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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
1kphSAHCyclopropane mycolic acid synthase 12.1.1.79

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
1kphSAHCyclopropane mycolic acid synthase 12.1.1.791.000
2fk8SAMHydroxymycolate synthase MmaA42.1.10.568
3ha7B32Hydroxymycolate synthase MmaA42.1.10.558
3ha3SAHHydroxymycolate synthase MmaA42.1.10.553
3ha5SFGHydroxymycolate synthase MmaA42.1.10.532
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.501
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.493
2idkC2FGlycine N-methyltransferase2.1.1.200.491
3k7mFAD6-hydroxy-L-nicotine oxidase/0.489
4necSAHPutative SAM-dependent methyltransferase/0.488
2a14SAHIndolethylamine N-methyltransferase2.1.1.490.487
1pq944BOxysterols receptor LXR-beta/0.486
4r6xSAHPhosphoethanolamine N-methyltransferase/0.486
2zfuSAHRibosomal RNA-processing protein 8/0.484
1ve3SAMUncharacterized protein/0.482
3n6uTSUHTH-type transcriptional regulator TsaR/0.482
4g67SAHUncharacterized ACR, COG1565 superfamily/0.482
2g0bNLTLong-chain N-acyl amino acid synthase/0.481
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.481
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.481
4y3jHICEndothiapepsin3.4.23.220.481
4nyiGNPGTPase HRas/0.480
1kiaSAMGlycine N-methyltransferase2.1.1.200.479
3ou6SAMSAM-dependent methyltransferase/0.479
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.478
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.478
1wy7SAHUncharacterized protein/0.478
2bzgSAHThiopurine S-methyltransferase2.1.1.670.478
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.477
1pd9CO4Dihydrofolate reductase1.5.1.30.476
3up0D7SaceDAF-12/0.476
1yf3SAHDNA adenine methylase/0.475
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.475
3e23SAMUncharacterized protein/0.475
1g60SAMModification methylase MboII2.1.1.720.474
3eksCY9Actin-5C/0.474
3kpjSAHPhenylethanolamine N-methyltransferase2.1.1.280.474
4f86SFGGeranyl diphosphate 2-C-methyltransferase2.1.1.2550.474
1booSAHModification methylase PvuII2.1.1.1130.471
3vc1SAHGeranyl diphosphate 2-C-methyltransferase2.1.1.2550.471
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.471
1rx8NAPDihydrofolate reductase1.5.1.30.470
2eg5SAH7-methylxanthosine synthase 1/0.470
5iqeGNPBifunctional AAC/APH2.3.10.470
3d84NDPDihydrofolate reductase1.5.1.30.469
3lbnGNPGTPase HRas/0.469
3qlsNDPDihydrofolate reductase1.5.1.30.469
1nbiSAMGlycine N-methyltransferase2.1.1.200.468
1v35NAIEnoyl-ACP reductase/0.468
3c3eGDP2-phospho-L-lactate transferase/0.468
3hxfBD9Geranylgeranyl transferase type-2 subunit beta2.5.1.600.468
4fgzSAHPhosphoethanolamine N-methyltransferase/0.468
1p8dCO1Oxysterols receptor LXR-beta/0.467
1vq1SAMRelease factor glutamine methyltransferase2.1.1.2970.467
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.467
4y35F90Endothiapepsin3.4.23.220.467
3ekuCY9Actin-5C/0.466
3o6o94MHeat shock protein 83/0.466
1diuBDMDihydrofolate reductase1.5.1.30.465
1hb1OCVIsopenicillin N synthase1.21.3.10.465
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.465
3ou7SAMSAM-dependent methyltransferase/0.465
3rs5GNPGTPase HRas/0.465
3t7x4SHEndothiapepsin3.4.23.220.465
3tm5SFGUncharacterized protein/0.465
4dvq1CACytochrome P450 11B2, mitochondrial1.14.15.40.465
1aiqCB3Thymidylate synthase/0.464
1kzjCB3Thymidylate synthase/0.464
2iviACWIsopenicillin N synthase1.21.3.10.464
2y60M8FIsopenicillin N synthase1.21.3.10.464
1s1cGNPTransforming protein RhoA/0.463
2h2qNAPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.463
4dvi2IWTankyrase-12.4.2.300.463
1n83CLRNuclear receptor ROR-alpha/0.462
2jb4A14Isopenicillin N synthase1.21.3.10.462
2r8pT6FTransketolase 1/0.462
3gyaCOAGCN5-related N-acetyltransferase/0.462
3oivGNPGTPase HRas/0.462
3zoiM2WIsopenicillin N synthase1.21.3.10.462
4wqmFADToluene-4-monooxygenase electron transfer component1.18.1.30.462
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.461
5dp2NAPCurF/0.461
1ia1NDPDihydrofolate reductase1.5.1.30.460
1w06W05Isopenicillin N synthase1.21.3.10.460
3elySAHMethyltransferase/0.460
3tljSAHUncharacterized protein/0.460
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.460
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.460
1drhNAPDihydrofolate reductase1.5.1.30.459
1q5mNDPProstaglandin-E(2) 9-reductase1.1.1.1890.459
2gjlFMNNitronate monooxygenase1.13.12.160.459
3tm4SAMUncharacterized protein/0.459
4i6gFADCryptochrome-2/0.459
4o1mNADEnoyl-acyl carrier reductase/0.459
4z24FADPutative GMC-type oxidoreductase R13510.459
5bw4SAMUncharacterized protein/0.459
1bc5SAHChemotaxis protein methyltransferase2.1.1.800.458
1xduSFGAclacinomycin 10-hydroxylase RdmB4.1.10.458
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.458
3v4fGNPGTPase HRas/0.458
4an4DUDPutative glycosyl transferase/0.458
4c67L5SBromodomain-containing protein 4/0.458
4kxjP34Nucleoprotein/0.458
4l1xNAPAldo-keto reductase family 1 member C2/0.458
4nyjGNPGTPase HRas/0.458
1qiqACCIsopenicillin N synthase1.21.3.10.457
2fhnBNIAvidin-related protein 4/5/0.457
3b8z294A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.457
3s1sSAHRestriction endonuclease BpuSI/0.457
3vc2SAHGeranyl diphosphate 2-C-methyltransferase2.1.1.2550.457
4mitGTPRho-related protein racC/0.457
4rtoSFGDNA adenine methylase2.1.1.720.457
4yaf2AMNADPH--cytochrome P450 reductase/0.457
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.456
1hb3SCVIsopenicillin N synthase1.21.3.10.456
1rx1NAPDihydrofolate reductase1.5.1.30.456
2e8sSAHDiphthine synthase/0.456
2hvdADPNucleoside diphosphate kinase A2.7.4.60.456
2ob0ACON-alpha-acetyltransferase 50/0.456
2r8oT5XTransketolase 1/0.456
3ljtLA3A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.456
3sfh1DIHistone deacetylase 83.5.1.980.456
4gdcNDPUDP-galactopyranose mutase/0.456
4ja1NGHStromelysin-13.4.24.170.456
2rh1CAUBeta-2 adrenergic receptor/0.456
1bk0ACVIsopenicillin N synthase1.21.3.10.455
1fkwPURAdenosine deaminase3.5.4.40.455
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.455
1upw444Oxysterols receptor LXR-beta/0.455
2prh238Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.455
3pbzF02Endothiapepsin3.4.23.220.455
3v0o4GWHisto-blood group ABO system transferase/0.455
4bixADPSensor histidine kinase CpxA/0.455
4pnmNU1Tankyrase-22.4.2.300.455
5iqiGNPBifunctional AAC/APH2.3.10.455
3ny8JRZBeta-2 adrenergic receptor/0.455
1qjfACSIsopenicillin N synthase1.21.3.10.454
2xlrFADPutative flavin-containing monooxygenase/0.454
2ykeYKEHeat shock protein HSP 90-alpha/0.454
3mtwM3RXaa-Pro dipeptidase, putative/0.454
4yd7F5NEndothiapepsin3.4.23.220.454
1pqc444Oxysterols receptor LXR-beta/0.453
1sg9SAMRelease factor glutamine methyltransferase2.1.1.2970.453
1uy9PU6Heat shock protein HSP 90-alpha/0.453
2wvlGDDMannosyl-3-phosphogylcerate synthase/0.453
3akn11DFatty acid-binding protein, intestinal/0.453
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.453
3rs7GNPGTPase HRas/0.453
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
1fdsESTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.452
1nw5SAMModification methylase RsrI2.1.1.720.452
2ih2NEAModification methylase TaqI2.1.1.720.452
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.452
3uj8SFGPhosphoethanolamine N-methyltransferase/0.452
4b4dFADFerredoxin-NADP reductase/0.452
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
1uzwCDHIsopenicillin N synthase1.21.3.10.451
2c20NADUDP-glucose 4-epimerase/0.451
2z97CAMCamphor 5-monooxygenase1.14.15.10.451
3gwfNAPCyclohexanone monooxygenase/0.451
3k5gBJCBeta-secretase 13.4.23.460.451
4mv8ACPBiotin carboxylase6.3.4.140.451
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
1dyjDDFDihydrofolate reductase1.5.1.30.450
1i2bNADUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.450
1r00SAHAclacinomycin 10-hydroxylase RdmB4.1.10.450
2f8lSAMLmo1582 protein/0.450
2okcSAMProbable type I restriction enzyme BthVORF4518P M protein2.1.1.720.450
2p41SAHGenome polyprotein/0.450
3hxbBD5Geranylgeranyl transferase type-2 subunit beta2.5.1.600.450
4elb34RDihydrofolate reductase/0.450
4fw05KJNitric oxide synthase, brain1.14.13.390.450
4gddNAIUDP-galactopyranose mutase/0.450
5c80URIUridine phosphorylase/0.450
1qipGNBLactoylglutathione lyase4.4.1.50.449
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.449
1u1d181Uridine phosphorylase2.4.2.30.449
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.449
3n0hTOPDihydrofolate reductase1.5.1.30.449
4bb3KKAIsopenicillin N synthase1.21.3.10.449
4iarERM5-hydroxytryptamine receptor 1B/0.449
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.449
5d6lCAUBeta-2 adrenergic receptor/0.449
4ldeP0GBeta-2 adrenergic receptor/0.449
1b3dS27Stromelysin-13.4.24.170.448
1mvtDTMDihydrofolate reductase1.5.1.30.448
1wxyFRKAdenosine deaminase3.5.4.40.448
2ahvCOAAcetate CoA-transferase YdiF2.8.3.80.448
2ejzSAHDiphthine synthase/0.448
2w9hTOPDihydrofolate reductase1.5.1.30.448
3af0GDPPantothenate kinase2.7.1.330.448
3e6eDCSAlanine racemase/0.448
3kslSZHProtein farnesyltransferase subunit beta2.5.1.580.448
3qj5022Alcohol dehydrogenase class-31.1.1.10.448
3tnfGNPRas-related protein Rab-8A/0.448
3vtbTKAVitamin D3 receptor/0.448
4alhA9PBromodomain-containing protein 2/0.448
4eueNAITrans-2-enoyl-CoA reductase [NADH]/0.448
1db48INPhospholipase A2, membrane associated/0.447
1wbpADPSRSF protein kinase 12.7.11.10.447
2b37NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
2c12FADNitroalkane oxidase1.7.3.10.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3pllF06Endothiapepsin3.4.23.220.447
3pt9SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.447
3vrwYS5Vitamin D3 receptor/0.447
4mwzSAMPhosphoethanolamine N-methyltransferase, putative/0.447
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.447
1cxzGSPTransforming protein RhoA/0.446
1d3hA26Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
1jnrFADAdenylylsulfate reductase, subunit A (AprA)/0.446
1qtiGNTAcetylcholinesterase3.1.1.70.446
2oc4IMHPurine nucleoside phosphorylase2.4.2.10.446
2vbpVB1Isopenicillin N synthase1.21.3.10.446
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.446
3p9kSAHCaffeic acid O-methyltransferase/0.446
3w0aDS5Vitamin D3 receptor/0.446
4a87NARMajor pollen allergen Bet v 1-A/0.446
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.446
4kvgGTPRas-related protein Rap-1A/0.446
4lhwGNPRas-related protein Rab-8A/0.446
4q0kGA3Phytohormone-binding protein/0.446
4rphGDUUDP-galactopyranose mutase5.4.99.90.446
5a2yUTPMitochondrial poly(A) polymerase/0.446
5epeSAHUncharacterized protein/0.446
5hwpCOAHydroxymethylglutaryl-CoA synthase/0.446
1m78NDPDihydrofolate reductase1.5.1.30.445
1tvrTB9Gag-Pol polyprotein2.7.7.490.445
1zdwFLVPrenyltransferase/0.445
1zx1CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.445
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.445
2pncCLUPrimary amine oxidase, liver isozyme/0.445
2qg2A91Heat shock protein HSP 90-alpha/0.445
2wo7ASVIsopenicillin N synthase1.21.3.10.445
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.445
4blwSAHRibosomal RNA large subunit methyltransferase J/0.445
4nbwNADShort-chain dehydrogenase/reductase SDR/0.445
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.445
5i39FADL-amino acid deaminase/0.445
1b87ACOAac(6')-Ii protein/0.444
1ie8KH1Vitamin D3 receptor/0.444
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.444
1tkaN3TTransketolase 12.2.1.10.444
2b8tTHMThymidine kinase/0.444
2bfqAR6[Protein ADP-ribosylglutamate] hydrolase AF_15213.2.20.444
2r0pK2CPutative FAD-monooxygenase/0.444
2ym1FADPhenylacetone monooxygenase1.14.13.920.444
3zkyWT4Isopenicillin N synthase1.21.3.10.444
4bfxZVXPantothenate kinase2.7.1.330.444
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.444
4jkt04AGlutaminase kidney isoform, mitochondrial3.5.1.20.444
4y3zF41Endothiapepsin3.4.23.220.444
4y4jLNREndothiapepsin3.4.23.220.444
4zu44TGWxcM-like protein/0.444
5jadFB2Platelet-activating factor acetylhydrolase3.1.1.470.444
5d5bCAUBeta-2 adrenergic receptor/0.444
1gj5130Prothrombin3.4.21.50.443
1m8h6NINitric oxide synthase, inducible1.14.13.390.443
2bdyUNBProthrombin3.4.21.50.443
2bmeGNPRas-related protein Rab-4A/0.443
2bu9HFVIsopenicillin N synthase1.21.3.10.443
2fiwACOGCN5-related N-acetyltransferase:Aminotransferase, class-II/0.443
2w3bNDPDihydrofolate reductase1.5.1.30.443
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.443
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.443
3up3XCAaceDAF-12/0.443
4a7b3W5Collagenase 33.4.240.443
4iv0SAMPhosphoethanolamine N-methyltransferase, putative/0.443
5dhaGNPGTP-binding nuclear protein Ran/0.443
1dc6NADGlyceraldehyde-3-phosphate dehydrogenase A/0.442
1fduESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1fwkADPHomoserine kinase2.7.1.390.442
1j4jACOAcetyltransferase2.3.10.442
1s3vTQDDihydrofolate reductase1.5.1.30.442
1votHUPAcetylcholinesterase3.1.1.70.442
1ygkRRCPyridoxal kinase2.7.1.350.442
2aclL05Oxysterols receptor LXR-alpha/0.442
2c9zQUEAnthocyanidin 3-O-glucosyltransferase 22.4.1.1150.442
2wi72KLHeat shock protein HSP 90-alpha/0.442
3ey4352Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3frkTQPQdtB/0.442
3qvpFADGlucose oxidase1.1.3.40.442
3reoSAH(Iso)eugenol O-methyltransferase2.1.1.1460.442
3uj7SAMPhosphoethanolamine N-methyltransferase/0.442
4f0e0RUPoly [ADP-ribose] polymerase 152.4.2.300.442
4i4b1CV3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.442
4jucTPPBenzoylformate decarboxylase4.1.1.70.442
4ktl1CQCytochrome P450/0.442
4rlh0WEEnoyl-[acyl-carrier-protein] reductase [NADH]/0.442
4zeaIMIEndothiapepsin3.4.23.220.442
1mczRMNBenzoylformate decarboxylase4.1.1.70.441
1n06ADPRiboflavin kinase2.7.1.260.441
1o6qR17Squalene--hopene cyclase4.2.1.1290.441
1pq6965Oxysterols receptor LXR-beta/0.441
2pa7TYDTDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase5.3.2.30.441
2xegCI9Glutamate carboxypeptidase 23.4.17.210.441
3nw2H4BNitric oxide synthase, inducible1.14.13.390.441
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.441
3w0yDS4Vitamin D3 receptor/0.441
4g95OAGDihydrofolate reductase1.5.1.30.441
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
3sn6P0GBeta-2 adrenergic receptor/0.441
1af7SAHChemotaxis protein methyltransferase2.1.1.800.440
1biwS80Stromelysin-13.4.24.170.440
1ez0NAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.440
1h60STRPentaerythritol tetranitrate reductase/0.440
1hvyD16Thymidylate synthase2.1.1.450.440
1rfuADPPyridoxal kinase2.7.1.350.440
2a0yDIHPurine nucleoside phosphorylase2.4.2.10.440
2gdzNAD15-hydroxyprostaglandin dehydrogenase [NAD(+)]1.1.1.1410.440
3e33ED7Protein farnesyltransferase subunit beta2.5.1.580.440
3eluSAMMethyltransferase/0.440
3fznD7KBenzoylformate decarboxylase4.1.1.70.440
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.440
3k7tFAD6-hydroxy-L-nicotine oxidase/0.440
3njuANNAcidic phospholipase A2 33.1.1.40.440
3t4hMD5Alpha-ketoglutarate-dependent dioxygenase AlkB1.14.11.330.440
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
4elb34SDihydrofolate reductase/0.440
4ttjFMCPurine nucleoside phosphorylase DeoD-type/0.440
4y3qF02Endothiapepsin3.4.23.220.440
5iqdGNPBifunctional AAC/APH2.3.10.440
5jjrSAHGenome polyprotein/0.440