1.5.1.30.446
4li71XPTankyrase-12.4.2.300.446
1jtuLYBThymidylate synthase/0.445
1k27MTMS-methyl-5'-thioadenosine phosphorylase/0.445
1rdtL79Retinoic acid receptor RXR-alpha/0.445
1wdkACO3-ketoacyl-CoA thiolase/0.445
1yhoTRRDihydrofolate reductase1.5.1.30.445
2bfaCB3Pteridine reductase 11.5.1.330.445
2gzl2AA2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.445
2w6zL21Biotin carboxylase6.3.4.140.445
3ansS38Bifunctional epoxide hydrolase 23.3.2.100.445
3b9lAZZSerum albumin/0.445
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.445
3oapREARetinoic acid receptor RXR-alpha/0.445
3v49PK0Androgen receptor/0.445
4gtt7TQGeranylgeranyl transferase type-2 subunit beta2.5.1.600.445
4lngJANCaaX farnesyltransferase beta subunit Ram1/0.445
4lsjLSJGlucocorticoid receptor/0.445
1kceCB3Thymidylate synthase/0.444
1kt5RTLRetinol-binding protein 4/0.444
1ohkCOPDihydrofolate reductase1.5.1.30.444
1t47NTD4-hydroxyphenylpyruvate dioxygenase1.13.11.270.444
1u0hFOKAdenylate cyclase type 2/0.444
1u0hFOKAdenylate cyclase type 5/0.444
1yqj6NPMitogen-activated protein kinase 14/0.444
2aa2AS4Mineralocorticoid receptor/0.444
2vbpVB1Isopenicillin N synthase1.21.3.10.444
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3pghFLPProstaglandin G/H synthase 21.14.99.10.444
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4k4fK4FTankyrase-12.4.2.300.444
4twnB96Ephrin type-A receptor 32.7.10.10.444
1cjuFOKAdenylate cyclase type 2/0.443
1cjuFOKAdenylate cyclase type 5/0.443
1rx7FOLDihydrofolate reductase1.5.1.30.443
1toiHCIAspartate aminotransferase2.6.1.10.443
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
3nmpPYVAbscisic acid receptor PYL2/0.443
3sigAR6Uncharacterized protein/0.443
3wizLC6Bcl-2-like protein 1/0.443
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4kd79DRDihydrofolate reductase1.5.1.30.443
1fkxPRHAdenosine deaminase3.5.4.40.442
1fw0KAIGlutamate receptor 2/0.442
2bf7HBIPteridine reductase 11.5.1.330.442
2bp1NDPAflatoxin B1 aldehyde reductase member 2/0.442
2fyuFDNCytochrome b/0.442
2w3mFOLDihydrofolate reductase1.5.1.30.442
3repATPIntegrin-linked protein kinase2.7.11.10.442
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.442
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
1kqwRTLCellular retinol-binding protein type II/0.441
1lkeDOGBilin-binding protein/0.441
1toxNADDiphtheria toxin/0.441
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.441
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2fpcSCGStrictosidine synthase4.3.3.20.441
2hl2SSAThreonine--tRNA ligase6.1.1.30.441
3d80Q22Dihydrofolate reductase1.5.1.30.441
3qn1A8SAbscisic acid receptor PYR1/0.441
4dsbA8SAbscisic acid receptor PYL3/0.441
5cuqNSCGenome polyprotein/0.441
1cqp803Integrin alpha-L/0.440
1ldqSHMAvidin/0.440
1oriSAHProtein arginine N-methyltransferase 1/0.440
1qnfHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.440
1s9qOHTEstrogen-related receptor gamma/0.440
1stdBFSScytalone dehydratase4.2.1.940.440
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.440
2aaxPDNMineralocorticoid receptor/0.440
2blcCP7Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
2f6rACOBifunctional coenzyme A synthase/0.440
2qhxFE1Pteridine reductase 11.5.1.330.440
2vqjTFGHistone deacetylase 43.5.1.980.440
2zf4PPYUncharacterized protein/0.440
2zhw12UProthrombin3.4.21.50.440
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.440
3l3rOAGDihydrofolate reductase1.5.1.30.440
3zze6XPHepatocyte growth factor receptor2.7.10.10.440
4g1nNZTPyruvate kinase PKM2.7.1.400.440
4iarERM5-hydroxytryptamine receptor 1B/0.440
5difGNPGTP-binding nuclear protein Ran/0.440