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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
1azlFMNFlavodoxin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1azlFMNFlavodoxin/1.000
1akrFMNFlavodoxin/0.765
1akwFMNFlavodoxin/0.646
1j9gFMNFlavodoxin/0.587
4fx2FMNFlavodoxin/0.576
1fx1FMNFlavodoxin/0.569
1wsbFMNFlavodoxin/0.560
3f6rFMNFlavodoxin/0.560
1c7fFMNFlavodoxin/0.548
5fx2FMNFlavodoxin/0.547
1bu5RBFFlavodoxin/0.544
1j8qFMNFlavodoxin/0.543
2fx2FMNFlavodoxin/0.541
1akuFMNFlavodoxin/0.540
5tgzFMNCannabinoid receptor 1/0.534
4y7cFMNNADPH--cytochrome P450 reductase/0.531
5xraFMNCannabinoid receptor 1/0.521
3kaqFMNFlavodoxin/0.513
3kapFMNFlavodoxin/0.509
1xyvFMNFlavodoxin/0.506
1xyyFMNFlavodoxin/0.495
3ojxFMNNADPH--cytochrome P450 reductase/0.493
3q9bB3NAcetylpolyamine amidohydrolase/0.487
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.481
1cznFMNFlavodoxin/0.479
3nytULPUDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.479
2fcrFMNFlavodoxin/0.477
1j9zFMNNADPH--cytochrome P450 reductase/0.476
2v9cMREFMN-dependent NADH-azoreductase 1/0.467
2v13C40Renin3.4.23.150.466
3af1GDPPantothenate kinase2.7.1.330.465
1m4iCOAAminoglycoside 2'-N-acetyltransferase2.3.10.463
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3fhxPLPPyridoxal kinase2.7.1.350.463
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
4oztP1AEcdysone receptor, putative/0.462
2gv8NDPThiol-specific monooxygenase1.14.130.461
5xr8FMNCannabinoid receptor 1/0.461
1ahnFMNFlavodoxin 1/0.460
2zevIPEGeranylgeranyl pyrophosphate synthase/0.460
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.460
2cvzNDP3-hydroxyisobutyrate dehydrogenase/0.459
2ejzSAHDiphthine synthase/0.459
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.459
1h69ARHNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.458
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.458
3i8p8403-oxoacyl-[acyl-carrier-protein] synthase 22.3.1.1790.458
1jqdSAHHistamine N-methyltransferase2.1.1.80.457
1rkwPNTHTH-type transcriptional regulator QacR/0.456
4brgGNPEctonucleoside triphosphate diphosphohydrolase I/0.456
4ej1FOLDihydrofolate reductase1.5.1.30.455
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.454
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.454
2r8oT5XTransketolase 1/0.453
2xjeU5PCytosolic purine 5'-nucleotidase3.1.3.50.453
3dhaC6LN-acyl homoserine lactonase AiiA3.1.1.810.453
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.452
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.452
1ykgFMNSulfite reductase [NADPH] flavoprotein alpha-component/0.452
1uyiPUZHeat shock protein HSP 90-alpha/0.451
2xuhTZ4Acetylcholinesterase3.1.1.70.451
4bfwZVWPantothenate kinase2.7.1.330.451
1z6tADPApoptotic protease-activating factor 1/0.450
3gr8FMNNADPH dehydrogenase/0.450
1gpuTHDTransketolase 12.2.1.10.449
3ggs2FDPurine nucleoside phosphorylase2.4.2.10.449
4bixADPSensor histidine kinase CpxA/0.449
1fmjRTLRetinol dehydratase/0.448
1ofvFMNFlavodoxin/0.448
2rc6NAPFerredoxin--NADP reductase/0.448
2w6cBM4Acetylcholinesterase3.1.1.70.448
3b9oFMNAlkane monoxygenase/0.448
3g5sFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.448
4a31MYAGlycylpeptide N-tetradecanoyltransferase/0.448
4oxxFMNCindoxin/0.447
1wl4COAAcetyl-CoA acetyltransferase, cytosolic2.3.1.90.446
2ha6SCKAcetylcholinesterase3.1.1.70.446
2r8pT6FTransketolase 1/0.446
2xysSY9Soluble acetylcholine receptor/0.446
3esyFMNFlavodoxin/0.446
3w5hFADNADH-cytochrome b5 reductase 31.6.2.20.446
2c20NADUDP-glucose 4-epimerase/0.445
2mokFMNFlavodoxin 1/0.445
2mt9FMNFlavodoxin 2/0.445
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3eszFMNFlavodoxin/0.445
1qorNDPQuinone oxidoreductase 1/0.444
2h3wHC5Carnitine O-acetyltransferase2.3.1.70.444
2xufTZ4Acetylcholinesterase3.1.1.70.444
3c1kT15Prothrombin3.4.21.50.444
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
2op18PCEnoyl-ACP reductase/0.443
4efuEFUHeat shock protein HSP 90-alpha/0.443
1a26CNAPoly [ADP-ribose] polymerase 12.4.2.300.442
1akaPLPAspartate aminotransferase, mitochondrial2.6.1.10.442
1uydPU8Heat shock protein HSP 90-alpha/0.442
2rr1W8RGenome polyprotein/0.442
2zs9ADPPantothenate kinase2.7.1.330.442
1ay0TPPTransketolase 12.2.1.10.441
1m9nAMZBifunctional purine biosynthesis protein PURH2.1.2.30.441
1s20NAD2,3-diketo-L-gulonate reductase1.1.1.1300.441
2ed3SAHDiphthine synthase/0.441
2r5nTPPTransketolase 1/0.441
2w6pOA4Biotin carboxylase6.3.4.140.441
2wp9CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.441
2wp9CBESuccinate dehydrogenase cytochrome b556 subunit/0.441
3fktSIIBeta-secretase 13.4.23.460.441
3pvcFADtRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC/0.441
4br0AU1Ectonucleoside triphosphate diphosphohydrolase 2/0.441
5a4vQUEGlutathione S-transferase F22.5.1.180.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
3dhcCYKN-acyl homoserine lactonase AiiA3.1.1.810.440
3h3qH13Collagen type IV alpha-3-binding protein/0.440
4jqh1MFAlr2278 protein/0.440
4twnB96Ephrin type-A receptor 32.7.10.10.440
4xbfFADLysine-specific histone demethylase 1A10.440