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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3eya TDP Pyruvate dehydrogenase [ubiquinone] 1.2.5.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 1.137
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 1.046
1y9d TPPPyruvate oxidase 1.2.3.3 0.838
2ezt TDMPyruvate oxidase 1.2.3.3 0.768
5ahk TPPAcetolactate synthase II, large subunit / 0.763
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.762
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.762
2ag1 TPPBenzaldehyde lyase / 0.752
1pox TPPPyruvate oxidase 1.2.3.3 0.751
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.748
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.748
2uz1 TPPBenzaldehyde lyase / 0.746
1pow TPPPyruvate oxidase 1.2.3.3 0.741
3d7k D7KBenzaldehyde lyase / 0.737
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.736
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.736
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.732
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.732
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.731
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.726
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.725
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.720
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.720
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.720
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.720
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.720
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.716
4qpz TPPBenzaldehyde lyase / 0.714
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.713
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.713
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.709
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.709
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.708
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.708
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.707
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.707
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.706
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.706
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.706
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.706
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.706
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.706
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.704
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.699
2pan TDPGlyoxylate carboligase 4.1.1.47 0.698
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.697
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.697
3iae D7KBenzaldehyde lyase / 0.696
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.694
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.694
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.693
2ez9 TDKPyruvate oxidase 1.2.3.3 0.692
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.692
2r8o T5XTransketolase 1 / 0.691
5c4i TPPOxalate oxidoreductase subunit alpha / 0.686
5c4i TPPOxalate oxidoreductase subunit beta / 0.686
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.683
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.683
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.682
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.681
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.680
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.675
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.675
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.674
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.673
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.671
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.671
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.671
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.669
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.669
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.668
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.668
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.667
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.667
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.666
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.666
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.665
3upt TPPTransketolase / 0.665
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.665
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.663
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.663
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.662
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.662
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.661
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.660
2r5n TPPTransketolase 1 / 0.660
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.659
1ngs TPPTransketolase 1 2.2.1.1 0.657
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.657
2r8p T6FTransketolase 1 / 0.657
4cok TPPPyruvate decarboxylase / 0.657
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.657
1trk TPPTransketolase 1 2.2.1.1 0.656
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.656
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.656
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.655
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.654
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.654
1gpu THDTransketolase 1 2.2.1.1 0.653
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.651
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.651
3m0e ATPTranscriptional regulator (NtrC family) / 0.650