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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
1azlFMNFlavodoxin

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1azlFMNFlavodoxin/1.000
1akrFMNFlavodoxin/0.772
1akwFMNFlavodoxin/0.639
1j9gFMNFlavodoxin/0.599
4fx2FMNFlavodoxin/0.588
3f90FMNFlavodoxin/0.581
1fx1FMNFlavodoxin/0.580
1wsbFMNFlavodoxin/0.571
3f6rFMNFlavodoxin/0.568
5fx2FMNFlavodoxin/0.558
1c7fFMNFlavodoxin/0.557
1j8qFMNFlavodoxin/0.554
2fx2FMNFlavodoxin/0.552
1akuFMNFlavodoxin/0.551
1bu5RBFFlavodoxin/0.550
5tgzFMNCannabinoid receptor 1/0.548
4y7cFMNNADPH--cytochrome P450 reductase/0.536
3f6sFMNFlavodoxin/0.532
3ojxFMNNADPH--cytochrome P450 reductase/0.532
5xraFMNCannabinoid receptor 1/0.531
3kaqFMNFlavodoxin/0.524
3kapFMNFlavodoxin/0.520
1xyvFMNFlavodoxin/0.516
3q9bB3NAcetylpolyamine amidohydrolase/0.503
1xyyFMNFlavodoxin/0.502
2r8pT6FTransketolase 1/0.498
4n82FMNRibonucleotide reductase (NrdI family protein), putative/0.497
2v13C40Renin3.4.23.150.493
1cznFMNFlavodoxin/0.489
1j9zFMNNADPH--cytochrome P450 reductase/0.489
2v5uFMNFlavodoxin/0.488
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.488
2fcrFMNFlavodoxin/0.486
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.478
2r8oT5XTransketolase 1/0.476
3af1GDPPantothenate kinase2.7.1.330.476
2y60M8FIsopenicillin N synthase1.21.3.10.473
4bfwZVWPantothenate kinase2.7.1.330.472
4oztP1AEcdysone receptor, putative/0.472
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.470
1ahnFMNFlavodoxin 1/0.469
1fmjRTLRetinol dehydratase/0.469
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.469
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.469
1h69ARHNAD(P)H dehydrogenase [quinone] 11.6.5.20.468
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.468
1qorNDPQuinone oxidoreductase 1/0.466
2g8yNADHydroxycarboxylate dehydrogenase B/0.466
2iviACWIsopenicillin N synthase1.21.3.10.465
2pncCLUPrimary amine oxidase, liver isozyme/0.465
3af0GDPPantothenate kinase2.7.1.330.465
1bk0ACVIsopenicillin N synthase1.21.3.10.464
1m4iCOAAminoglycoside 2'-N-acetyltransferase2.3.10.463
1h63FMNPentaerythritol tetranitrate reductase/0.462
2w6pOA4Biotin carboxylase6.3.4.140.462
2xveFADPutative flavin-containing monooxygenase/0.462
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
2mt9FMNFlavodoxin 2/0.461
1pq944BOxysterols receptor LXR-beta/0.460
1z6tADPApoptotic protease-activating factor 1/0.460
3gr8FMNNADPH dehydrogenase/0.459
4eb5PLPCysteine desulfurase IscS 2/0.459
2rc6NAPFerredoxin--NADP reductase/0.458
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.458
4bixADPSensor histidine kinase CpxA/0.458
1ofvFMNFlavodoxin/0.457
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.457
4oxxFMNCindoxin/0.457
5xr8FMNCannabinoid receptor 1/0.457
2zs9ADPPantothenate kinase2.7.1.330.456
3irhDTPHD domain protein/0.456
4uugPXGBranched-chain amino acid aminotransferase, putative/0.456
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.456
5irnADPNucleotide binding oligomerization domain containing 2/0.456
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.455
2xviFADPutative flavin-containing monooxygenase/0.455
3c1kT15Prothrombin3.4.21.50.455
3qfrFMNNADPH--cytochrome P450 reductase/0.455
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.454
2c20NADUDP-glucose 4-epimerase/0.454
2ha6SCKAcetylcholinesterase3.1.1.70.454
2mokFMNFlavodoxin 1/0.454
2q1tNADPutative nucleotide sugar epimerase/ dehydratase/0.454
2w6cBM4Acetylcholinesterase3.1.1.70.454
3abxRCBGlucanase/0.454
3fktSIIBeta-secretase 13.4.23.460.454
5fm7ADPRuvB-like helicase/0.454
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.453
2ed3SAHDiphthine synthase/0.453
1ykgFMNSulfite reductase [NADPH] flavoprotein alpha-component/0.452
2ohiFMNType A flavoprotein FprA10.451
2xlrFADPutative flavin-containing monooxygenase/0.451
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.451
4uwmFMN3,6-diketocamphane 1,6 monooxygenase1.14.130.451
5a4vQUEGlutathione S-transferase F22.5.1.180.451
1pqc444Oxysterols receptor LXR-beta/0.450
1q23FUAChloramphenicol acetyltransferase2.3.1.280.450
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.450
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.450
1obnASVIsopenicillin N synthase1.21.3.10.449
2po7CHDFerrochelatase, mitochondrial4.99.1.10.449
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.449
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.449
4twnB96Ephrin type-A receptor 32.7.10.10.449
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.448
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.448
2xvfFADPutative flavin-containing monooxygenase/0.448
2yneYNEGlycylpeptide N-tetradecanoyltransferase/0.448
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.448
3esyFMNFlavodoxin/0.448
3jsxCC2NAD(P)H dehydrogenase [quinone] 11.6.5.20.448
3uk6ADPRuvB-like 23.6.4.120.448
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.448
1h42FADFerredoxin--NADP reductase1.18.1.20.447
2ejzSAHDiphthine synthase/0.447
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.447
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.447
3eszFMNFlavodoxin/0.447
3n3aFMNProtein NrdI/0.447
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.447
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.446
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.446
2r2mI50Prothrombin3.4.21.50.446
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.446
3aosJH2Hemolymph juvenile hormone binding protein/0.446
4araC56Acetylcholinesterase3.1.1.70.446
4friDWABeta-secretase 13.4.23.460.446
4uy6SAHHistidine N-alpha-methyltransferase/0.446
1hb3SCVIsopenicillin N synthase1.21.3.10.445
2msdGNPMHC class I alpha chain/0.445
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.445
3ha3SAHHydroxymycolate synthase MmaA42.1.10.445
4driRAPSerine/threonine-protein kinase mTOR2.7.11.10.445
4driRAPPeptidyl-prolyl cis-trans isomerase FKBP55.2.1.80.445
1lwiNAP3-alpha-hydroxysteroid dehydrogenase1.1.1.500.444
2a57CRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2j83BATUlilysin3.4.240.444
2po3T4K4-dehydrase/0.444
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.444
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.444
4r81FMNPredicted NADH dehydrogenase/0.444
1fmlRTLRetinol dehydratase/0.443
2v5aLZLBiotin carboxylase6.3.4.140.443
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3mj4URMUDP-galactopyranose mutase/0.443
3tfyCOAN-alpha-acetyltransferase 502.3.10.443
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.443
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.443
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.443
4jtqNAPAldo-keto reductase family 1 member C2/0.443
3oqkS52Renin3.4.23.150.442
4a2zVIQGlycylpeptide N-tetradecanoyltransferase/0.442
4bb3KKAIsopenicillin N synthase1.21.3.10.442
4d965PAD-cysteine desulfhydrase/0.442
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1qzyTDEMethionine aminopeptidase 2/0.441
1rkwPNTHTH-type transcriptional regulator QacR/0.441
1v3q2DIPurine nucleoside phosphorylase2.4.2.10.441
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3f03FMNPentaerythritol tetranitrate reductase/0.441
4bftZVTPantothenate kinase2.7.1.330.441
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.441
1gg5E09NAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
1qjfACSIsopenicillin N synthase1.21.3.10.440
1ry0PG2Aldo-keto reductase family 1 member C3/0.440
1t4u81AProthrombin3.4.21.50.440
1x8lOXRRetinol dehydratase/0.440
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.440
2vcmM11Isopenicillin N synthase1.21.3.10.440
2xufTZ4Acetylcholinesterase3.1.1.70.440
2xuhTZ4Acetylcholinesterase3.1.1.70.440
2ykiYKIHeat shock protein HSP 90-alpha/0.440
3hr4FMNNitric oxide synthase, inducible1.14.13.390.440
3r5yF42Uncharacterized protein/0.440
4drjRAPSerine/threonine-protein kinase mTOR2.7.11.10.440
4drjRAPPeptidyl-prolyl cis-trans isomerase FKBP45.2.1.80.440
4f3gKAIGlutamate receptor 3/0.440