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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3gr8FMNNADPH dehydrogenase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3gr8FMNNADPH dehydrogenase/1.000
3hf3FMNChromate reductase/0.599
3kruFMNNADH:flavin oxidoreductase/NADH oxidase/0.587
1z48FMNNADPH dehydrogenase/0.575
1z44FMNNADPH dehydrogenase/0.563
3hgsFMN12-oxophytodienoate reductase 31.3.1.420.559
3f03FMNPentaerythritol tetranitrate reductase/0.547
1z41FMNNADPH dehydrogenase/0.542
3p8jFMNPentaerythritol tetranitrate reductase/0.540
3p62FMNPentaerythritol tetranitrate reductase/0.538
3p74FMNPentaerythritol tetranitrate reductase/0.536
3p84FMNPentaerythritol tetranitrate reductase/0.533
1icsFMN12-oxophytodienoate reductase 11.3.1.420.530
3l5lFMNXenobiotic reductase/0.526
2gouFMNNADH:flavin oxidoreductase Sye1/0.519
1h63FMNPentaerythritol tetranitrate reductase/0.517
3tjlFMNNADPH dehydrogenase/0.514
4qnwFMNChanoclavine-I aldehyde reductase easA/0.514
1h51FMNPentaerythritol tetranitrate reductase/0.508
1icqFMN12-oxophytodienoate reductase 11.3.1.420.502
2abbFMNPentaerythritol tetranitrate reductase/0.501
1x8lOXRRetinol dehydratase/0.499
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.499
1vyrFMNPentaerythritol tetranitrate reductase/0.498
4xguADPPutative pachytene checkpoint protein 2/0.497
2h8xFMNXenA/0.495
4rnwFMNNADPH dehydrogenase 11.6.99.10.492
2g25TDKPyruvate dehydrogenase E1 component1.2.4.10.491
4utlFNRXenobiotic reductase/0.491
1h50FMNPentaerythritol tetranitrate reductase/0.490
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.488
4jicFMNGTN Reductase/0.487
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.487
1bwlFMNNADPH dehydrogenase 11.6.99.10.486
1d0lBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.486
3b05FNRIsopentenyl-diphosphate delta-isomerase/0.486
4m5pFMNNADPH dehydrogenase/0.486
4df2FMNNADPH dehydrogenase/0.485
4awtFMNNADH:flavin oxidoreductase Sye1/0.484
2zrvFNRIsopentenyl-diphosphate delta-isomerase/0.483
2zryFNRIsopentenyl-diphosphate delta-isomerase/0.483
3hgrFMN12-oxophytodienoate reductase 11.3.1.420.483
4uthFMNXenobiotic reductase/0.482
2g8yNADHydroxycarboxylate dehydrogenase B/0.481
2zrzFNRIsopentenyl-diphosphate delta-isomerase/0.481
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.480
4bfxZVXPantothenate kinase2.7.1.330.478
4mv8ACPBiotin carboxylase6.3.4.140.478
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.477
3u9eCOALmo1369 protein/0.476
4awsFMNNADH:flavin oxidoreductase Sye1/0.476
4qaiFMNNADPH dehydrogenase/0.476
1kbiFMNCytochrome b2, mitochondrial1.1.2.30.475
2gjlFMNNitronate monooxygenase1.13.12.160.475
2gjnFMNNitronate monooxygenase1.13.12.160.475
2q1wNADPutative nucleotide sugar epimerase/ dehydratase/0.475
3b03VNRIsopentenyl-diphosphate delta-isomerase/0.475
4ycpFMNtRNA-dihydrouridine(16) synthase/0.475
4yl2FMNLactate oxidase/0.475
2gqaFMNNADH:flavin oxidoreductase Sye1/0.473
4gxs0YSGlutamate receptor 2/0.473
2r5nTPPTransketolase 1/0.472
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.472
3p82FMNPentaerythritol tetranitrate reductase/0.472
1q45FMN12-oxophytodienoate reductase 31.3.1.420.471
2ojtUBAGlutamate receptor ionotropic, kainate 1/0.470
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.470
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.470
1kbjFMNCytochrome b2, mitochondrial1.1.2.30.469
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.469
3p67FMNPentaerythritol tetranitrate reductase/0.469
3hk1B64Fatty acid-binding protein, adipocyte/0.468
4utkFNRXenobiotic reductase/0.468
1vjiFMN12-oxophytodienoate reductase 11.3.1.420.467
2iyfERYOleandomycin glycosyltransferase2.4.10.467
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.467
3b04OOPIsopentenyl-diphosphate delta-isomerase/0.467
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.466
1o0sNAINAD-dependent malic enzyme, mitochondrial1.1.1.380.465
3otwCOAPhosphopantetheine adenylyltransferase/0.465
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.465
3n19FNRXenobiotic reductase/0.464
4bfvZVVPantothenate kinase2.7.1.330.464
2e77FMNLactate oxidase/0.463
2g28TDKPyruvate dehydrogenase E1 component1.2.4.10.463
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.463
2q3oFMN12-oxophytodienoate reductase 31.3.1.420.463
3tr05GPGuanylate kinase/0.463
3atzFMNProstaglandin F2a synthase/0.462
4k7yFMNNADPH dehydrogenase 11.6.99.10.462
2vnjFADNADPH:ferredoxin reductase/0.461
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.461
4rnxFMNNADPH dehydrogenase 11.6.99.10.461
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.460
2g1n1IGRenin3.4.23.150.460
2zrxFMNIsopentenyl-diphosphate delta-isomerase/0.460
3p8iFMNPentaerythritol tetranitrate reductase/0.460
3s8pSAMHistone-lysine N-methyltransferase KMT5B2.1.1.430.460
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.460
4rjeFNRLactate oxidase/0.460
4rnvFMNNADPH dehydrogenase 11.6.99.10.460
1qorNDPQuinone oxidoreductase 1/0.459
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.459
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.459
2ejvNADL-threonine 3-dehydrogenase/0.459
4uymVOR14-alpha sterol demethylase Cyp51B/0.459
2pncCLUPrimary amine oxidase, liver isozyme/0.458
1icpFMN12-oxophytodienoate reductase 11.3.1.420.457
2igoFADPyranose 2-oxidase/0.457
2ohjFMNType A flavoprotein FprA10.457
2w02ATPAcsD/0.457
3zkyWT4Isopenicillin N synthase1.21.3.10.457
4xnw2IDP2Y purinoceptor 1/0.457
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.456
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.456
1udaUFGUDP-glucose 4-epimerase5.1.3.20.455
2iko7IGRenin3.4.23.150.455
2po7CHDFerrochelatase, mitochondrial4.99.1.10.455
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.455
3muoZPRProlyl endopeptidase/0.455
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.455
4mv1ADPBiotin carboxylase6.3.4.140.455
4tmcFMNOld yellow enzyme/0.455
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.454
1ta6177Prothrombin3.4.21.50.454
1vhnFMNtRNA-dihydrouridine synthase/0.454
2ed3SAHDiphthine synthase/0.454
3q9bB3NAcetylpolyamine amidohydrolase/0.454
3zhrTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.454
4bzbDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.454
1fxsNAPGDP-L-fucose synthase/0.453
1x1bSAHC-20 methyltransferase/0.453
1yqxNAPSinapyl alcohol dehydrogenase/0.453
2zs9ADPPantothenate kinase2.7.1.330.453
3ingNDPHomoserine dehydrogenase related protein/0.453
3ojxFMNNADPH--cytochrome P450 reductase/0.453
3qt62P0Mevalonate diphosphate decarboxylase/0.453
4wpuGDPPhosphoenolpyruvate carboxykinase [GTP]/0.453
1fmlRTLRetinol dehydratase/0.452
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.452
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.452
2qf2GDPPhosphoenolpyruvate carboxykinase, cytosolic [GTP]4.1.1.320.452
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.452
3b9oFMNAlkane monoxygenase/0.452
3ig6438Urokinase-type plasminogen activator3.4.21.730.452
4bfsZVSPantothenate kinase2.7.1.330.452
1g7vPAI2-dehydro-3-deoxyphosphooctonate aldolase2.5.1.550.451
1h74ADPHomoserine kinase2.7.1.390.451
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.451
2vn1FK5Peptidylprolyl isomerase/0.451
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.451
3e39FMNNitroreductase/0.451
3fr5I4AFatty acid-binding protein, adipocyte/0.451
4ocvANPAminoglycoside phosphotransferase/0.451
1ftlDNQGlutamate receptor 2/0.450
2ebaFADPutative glutaryl-CoA dehydrogenase/0.450
2w6qOA5Biotin carboxylase6.3.4.140.450
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.450
3gkaFMNN-ethylmaleimide reductase/0.450
4hmvWUBPhenazine biosynthesis protein PhzG1.40.450
4rnuFMNNADPH dehydrogenase 11.6.99.10.450
5fd8A5APutative carboxypeptidase yocD/0.450
1fmjRTLRetinol dehydratase/0.449
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1h66FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1r6uTYMTryptophan--tRNA ligase, cytoplasmic6.1.1.20.449
1trkTPPTransketolase 12.2.1.10.449
3r96ACOMccE protein/0.449
3triNAPPyrroline-5-carboxylate reductase/0.449
4bv9NDPKetimine reductase mu-crystallin1.5.1.250.449
4q71FADBifunctional protein PutA/0.449
1e7qNAPGDP-L-fucose synthase/0.448
2g1s4IGRenin3.4.23.150.448
2geuCOKPantothenate kinase2.7.1.330.448
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.448
2x7hPFNProstaglandin reductase 310.448
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.448
3c1kT15Prothrombin3.4.21.50.448
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.448
3zbrNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.448
1ay0TPPTransketolase 12.2.1.10.447
1q6t600Tyrosine-protein phosphatase non-receptor type 13.1.3.480.447
1tqf32PBeta-secretase 13.4.23.460.447
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.447
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.447
3fktSIIBeta-secretase 13.4.23.460.447
3nutSAHPrecorrin-3 methylase/0.447
3rudNADUDP-N-acetylglucosamine 4-epimerase/0.447
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.447
4lcjNADC-terminal-binding protein 2/0.447
1b2lNDCAlcohol dehydrogenase1.1.1.10.446
1szgFNSCytochrome b2, mitochondrial1.1.2.30.446
2x0iNAIMalate dehydrogenase/0.446
2z1mNDPGDP-mannose 4,6-dehydratase/0.446
3tjzGNPADP-ribosylation factor 1/0.446
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.445
1x1aSAMC-20 methyltransferase/0.445
1xl8152Peroxisomal carnitine O-octanoyltransferase2.3.1.1370.445
2am22LGUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.445
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.445
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.445
2y6fM9FIsopenicillin N synthase1.21.3.10.445
3otbDGTProbable tRNA(His) guanylyltransferase2.7.7.790.445
3vg10GTBeta-secretase 13.4.23.460.445
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.445
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.445
5jscFADPutative acyl-CoA dehydrogenase/0.445
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.444
1f17NAIHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.444
1itzTPPTransketolase, chloroplastic2.2.1.10.444
1lrjUD1UDP-glucose 4-epimerase5.1.3.20.444
1rp7TZDPyruvate dehydrogenase E1 component1.2.4.10.444
2anb5GPGuanylate kinase2.7.4.80.444
2du2FMNLactate oxidase/0.444
3h3r14HCollagen type IV alpha-3-binding protein/0.444
3qviK95HAP protein/0.444
3to3ATPPetrobactin biosynthesis protein AsbB/0.444
5b0oADPFlagellum-specific ATP synthase3.6.3.140.444
1jcq739Protein farnesyltransferase subunit beta2.5.1.580.443
2v59LZKBiotin carboxylase6.3.4.140.443
4b63FADL-ornithine N(5)-monooxygenase/0.443
4dieC5PCytidylate kinase/0.443
4m9aFDAAcyl-CoA dehydrogenase/0.443
1bwsNDPGDP-L-fucose synthase/0.442
1yqzCOACoenzyme A disulfide reductase/0.442
2zc922UProthrombin3.4.21.50.442
3eteNDPGlutamate dehydrogenase 1, mitochondrial1.4.1.30.442
3lqfNADGalactitol dehydrogenase/0.442
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.442
4h6kFMNNADPH dehydrogenase 11.6.99.10.442
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.442
4itmATPTetraacyldisaccharide 4'-kinase/0.442
4iv6FDAIsovaleryl-CoA dehydrogenase/0.442
4z4pSAHHistone-lysine N-methyltransferase 2D2.1.1.430.442
1a8pFADFerredoxin--NADP reductase/0.441
1e79ATPATP synthase subunit alpha, mitochondrial/0.441
1e79ATPATP synthase subunit beta, mitochondrial3.6.3.140.441
1g1aNADdTDP-glucose 4,6-dehydratase/0.441
1i5cADPChemotaxis protein CheA2.7.13.30.441
1sa4JANProtein farnesyltransferase subunit beta2.5.1.580.441
2j6xFMNLactate oxidase/0.441
2lbaCHOFatty acid binding protein 6/0.441
2v58LZJBiotin carboxylase6.3.4.140.441
2y66N04UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.441
3cluFADElectron transfer flavoprotein subunit alpha/0.441
3q7fED2Uncharacterized protein/0.441
1dr2TAPDihydrofolate reductase1.5.1.30.440
2dfvNADL-threonine 3-dehydrogenase/0.440
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.440
2r2mI50Prothrombin3.4.21.50.440
2v3oI26Prothrombin3.4.21.50.440
2xlpFADPutative flavin-containing monooxygenase/0.440
2zfaFMNLactate oxidase/0.440
3fsuFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.440
3gyeFMNDihydroorotate dehydrogenase (fumarate)/0.440
3te5NAI5'-AMP-activated protein kinase subunit gamma/0.440
3zcsCAWGlycogen phosphorylase, muscle form2.4.1.10.440
4askK0ILysine-specific demethylase 6B1.14.110.440
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4l9kEHFSerum albumin/0.440
4y9uNAPNADPH--cytochrome P450 reductase/0.440