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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
3o0nTTPVitamin B12-dependent ribonucleotide reductase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3o0nTTPVitamin B12-dependent ribonucleotide reductase/1.000
3o0oTTPVitamin B12-dependent ribonucleotide reductase/0.551
3o0qTTPVitamin B12-dependent ribonucleotide reductase/0.523
1xjeTTPVitamin B12-dependent ribonucleotide reductase/0.474
1h8hADPATP synthase subunit alpha, mitochondrial/0.471
1h8hADPATP synthase subunit beta, mitochondrial3.6.3.140.471
4ix5ANPUncharacterized protein/0.470
4l9kEHFSerum albumin/0.467
2zynBCDPeriplasmic binding protein/0.465
1xjjDGTVitamin B12-dependent ribonucleotide reductase/0.463
1xjnDTPVitamin B12-dependent ribonucleotide reductase/0.462
1h63FMNPentaerythritol tetranitrate reductase/0.457
2ywvADPPhosphoribosylaminoimidazole-succinocarboxamide synthase/0.457
2yyiFAD4-hydroxyphenylacetate 3-monooxygenase oxygenase component1.14.14.90.457
2dcnADP2-keto-3-deoxy-gluconate kinase/0.456
4b8wNAPGDP-L-fucose synthase1.1.1.2710.455
4tl7ATPCircadian clock protein kinase KaiC2.7.11.10.455
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.451
2e1mFADL-glutamate oxidase/0.451
2p4yC03Peroxisome proliferator-activated receptor gamma/0.451
4nr42LKCREB-binding protein/0.450
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.449
2abbFMNPentaerythritol tetranitrate reductase/0.449
2vcmM11Isopenicillin N synthase1.21.3.10.449
2xzwATPNitrogen regulatory protein P-II/0.449
4a33MYAGlycylpeptide N-tetradecanoyltransferase/0.449
3copADPGlycogen synthase2.4.1.210.448
1pdhFASp-hydroxybenzoate hydroxylase/0.447
1vyrFMNPentaerythritol tetranitrate reductase/0.447
2wghDTPRibonucleoside-diphosphate reductase large subunit1.17.4.10.447
3nszANPCasein kinase II subunit alpha2.7.11.10.447
3da1FADGlycerol-3-phosphate dehydrogenase/0.446
4h8nNDPNADPH-dependent conjugated polyketone reductase C2/0.446
4h9814QUncharacterized protein/0.446
4ki8ADP60 kDa chaperonin/0.446
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.445
3cx4ADPGlycogen synthase2.4.1.210.445
3qdd94MHeat shock protein HSP 90-alpha/0.445
4eajATP5'-AMP-activated protein kinase subunit gamma-1/0.445
4ruoBIVVitamin D3 receptor A/0.445
3wowANPCasein kinase II subunit alpha2.7.11.10.444
4l8u9AZSerum albumin/0.444
4xcvNDPProbable hydroxyacid dehydrogenase protein/0.443
1hb3SCVIsopenicillin N synthase1.21.3.10.442
2vojNADAlanine dehydrogenase1.4.1.10.442
2zfaFMNLactate oxidase/0.442
3cukFADD-amino-acid oxidase1.4.3.30.442
3tk0FADFAD-linked sulfhydryl oxidase ALR1.8.3.20.442
4dieC5PCytidylate kinase/0.442
4tlbAGSCircadian clock protein kinase KaiC2.7.11.10.442
1q43CMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2/0.441
1v9aSAHUncharacterized protein/0.441
2jj1ADPATP synthase subunit alpha, mitochondrial/0.441
2jj1ADPATP synthase subunit beta, mitochondrial3.6.3.140.441
2vbpVB1Isopenicillin N synthase1.21.3.10.441
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.441
1jolFFODihydrofolate reductase1.5.1.30.440
3g8dADPBiotin carboxylase6.3.4.140.440
4zs2FLUAlpha-ketoglutarate-dependent dioxygenase FTO/0.440