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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
2fx2FMNFlavodoxin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2fx2FMNFlavodoxin/1.000
1j8qFMNFlavodoxin/0.667
1wsbFMNFlavodoxin/0.634
1xyvFMNFlavodoxin/0.624
1akwFMNFlavodoxin/0.610
1j9gFMNFlavodoxin/0.610
5tgzFMNCannabinoid receptor 1/0.606
1fx1FMNFlavodoxin/0.593
3f6rFMNFlavodoxin/0.589
4fx2FMNFlavodoxin/0.587
3kaqFMNFlavodoxin/0.584
1bu5RBFFlavodoxin/0.583
1azlFMNFlavodoxin/0.582
1akuFMNFlavodoxin/0.578
1xyyFMNFlavodoxin/0.570
3kapFMNFlavodoxin/0.570
5fx2FMNFlavodoxin/0.566
3f90FMNFlavodoxin/0.526
5xraFMNCannabinoid receptor 1/0.524
1c7fFMNFlavodoxin/0.523
4oxxFMNCindoxin/0.505
1gpuTHDTransketolase 12.2.1.10.503
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.501
2a2cADPN-acetylgalactosamine kinase2.7.1.1570.497
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.489
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.488
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.486
3mauPLRPutative sphingosine-1-phosphate lyase/0.482
2fcrFMNFlavodoxin/0.481
2mt9FMNFlavodoxin 2/0.479
4c73TLH3-oxoacyl-ACP synthase/0.478
1tkcM6TTransketolase 12.2.1.10.477
2q7oIMHPurine nucleoside phosphorylase2.4.2.10.477
3dylIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.477
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.477
4b4w9L9Bifunctional protein FolD/0.476
3fhxPLPPyridoxal kinase2.7.1.350.475
1iayAVG1-aminocyclopropane-1-carboxylate synthase 24.4.1.140.472
1mrkFMCRibosome-inactivating protein alpha-trichosanthin3.2.2.220.472
3p1799PProthrombin3.4.21.50.472
1g63FMNEpidermin decarboxylase4.1.10.470
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.469
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.469
2hp2KE4Glutamate-1-semialdehyde 2,1-aminomutase5.4.3.80.468
3zv7NHGAcetylcholinesterase3.1.1.70.468
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.467
2r8pT6FTransketolase 1/0.467
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.467
4js0GNPCell division control protein 42 homolog/0.467
1cznFMNFlavodoxin/0.466
3dyqIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.466
3junAJDPhenazine biosynthesis protein A/B/0.466
3eksCY9Actin-5C/0.465
3uweVJJAldo-keto reductase family 1 member C3/0.465
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.463
1q84TZ4Acetylcholinesterase3.1.1.70.463
4mrm2BYGamma-aminobutyric acid type B receptor subunit 1/0.463
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.462
1qtiGNTAcetylcholinesterase3.1.1.70.462
2zf051UProthrombin3.4.21.50.462
3uzzTES3-oxo-5-beta-steroid 4-dehydrogenase/0.462
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.462
1w6rGNTAcetylcholinesterase3.1.1.70.461
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.461
3aosJH2Hemolymph juvenile hormone binding protein/0.461
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.461
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.461
4baoMVFProthrombin3.4.21.50.461
1pqc444Oxysterols receptor LXR-beta/0.460
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.460
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.460
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.460
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.460
4m0cFMNFMN-dependent NADH-azoreductase 1/0.460
1cjkFOKAdenylate cyclase type 2/0.459
1cjkFOKAdenylate cyclase type 5/0.459
1f20FADNitric oxide synthase, brain1.14.13.390.459
2jf0HBPAcetylcholinesterase3.1.1.70.459
3q9bB3NAcetylpolyamine amidohydrolase/0.459
3zj0ACOPutative acetyltransferase OgpAT/0.459
5xr8FMNCannabinoid receptor 1/0.459
4h6pFMNChromate reductase/0.458
1pq944BOxysterols receptor LXR-beta/0.457
2j3qTFLAcetylcholinesterase3.1.1.70.457
1dggNDPCatalase1.11.1.60.456
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.456
2g1a5HGClass B acid phosphatase3.1.3.20.456
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.456
3gr8FMNNADPH dehydrogenase/0.456
3iu9T07Methionine aminopeptidase 2/0.456
3wqmB29Diterpene synthase3.1.7.80.456
4b117I1Glycylpeptide N-tetradecanoyltransferase/0.456
4c72TLG3-oxoacyl-ACP synthase/0.456
3uonQNBMuscarinic acetylcholine receptor M2/0.456
2gfxPMN3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.455
2r8oT5XTransketolase 1/0.455
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.455
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.455
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.455
3mauEXTPutative sphingosine-1-phosphate lyase/0.455
1xh7R96cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.454
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.454
2zgb21UProthrombin3.4.21.50.454
4bfyZVYPantothenate kinase2.7.1.330.454
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1zgv501Prothrombin3.4.21.50.453
2cekN8TAcetylcholinesterase3.1.1.70.453
2ejzSAHDiphthine synthase/0.453
2fxuBIDActin, alpha skeletal muscle/0.453
2vbpVB1Isopenicillin N synthase1.21.3.10.453
3dvaTPWPyruvate dehydrogenase E1 component subunit alpha1.2.4.10.453
3dvaTPWPyruvate dehydrogenase E1 component subunit beta1.2.4.10.453
3fsjD7KBenzoylformate decarboxylase4.1.1.70.453
1a9cGTPGTP cyclohydrolase 13.5.4.160.452
1b9iPXG3-amino-5-hydroxybenzoate synthase4.2.1.1440.452
1ykgFMNSulfite reductase [NADPH] flavoprotein alpha-component/0.452
2r5nTPPTransketolase 1/0.452
2v2zADP4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.452
3nx2FERFerulic acid decarboxylase/0.452
3v2uATPProtein GAL3/0.452
4c717RD3-oxoacyl-ACP synthase/0.452
4oztP1AEcdysone receptor, putative/0.452
2cn0F25Prothrombin3.4.21.50.451
2i4qUA4Renin3.4.23.150.451
3pkeY10Methionine aminopeptidase 2/0.451
4b1hAR6Poly(ADP-ribose) glycohydrolase3.2.1.1430.451
5cmx0G6Prothrombin3.4.21.50.451
1cjvFOKAdenylate cyclase type 2/0.450
1cjvFOKAdenylate cyclase type 5/0.450
1zgbA1EAcetylcholinesterase3.1.1.70.450
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.450
3iexGMPPurine nucleoside phosphorylase/0.450
3ntrNADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase1.1.1.180.450
3qvrFADGlucose oxidase1.1.3.40.450
4fhd0TTSpore photoproduct lyase/0.450
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.450
5ilwURIRibosome inactivating protein/0.450
1obnASVIsopenicillin N synthase1.21.3.10.449
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.449
2ffqGSPRas-related protein Rab-6B/0.449
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.449
4l091URTankyrase-22.4.2.300.449
1h22E10Acetylcholinesterase3.1.1.70.448
1tkaN3TTransketolase 12.2.1.10.448
1x8lOXRRetinol dehydratase/0.448
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.448
3rvhHQ2Lysine-specific demethylase 4A1.14.110.448
3u57DH8Raucaffricine-O-beta-D-glucosidase3.2.1.1250.448
3wquATPCell division protein FtsA/0.448
4bmpFMNProtein NrdI/0.448
4imfSI3N-acetylneuraminate lyase/0.448
1mrqSTRAldo-keto reductase family 1 member C1/0.447
1tkbN1TTransketolase 12.2.1.10.447
2bu9HFVIsopenicillin N synthase1.21.3.10.447
2op18PCEnoyl-ACP reductase/0.447
3c1kT15Prothrombin3.4.21.50.447
4bj9UHBTankyrase-22.4.2.300.447
4eqrCOACoenzyme A disulfide reductase/0.447
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.447
5cxv0HKMuscarinic acetylcholine receptor M1/0.447
1bk0ACVIsopenicillin N synthase1.21.3.10.446
1gj5130Prothrombin3.4.21.50.446
1mueCDDProthrombin3.4.21.50.446
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.446
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.446
1zgcA2EAcetylcholinesterase3.1.1.70.446
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2vyqFADFerredoxin--NADP reductase1.18.1.20.446
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.446
3br3ETHTH-type transcriptional regulator QacR/0.446
3g0yP9A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.446
3hxcBD6Geranylgeranyl transferase type-2 subunit beta2.5.1.600.446
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3k8q22APurine nucleoside phosphorylase2.4.2.10.446
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
3pfhT3QdTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase2.1.1.2350.446
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4epq0RRPoly(ADP-ribose) glycohydrolase/0.446
4ey6GNTAcetylcholinesterase3.1.1.70.446
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.445
1rzuADPGlycogen synthase 12.4.1.210.445
1tilATPAnti-sigma F factor/0.445
2ckmAA7Acetylcholinesterase3.1.1.70.445
2jgsBTNAvidin/0.445
2v5uFMNFlavodoxin/0.445
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3cotSTR3-oxo-5-beta-steroid 4-dehydrogenase/0.445
3ekuCY9Actin-5C/0.445
3qeoLLTDeoxycytidine kinase2.7.1.740.445
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.445
5a8aADPRiboflavin biosynthesis protein RibF2.7.1.260.445
1culFOKAdenylate cyclase type 2/0.444
1culFOKAdenylate cyclase type 5/0.444
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.444
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.444
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.444
2cv2GSUGlutamate--tRNA ligase6.1.1.170.444
2ed3SAHDiphthine synthase/0.444
2fj1CTCTetracycline repressor protein class D/0.444
2zdv37UProthrombin3.4.21.50.444
2zff53UProthrombin3.4.21.50.444
3fapARDPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.444
3fapARDSerine/threonine-protein kinase mTOR2.7.11.10.444
3fktSIIBeta-secretase 13.4.23.460.444
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.444
3u8fFGMRibosome inactivating protein/0.444
4iomFOLFormate--tetrahydrofolate ligase/0.444
1jwtBLIProthrombin3.4.21.50.443
1mmkH4BPhenylalanine-4-hydroxylase1.14.16.10.443
1svlADPLarge T antigen3.6.40.443
2aj4ANPGalactokinase2.7.1.60.443
2g1n1IGRenin3.4.23.150.443
2xukTZ5Acetylcholinesterase3.1.1.70.443
3dux64UProthrombin3.4.21.50.443
3gyf51PDihydrofolate reductase1.5.1.30.443
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
4bb3KKAIsopenicillin N synthase1.21.3.10.443
4ft4SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.443
4ihiNADProbable pyrroline-5-carboxylate dehydrogenase RocA/0.443
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.443
5c4fUPGHisto-blood group ABO system transferase/0.443
1ja0FADNADPH--cytochrome P450 reductase/0.442
1p5rCOAFormyl-CoA:oxalate CoA-transferase/0.442
1t7o152Carnitine O-acetyltransferase2.3.1.70.442
1w4lGL8Acetylcholinesterase3.1.1.70.442
1z6tADPApoptotic protease-activating factor 1/0.442
2c20NADUDP-glucose 4-epimerase/0.442
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.442
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.442
2v3hI25Prothrombin3.4.21.50.442
2vq7NAPPutative flavin-containing monooxygenase/0.442
2zgx29UProthrombin3.4.21.50.442
1j9zFADNADPH--cytochrome P450 reductase/0.441
1odcA8BAcetylcholinesterase3.1.1.70.441
1rszDIHPurine nucleoside phosphorylase2.4.2.10.441
1ry0PG2Aldo-keto reductase family 1 member C3/0.441
1ycfFMNNitric oxide reductase10.441
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.441
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.441
3e4vFMNUncharacterized protein/0.441
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3h2sNDPPutative NADH-flavin reductase/0.441
3hy9098A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.441
3keuATPPyridoxal kinase2.7.1.350.441
4afgQMRAchbp/0.441
1foaUD1Alpha-1,3-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase2.4.1.1010.440
1w6jR71Lanosterol synthase5.4.99.70.440
2evcFC3Methionine aminopeptidase/0.440
2f2sCOAAcetyl-CoA acetyltransferase, mitochondrial2.3.1.90.440
2gywOBIAcetylcholinesterase3.1.1.70.440
3djjFADGlutathione reductase, mitochondrial1.8.1.70.440
3ho9N3A3-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.440
4araC56Acetylcholinesterase3.1.1.70.440
4ey7E20Acetylcholinesterase3.1.1.70.440
4n3l2FNProthrombin3.4.21.50.440