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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
1kbiFMNCytochrome b2, mitochondrial1.1.2.3

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1kbiFMNCytochrome b2, mitochondrial1.1.2.31.000
1fcbFMNCytochrome b2, mitochondrial1.1.2.30.675
1kbjFMNCytochrome b2, mitochondrial1.1.2.30.631
1szgFNSCytochrome b2, mitochondrial1.1.2.30.610
1szfFMNCytochrome b2, mitochondrial1.1.2.30.609
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.594
2oz0FMNCytochrome b2, mitochondrial1.1.2.30.587
1goxFMNPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.577
1qcwFNSCytochrome b2, mitochondrial1.1.2.30.569
2e77FMNLactate oxidase/0.569
2nliFMNLactate oxidase/0.564
5ebuFMNLactate oxidase/0.558
1h50FMNPentaerythritol tetranitrate reductase/0.537
2j6xFMNLactate oxidase/0.535
4rjeFNRLactate oxidase/0.529
4yl2FMNLactate oxidase/0.526
3p62FMNPentaerythritol tetranitrate reductase/0.524
3f03FMNPentaerythritol tetranitrate reductase/0.519
3hf3FMNChromate reductase/0.518
1vyrFMNPentaerythritol tetranitrate reductase/0.516
3hgoFMN12-oxophytodienoate reductase 31.3.1.420.512
1icqFMN12-oxophytodienoate reductase 11.3.1.420.508
1icpFMN12-oxophytodienoate reductase 11.3.1.420.505
3p74FMNPentaerythritol tetranitrate reductase/0.505
2abbFMNPentaerythritol tetranitrate reductase/0.503
2hs6FMN12-oxophytodienoate reductase 31.3.1.420.502
1h63FMNPentaerythritol tetranitrate reductase/0.501
4tmbFMNOld yellow enzyme/0.500
1z44FMNNADPH dehydrogenase/0.499
2du2FMNLactate oxidase/0.497
1h51FMNPentaerythritol tetranitrate reductase/0.494
3p67FMNPentaerythritol tetranitrate reductase/0.494
4jicFMNGTN Reductase/0.493
1icsFMN12-oxophytodienoate reductase 11.3.1.420.491
3p84FMNPentaerythritol tetranitrate reductase/0.491
1bwlFMNNADPH dehydrogenase 11.6.99.10.490
2gjlFMNNitronate monooxygenase1.13.12.160.490
4rnwFMNNADPH dehydrogenase 11.6.99.10.489
2zfaFMNLactate oxidase/0.487
2q3rFMN12-oxophytodienoate reductase 11.3.1.420.485
3p82FMNPentaerythritol tetranitrate reductase/0.485
4awtFMNNADH:flavin oxidoreductase Sye1/0.485
3hgrFMN12-oxophytodienoate reductase 11.3.1.420.484
4e2bFMNDehydrogenase/0.482
1vjiFMN12-oxophytodienoate reductase 11.3.1.420.481
2hs8FMN12-oxophytodienoate reductase 31.3.1.420.481
3p8iFMNPentaerythritol tetranitrate reductase/0.481
4h6kFMNNADPH dehydrogenase 11.6.99.10.481
4m5pFMNNADPH dehydrogenase/0.480
1z41FMNNADPH dehydrogenase/0.479
3p8jFMNPentaerythritol tetranitrate reductase/0.479
4e2dFMNDehydrogenase/0.479
4rnuFMNNADPH dehydrogenase 11.6.99.10.477
1f8fNADBenzyl alcohol dehydrogenase/0.475
4qaiFMNNADPH dehydrogenase/0.475
4rnvFMNNADPH dehydrogenase 11.6.99.10.475
1q45FMN12-oxophytodienoate reductase 31.3.1.420.473
2gjnFMNNitronate monooxygenase1.13.12.160.472
3gkaFMNN-ethylmaleimide reductase/0.472
1z48FMNNADPH dehydrogenase/0.470
2gqaFMNNADH:flavin oxidoreductase Sye1/0.469
1oycFMNNADPH dehydrogenase 11.6.99.10.467
4df2FMNNADPH dehydrogenase/0.467
4yr9NADL-threonine 3-dehydrogenase, mitochondrial1.1.1.1030.466
1bwkFMNNADPH dehydrogenase 11.6.99.10.465
3tjzGNPADP-ribosylation factor 1/0.465
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
1bwsNDPGDP-L-fucose synthase/0.463
2wwjY28Lysine-specific demethylase 4A/0.463
3atzFMNProstaglandin F2a synthase/0.463
4awsFMNNADH:flavin oxidoreductase Sye1/0.463
4iqlFMNEnoyl-(Acyl-carrier-protein) reductase II/0.463
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.462
1oyaFMNNADPH dehydrogenase 11.6.99.10.462
2anb5GPGuanylate kinase2.7.4.80.462
2gouFMNNADH:flavin oxidoreductase Sye1/0.462
3mx5UTPNucleoprotein/0.462
1adfTADAlcohol dehydrogenase E chain1.1.1.10.461
2bi8FADUDP-galactopyranose mutase5.4.99.90.461
2c54NADGDP-mannose 3,5-epimerase5.1.3.180.461
2fxv5GPXanthine phosphoribosyltransferase2.4.2.220.460
2oapANPType II secretion system protein (GspE-2)/0.460
4qnwFMNChanoclavine-I aldehyde reductase easA/0.460
4ycpFMNtRNA-dihydrouridine(16) synthase/0.460
4a3uFMNNADH:flavin oxidoreductase/NADH oxidase/0.459
4ambDUDPutative glycosyl transferase/0.459
4hmz18TdTDP-4-dehydro-6-deoxyglucose 3-epimerase5.1.3.270.459
4uthFMNXenobiotic reductase/0.459
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.459
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.458
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.457
2ien017Gag-Pol polyprotein3.4.23.160.457
2iibC5PAlpha-2,3/2,6-sialyltransferase/sialidase/0.457
3nl6TPSUncharacterized protein/0.457
3tjlFMNNADPH dehydrogenase/0.457
1dr2TAPDihydrofolate reductase1.5.1.30.456
3b70NAPEnoyl reductase LovC10.456
1w6hTITPlasmepsin-23.4.23.390.455
2g226IGRenin3.4.23.150.455
2g8yNADHydroxycarboxylate dehydrogenase B/0.455
4utlFNRXenobiotic reductase/0.455
2yd0BESEndoplasmic reticulum aminopeptidase 13.4.110.453
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.453
1p9wANPType II secretion system protein E/0.452
2qzlIXSBeta-secretase 13.4.23.460.452
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.452
4tmcFMNOld yellow enzyme/0.452
4utkFNRXenobiotic reductase/0.452
1rneC60Renin3.4.23.150.451
3kruFMNNADH:flavin oxidoreductase/NADH oxidase/0.451
3l5lFMNXenobiotic reductase/0.451
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.450
2b4tAESGlyceraldehyde-3-phosphate dehydrogenase/0.450
3x2uATPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
4eb5PLPCysteine desulfurase IscS 2/0.450
5e7oMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.450
2gesCOKPantothenate kinase2.7.1.330.449
4c13UMLUDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase/0.449
1g9dBABBotulinum neurotoxin type B3.4.24.690.448
3hgsFMN12-oxophytodienoate reductase 31.3.1.420.448
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.448
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.448
4xw4ANPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
1t9gFADMedium-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.70.447
2vbdV10Isopenicillin N synthase1.21.3.10.447
3enkUPGUDP-glucose 4-epimerase/0.447
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.447
5c3aURMHisto-blood group ABO system transferase/0.447
1i59ANPChemotaxis protein CheA2.7.13.30.446
3qe2FMNNADPH--cytochrome P450 reductase/0.446
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.446
4dmmNAP3-oxoacyl-[acyl-carrier-protein] reductase/0.446
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.446
4opgFDAConserved Archaeal protein/0.446
4wdgA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
1fxsNAPGDP-L-fucose synthase/0.445
1tehNADAlcohol dehydrogenase class-31.1.1.10.445
1xe55FEPlasmepsin-23.4.23.390.445
1xe65FPPlasmepsin-23.4.23.390.445
2hrbNAPCarbonyl reductase [NADPH] 31.1.1.1840.445
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.445
4hmvWUBPhenazine biosynthesis protein PhzG1.40.445
4q71FADBifunctional protein PutA/0.445
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.444
2g1r3IGRenin3.4.23.150.444
2ignFADPyranose 2-oxidase/0.444
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.444
3lqfNADGalactitol dehydrogenase/0.444
4a802ANMajor pollen allergen Bet v 1-A/0.444
4c4oNADSADH/0.444
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4qxp1YEStimulator of interferon genes protein/0.444
4xguADPPutative pachytene checkpoint protein 2/0.444
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.443
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.443
2ewmNAD(S)-1-Phenylethanol dehydrogenase1.1.1.3110.443
2fzwNADAlcohol dehydrogenase class-31.1.1.10.443
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
3gr8FMNNADPH dehydrogenase/0.443
3n19FNRXenobiotic reductase/0.443
3tr05GPGuanylate kinase/0.443
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.443
1mjaCOAHistone acetyltransferase ESA1/0.442
1p0hACOMycothiol acetyltransferase2.3.1.1890.442
1xvaSAMGlycine N-methyltransferase2.1.1.200.442
2fj1CTCTetracycline repressor protein class D/0.442
2i4qUA4Renin3.4.23.150.442
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.442
2z1qFADAcyl-CoA dehydrogenase/0.442
3oqfS51Renin3.4.23.150.442
3uozFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
3zhtTD9Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.442
1w19T5P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2g247IGRenin3.4.23.150.441
2q2vNADBeta-D-hydroxybutyrate dehydrogenase/0.441
2trtTACTetracycline repressor protein class D/0.441
3lqsPSZD-alanine aminotransferase2.6.1.210.441
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.441
4x7wMVIMycinamicin III 3''-O-methyltransferase2.1.1.2370.441
1bil0IURenin3.4.23.150.440
1j21ATPArgininosuccinate synthase/0.440
1t2cNAIL-lactate dehydrogenase1.1.1.270.440
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.440
2dgnDOIAdenylosuccinate synthetase isozyme 1/0.440
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
3imgBZ3Pantothenate synthetase6.3.2.10.440
3jv7NADSecondary alcohol dehydrogenase/0.440
3q43D66M1 family aminopeptidase3.4.110.440
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.440
3v2uATPProtein GAL3/0.440
4f1l0RYPoly [ADP-ribose] polymerase 142.4.2.300.440
4h8aNAIUreidoglycolate dehydrogenase (NAD(+))1.1.1.3500.440
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.440