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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
3m6vSAMRibosomal RNA small subunit methyltransferase F

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3m6vSAMRibosomal RNA small subunit methyltransferase F/1.000
3m6wSAMRibosomal RNA small subunit methyltransferase F/0.584
2yxlSFG450aa long hypothetical fmu protein/0.560
4fzvSAM5-methylcytosine rRNA methyltransferase NSUN42.1.10.547
1sqfSAMRibosomal RNA small subunit methyltransferase B2.1.1.1760.539
4fp9SAM5-methylcytosine rRNA methyltransferase NSUN42.1.10.503
4wriOKAOkadaic acid binding protein 2-alpha/0.466
4bbyFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.461
4d03FADPhenylacetone monooxygenase1.14.13.920.456
1l3iSAHProbable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating)/0.455
3p8z36AGenome polyprotein2.1.1.560.455
5jscFADPutative acyl-CoA dehydrogenase/0.455
3mx5UTPNucleoprotein/0.454
1kh2ATPArgininosuccinate synthase/0.452
1korANPArgininosuccinate synthase/0.452
2yxuATPPyridoxal kinase2.7.1.350.452
2znnS44Peroxisome proliferator-activated receptor alpha/0.452
3efwAK8Aurora kinase A2.7.11.10.452
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.451
1esvLARActin, alpha skeletal muscle/0.449
1yb5NAPQuinone oxidoreductase1.6.5.50.449
3keuATPPyridoxal kinase2.7.1.350.448
4cpdNADAlcohol dehydrogenase/0.448
3a4tSFGtRNA (cytosine(48)-C(5))-methyltransferase2.1.10.447
2pj4414Carboxypeptidase B/0.445
3fhyATPPyridoxal kinase2.7.1.350.445
3q43D66M1 family aminopeptidase3.4.110.444
3t1tGDPProbable gliding protein mglA/0.444
4qxr1YEStimulator of interferon genes protein/0.444
1nhrFADNADH peroxidase1.11.1.10.443
2c12FADNitroalkane oxidase1.7.3.10.443
3mx2TTPNucleoprotein/0.442
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2plwSAMRibosomal RNA methyltransferase, putative/0.441
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.440
2fw3BUICarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.440
2vhwNAIAlanine dehydrogenase1.4.1.10.440
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.440
4kuhCAA3-hydroxybutyryl-CoA dehydrogenase/0.440