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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
5xr8FMNCannabinoid receptor 1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
5xr8FMNCannabinoid receptor 1/1.000
5xraFMNCannabinoid receptor 1/0.564
1akuFMNFlavodoxin/0.526
3fktSIIBeta-secretase 13.4.23.460.525
4y7cFMNNADPH--cytochrome P450 reductase/0.521
5tgzFMNCannabinoid receptor 1/0.511
4fx2FMNFlavodoxin/0.509
3f6rFMNFlavodoxin/0.508
1azlFMNFlavodoxin/0.507
1c7fFMNFlavodoxin/0.507
3ojxFMNNADPH--cytochrome P450 reductase/0.505
1wsbFMNFlavodoxin/0.499
4araC56Acetylcholinesterase3.1.1.70.492
1xyyFMNFlavodoxin/0.490
1mvtDTMDihydrofolate reductase1.5.1.30.489
1j8qFMNFlavodoxin/0.487
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.482
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.482
1rkwPNTHTH-type transcriptional regulator QacR/0.479
1akwFMNFlavodoxin/0.477
3kaqFMNFlavodoxin/0.477
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.476
1j9zFMNNADPH--cytochrome P450 reductase/0.475
1odcA8BAcetylcholinesterase3.1.1.70.475
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.474
4q0kGA3Phytohormone-binding protein/0.472
2fx2FMNFlavodoxin/0.471
3eksCY9Actin-5C/0.471
4j0v1H7Beta-secretase 13.4.23.460.471
4kxjP34Nucleoprotein/0.471
1kw8BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.470
1xyvFMNFlavodoxin/0.470
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.470
4b4vL34Bifunctional protein FolD/0.469
2ylrNAPPhenylacetone monooxygenase1.14.13.920.468
4p9dTMPDeoxycytidylate deaminase/0.468
3esyFMNFlavodoxin/0.467
1j9gFMNFlavodoxin/0.466
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.466
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.466
3h2sNDPPutative NADH-flavin reductase/0.466
3wquATPCell division protein FtsA/0.466
1ja1FMNNADPH--cytochrome P450 reductase/0.465
1q84TZ4Acetylcholinesterase3.1.1.70.465
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.465
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.465
4b7754MBeta-secretase 13.4.23.460.465
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.465
1e66HUXAcetylcholinesterase3.1.1.70.464
2a9z26AAdenosine kinase2.7.1.200.464
2il2LIXRenin3.4.23.150.464
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.464
3kmxG00Beta-secretase 13.4.23.460.464
3pkbY16Methionine aminopeptidase 2/0.464
4a81DXCMajor pollen allergen Bet v 1-A/0.464
3ck7ACXStarch-binding protein SusD/0.463
3e34ED1Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha/0.463
3e34ED1Protein farnesyltransferase subunit beta2.5.1.580.463
3sxjSAMPutative methyltransferase/0.463
4oxxFMNCindoxin/0.463
1bu5RBFFlavodoxin/0.462
1ofvFMNFlavodoxin/0.462
1s3uTQDDihydrofolate reductase1.5.1.30.462
3ekuCY9Actin-5C/0.462
3ohh3HHBeta-secretase 13.4.23.460.462
4oztP1AEcdysone receptor, putative/0.462
4z0pNDPNAD-dependent dehydrogenase/0.462
1ni12C5Protein farnesyltransferase subunit beta2.5.1.580.461
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.461
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.460
1sa5BMVProtein farnesyltransferase subunit beta2.5.1.580.460
2xupTZ5Acetylcholinesterase3.1.1.70.460
4qaiFMNNADPH dehydrogenase/0.460
1w87FADFerredoxin--NADP reductase1.18.1.20.459
4df2FMNNADPH dehydrogenase/0.459
1a9cGTPGTP cyclohydrolase 13.5.4.160.458
2r5nTPPTransketolase 1/0.458
2xuqTZ4Acetylcholinesterase3.1.1.70.458
3wycNAPMeso-diaminopimelate D-dehydrogenase1.4.1.160.458
2bb3SAHCobalamin biosynthesis precorrin-6Y methylase (CbiE)/0.457
2ha6SCKAcetylcholinesterase3.1.1.70.457
2x6o2TCTetracycline repressor protein class D/0.457
3p67FMNPentaerythritol tetranitrate reductase/0.457
4ef4C2EStimulator of interferon genes protein/0.457
4zu44TGWxcM-like protein/0.457
1cf3FADGlucose oxidase1.1.3.40.456
1q45FMN12-oxophytodienoate reductase 31.3.1.420.456
2g1n1IGRenin3.4.23.150.456
2v2zADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.456
2vqbFADPutative flavin-containing monooxygenase/0.456
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.456
3q9bB3NAcetylpolyamine amidohydrolase/0.456
4rvfTYDD-mycarose 3-C-methyltransferase/0.456
1h60STRPentaerythritol tetranitrate reductase/0.455
2hpvFMNFMN-dependent NADH-azoreductase1.70.455
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3h3qH13Collagen type IV alpha-3-binding protein/0.455
1drhNAPDihydrofolate reductase1.5.1.30.454
1j9zFADNADPH--cytochrome P450 reductase/0.454
1txtCAAHMG-CoA synthase/0.454
1v453DGPurine nucleoside phosphorylase2.4.2.10.454
2bn4FMNNADPH--cytochrome P450 reductase/0.454
2ea2F77Methionine aminopeptidase 2/0.454
2g1y5IGRenin3.4.23.150.454
3dziRGTADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.454
4fue7UPUrokinase-type plasminogen activator3.4.21.730.454
1n4qLYS_CYS_VAL_ILE_LEUGeranylgeranyl transferase type-1 subunit beta2.5.1.590.453
1ut6A8NAcetylcholinesterase3.1.1.70.453
1x1cSAHC-20 methyltransferase/0.453
1zgbA1EAcetylcholinesterase3.1.1.70.453
2g247IGRenin3.4.23.150.453
2vatCOAAcetyl-CoA--deacetylcephalosporin C acetyltransferase2.3.1.1750.453
3kruFMNNADH:flavin oxidoreductase/NADH oxidase/0.453
4lutDCSAlanine racemase/0.453
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.453
1dhfFOLDihydrofolate reductase1.5.1.30.452
1toiHCIAspartate aminotransferase2.6.1.10.452
1w6hTITPlasmepsin-23.4.23.390.452
3bw4FMNPutative 2-nitropropane dioxygenase/0.452
3nd6ATPPhosphopantetheine adenylyltransferase/0.452
4arbC57Acetylcholinesterase3.1.1.70.452
4ey7E20Acetylcholinesterase3.1.1.70.452
1n95FTHProtein farnesyltransferase subunit beta2.5.1.580.451
1o9bNAIQuinate/shikimate dehydrogenase/0.451
1pd9CO4Dihydrofolate reductase1.5.1.30.451
1rneC60Renin3.4.23.150.451
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.451
3hlwCE3Beta-lactamase/0.451
3jv7NADSecondary alcohol dehydrogenase/0.451
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.451
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.451
1bvrNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.450
2dhfDZFDihydrofolate reductase1.5.1.30.450
2ed4NAD4-hydroxyphenylacetate 3-monooxygenase reductase component1.5.1.360.450
2i4qUA4Renin3.4.23.150.450
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.450
2v16C47Renin3.4.23.150.450
3bw2FMNPutative 2-nitropropane dioxygenase/0.450
3junAJDPhenazine biosynthesis protein A/B/0.450
3lqsPSZD-alanine aminotransferase2.6.1.210.450
4e2dFMNDehydrogenase/0.450
4mr72BVGamma-aminobutyric acid type B receptor subunit 1/0.450
5c4fUPGHisto-blood group ABO system transferase/0.450
1h63FMNPentaerythritol tetranitrate reductase/0.449
1psa0ZLPepsin A3.4.23.10.449
2a9y26AAdenosine kinase2.7.1.200.449
2g21L1BRenin3.4.23.150.449
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.449
2gyuHI6Acetylcholinesterase3.1.1.70.449
2h6iCYS_VAL_LEU_SER_GERProtein farnesyltransferase subunit beta2.5.1.580.449
2npiATPmRNA cleavage and polyadenylation factor CLP1/0.449
3iu7FCDMethionine aminopeptidase 2/0.449
3tjlFMNNADPH dehydrogenase/0.449
4bfxZVXPantothenate kinase2.7.1.330.449
4c49HCYCorticosteroid-binding globulin/0.449
4fse0VABeta-secretase 13.4.23.460.449
4necSAHPutative SAM-dependent methyltransferase/0.449
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.449
4rnwFMNNADPH dehydrogenase 11.6.99.10.449
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.449
5irnADPNucleotide binding oligomerization domain containing 2/0.449
1rzuADPGlycogen synthase 12.4.1.210.448
1xe65FPPlasmepsin-23.4.23.390.448
2cndFADNitrate reductase [NADH]1.7.1.10.448
2ed3SAHDiphthine synthase/0.448
2ejzSAHDiphthine synthase/0.448
3ojwFMNNADPH--cytochrome P450 reductase/0.448
4bftZVTPantothenate kinase2.7.1.330.448
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.448
4v2gITCTetracycline repressor protein class D/0.448
1icpFMN12-oxophytodienoate reductase 11.3.1.420.447
1w6rGNTAcetylcholinesterase3.1.1.70.447
1x1bSAHC-20 methyltransferase/0.447
2gywOBIAcetylcholinesterase3.1.1.70.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.447
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.447
2zrvFNRIsopentenyl-diphosphate delta-isomerase/0.447
3qgf46FGenome polyprotein2.7.7.480.447
3tlc7MDMicrocin C7 self-immunity protein MccF/0.447
3vydVYDRenin3.4.23.150.447
4lu3AZMCarbonic anhydrase 144.2.1.10.447
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.446
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.446
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.446
1reqDCAMethylmalonyl-CoA mutase large subunit5.4.99.20.446
2e07SAHDiphthine synthase/0.446
2gesCOKPantothenate kinase2.7.1.330.446
3af0GDPPantothenate kinase2.7.1.330.446
3ccc7ACDipeptidyl peptidase 4/0.446
3fr5I4AFatty acid-binding protein, adipocyte/0.446
3p62FMNPentaerythritol tetranitrate reductase/0.446
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3vyfVYFRenin3.4.23.150.446
4ihl1F514-3-3 protein zeta/delta/0.446
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.445
1nuuNADNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.445
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.445
2bf7HBIPteridine reductase 11.5.1.330.445
2futH1SHeparin and heparin-sulfate lyase/0.445
3bgxMEFThymidylate synthase/0.445
3qe2FMNNADPH--cytochrome P450 reductase/0.445
4gv25MEPoly [ADP-ribose] polymerase 32.4.2.300.445
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.445
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.445
5hwoHMGHydroxymethylglutaryl-CoA synthase/0.445
1h5qNAPNADP-dependent mannitol dehydrogenase1.1.1.1380.444
1ix1BB2Peptide deformylase/0.444
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.444
1t7o152Carnitine O-acetyltransferase2.3.1.70.444
2cekN8TAcetylcholinesterase3.1.1.70.444
2f98NGVAklanonic acid methyl ester cyclase AcmA5.5.1.230.444
2fapRADPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
2fapRADSerine/threonine-protein kinase mTOR2.7.11.10.444
2vuuNAPNitrogen metabolite repression protein nmrA/0.444
2xukTZ5Acetylcholinesterase3.1.1.70.444
3d91REMRenin3.4.23.150.444
3koyZ97D-ornithine 4,5-aminomutase subunit beta/0.444
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.444
3opmLUIDipeptidyl peptidase 4/0.444
3vjlW94Dipeptidyl peptidase 4/0.444
1cneFADNitrate reductase [NADH]1.7.1.10.443
1cznFMNFlavodoxin/0.443
1t2cNAIL-lactate dehydrogenase1.1.1.270.443
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.443
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.443
2fs4PZ1Renin3.4.23.150.443
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.443
2g1r3IGRenin3.4.23.150.443
2ifaFMNUncharacterized protein/0.443
3lqfNADGalactitol dehydrogenase/0.443
3q7fED2Uncharacterized protein/0.443
3qviK95HAP protein/0.443
3wqmB29Diterpene synthase3.1.7.80.443
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.443
4qnwFMNChanoclavine-I aldehyde reductase easA/0.443
5a4vQUEGlutathione S-transferase F22.5.1.180.443
1aiqCB3Thymidylate synthase/0.442
1ppl1Z7Penicillopepsin-13.4.23.200.442
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.442
2fznFADBifunctional protein PutA1.5.5.20.442
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.442
2pncCLUPrimary amine oxidase, liver isozyme/0.442
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.442
2tplHPPTyrosine phenol-lyase4.1.99.20.442
3af3GCPPantothenate kinase2.7.1.330.442
3ndjJHZMethyltransferase/0.442
3oqkS52Renin3.4.23.150.442
3rsv3RSBeta-secretase 13.4.23.460.442
4gddNAIUDP-galactopyranose mutase/0.442
4m5pFMNNADPH dehydrogenase/0.442
1a8pFADFerredoxin--NADP reductase/0.441
1fx1FMNFlavodoxin/0.441
1k4mNADNicotinate-nucleotide adenylyltransferase2.7.7.180.441
1ni1HFPProtein farnesyltransferase subunit beta2.5.1.580.441
2ab8MTPAdenosine kinase2.7.1.200.441
2ctsCOACitrate synthase, mitochondrial2.3.3.10.441
2ewvADPTwitching motility protein PilT/0.441
2gevCOKPantothenate kinase2.7.1.330.441
2ikuLIYRenin3.4.23.150.441
2iviACWIsopenicillin N synthase1.21.3.10.441
2pk3GDDGDP-6-deoxy-D-mannose reductase/0.441
2vkeTACTetracycline repressor protein class D/0.441
2xujTZ5Acetylcholinesterase3.1.1.70.441
3f8sPF2Dipeptidyl peptidase 4/0.441
3kftNADPentaerythritol tetranitrate reductase/0.441
4b7zQ4QAcetylcholinesterase3.1.1.70.441
1jf0CZHObelin/0.440
1ypkCCRProthrombin3.4.21.50.440
2hv9SFGmRNA cap guanine-N7 methyltransferase2.1.1.560.440
2zgb21UProthrombin3.4.21.50.440
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.440
3n19FNRXenobiotic reductase/0.440
4bb3KKAIsopenicillin N synthase1.21.3.10.440
4e2xTYDMethyltransferase/0.440
4eu4COASuccinyl-CoA:acetate CoA-transferase/0.440
4jtqNAPAldo-keto reductase family 1 member C2/0.440