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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
5f2kSAHUncharacterized protein

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
5f2kSAHUncharacterized protein/1.000
2eg5SAH7-methylxanthosine synthase 1/0.551
2hq9FADMll6688 protein/0.495
2np7NEAModification methylase TaqI2.1.1.720.487
3gkjHC3Niemann-Pick C1 protein/0.482
1lriCLRBeta-elicitin cryptogein/0.481
3ox4NADAlcohol dehydrogenase 21.1.1.10.481
5dbgNADIridoid synthase1.3.1.990.479
2g1pSAHDNA adenine methylase2.1.1.720.478
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.475
4iarERM5-hydroxytryptamine receptor 1B/0.474
1nbiSAMGlycine N-methyltransferase2.1.1.200.473
3q44D50M1 family aminopeptidase3.4.110.472
5bp9SAHPutative methyltransferase protein/0.470
5emhNAPIridoid synthase1.3.1.990.470
3eeySAMrRNA methylase/0.469
4obwSAM2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial/0.469
5dcyNAPIridoid synthase1.3.1.990.468
2r0pK2CPutative FAD-monooxygenase/0.466
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.465
2f8lSAMLmo1582 protein/0.464
2zjwREFCasein kinase II subunit alpha2.7.11.10.464
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.464
1ojtFADDihydrolipoyl dehydrogenase/0.463
2v6gNAP3-oxo-Delta(4,5)-steroid 5-beta-reductase/0.463
1fdtESTEstradiol 17-beta-dehydrogenase 11.1.1.620.461
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.461
2ftoCB3Thymidylate synthase/0.460
3qvwNADMyo-inositol-1-phosphate synthase (Ino1)/0.460
4rvuNDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein)/0.460
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.459
3mw9NAIGlutamate dehydrogenase 1, mitochondrial1.4.1.30.459
2g20L1ARenin3.4.23.150.457
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.457
2iyaZIOOleandomycin glycosyltransferase/0.455
5dbfNDPIridoid synthase1.3.1.990.455
1xu7CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
3bgvSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.453
3w0yDS4Vitamin D3 receptor/0.453
4gbeSAHDNA adenine methylase2.1.1.720.453
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.453
1vjy460TGF-beta receptor type-12.7.11.300.452
3qlrNDPDihydrofolate reductase1.5.1.30.451
3qv2SAH5-cytosine DNA methyltransferase/0.451
4z44FADFlavin-dependent tryptophan halogenase PrnA1.14.19.90.451
5g53NECAdenosine receptor A2a/0.451
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.450
2xk9XK9Serine/threonine-protein kinase Chk22.7.11.10.450
3h0bB35Beta-secretase 13.4.23.460.450
4hfr14MCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
1ia9ANPTransient receptor potential cation channel subfamily M member 72.7.11.10.449
2b00GCHPhospholipase A2, major isoenzyme3.1.1.40.449
3czr3CZCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.449
1d7lRFLp-hydroxybenzoate hydroxylase/0.448
1x8lOXRRetinol dehydratase/0.448
2ih2NEAModification methylase TaqI2.1.1.720.448
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.448
3d91REMRenin3.4.23.150.448
3lpiZ74Beta-secretase 13.4.23.460.448
3up0D7SaceDAF-12/0.448
1f4gTP4Thymidylate synthase/0.447
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.447
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.447
1nv8SAMRelease factor glutamine methyltransferase2.1.1.2970.447
1qorNDPQuinone oxidoreductase 1/0.447
4da7AC2Purine nucleoside phosphorylase DeoD-type2.4.2.10.447
4impNDPPolyketide synthase extender modules 3-4/0.447
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.447
4qtuSAM18S rRNA (guanine(1575)-N(7))-methyltransferase/0.447
2cduFADNADH oxidase/0.446
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.445
3b5iSAHIndole-3-acetate O-methyltransferase 1/0.445
3ce31FNHepatocyte growth factor receptor2.7.10.10.445
4blwSAHRibosomal RNA large subunit methyltransferase J/0.445
1ipeNDPTropinone reductase 21.1.1.2360.444
1kiaSAMGlycine N-methyltransferase2.1.1.200.444
1yb5NAPQuinone oxidoreductase1.6.5.50.444
2rm2W43Genome polyprotein/0.444
3jynNDPQuinone oxidoreductase/0.444
3t2yFADSulfide-quinone reductase/0.444
3w2fNADNADH-cytochrome b5 reductase 31.6.2.20.444
4pooSAMPutative RNA methylase/0.444
5dp2NAPCurF/0.444
5je3SAHMethyl transferase/0.444
1f8sFADL-amino-acid oxidase1.4.3.20.443
1g0nNDPTetrahydroxynaphthalene reductase1.1.1.2520.443
1mjbACOHistone acetyltransferase ESA1/0.443
1ppjANYCytochrome b/0.443
3lpkZ76Beta-secretase 13.4.23.460.443
3t2kFADSulfide-quinone reductase/0.443
3vetADPnebramycin 5' synthase6.1.2.20.443
4e1bTXAThreonylcarbamoyl-AMP synthase2.7.7.870.443
4isk1JYThymidylate synthase/0.443
1lf3EH5Plasmepsin-23.4.23.390.442
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.442
2xpwOTCTetracycline repressor protein class D/0.442
2y0mACOHistone acetyltransferase KAT8/0.442
3biy01KHistone acetyltransferase p300/0.442
3cid318Beta-secretase 13.4.23.460.442
3g7jGTXGlutathione transferase GST1-4/0.442
3kpkFADSulfide-quinone reductase/0.442
4u8iFDAUDP-galactopyranose mutase/0.442
1fwmCB3Thymidylate synthase/0.441
1rzy5ASHistidine triad nucleotide-binding protein 130.441
1w1rZEACytokinin dehydrogenase 11.5.99.120.441
1w6hTITPlasmepsin-23.4.23.390.441
2oalFADFlavin-dependent tryptophan halogenase RebH1.14.19.90.441
2qo4CHDFatty acid-binding protein 10-A, liver basic/0.441
3clxX22E3 ubiquitin-protein ligase XIAP6.3.20.441
3ea4FABAcetolactate synthase, chloroplastic2.2.1.60.441
3lbySAHUncharacterized protein/0.441
3slz3TLPutative gag-pro-pol polyprotein/0.441
3vsxR32Renin3.4.23.150.441
1s3uTQDDihydrofolate reductase1.5.1.30.440
2aotSAHHistamine N-methyltransferase2.1.1.80.440
3n1s5GPPurine nucleoside phosphoramidase/0.440