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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
3dv0 TPW Pyruvate dehydrogenase E1 component subunit alpha 1.2.4.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 1.242
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 1.242
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 1.047
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 1.047
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 1.018
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 1.018
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.954
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.954
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.946
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.946
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.913
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.913
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.912
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.912
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.909
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.909
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.891
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.891
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.878
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.864
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.854
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.851
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.834
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.820
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.818
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.816
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.816
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.813
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.801
3upt TPPTransketolase / 0.799
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.786
2r8o T5XTransketolase 1 / 0.786
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.775
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.770
3ahj TPPProbable phosphoketolase / 0.768
1gpu THDTransketolase 1 2.2.1.1 0.766
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.766
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.764
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.761
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.758
1tkc M6TTransketolase 1 2.2.1.1 0.756
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.753
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.752
2r5n TPPTransketolase 1 / 0.750
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.750
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.747
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.746
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.746
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.745
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.745
1trk TPPTransketolase 1 2.2.1.1 0.744
3rim TPPTransketolase 2.2.1.1 0.743
5ahk TPPAcetolactate synthase II, large subunit / 0.743
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.743
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.742
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.742
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.742
3ahi HTLProbable phosphoketolase / 0.740
3m7i TPPTransketolase / 0.740
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.738
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.737
3m6l TPPTransketolase / 0.737
1ay0 TPPTransketolase 1 2.2.1.1 0.736
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.736
3ahe THDProbable phosphoketolase / 0.734
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.734
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.733
3m34 TPPTransketolase / 0.733
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.733
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.731
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.728
2uz1 TPPBenzaldehyde lyase / 0.728
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.726
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.722
2r8p T6FTransketolase 1 / 0.718
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.717
1ngs TPPTransketolase 1 2.2.1.1 0.715
2ag0 TPPBenzaldehyde lyase / 0.714
4qpz TPPBenzaldehyde lyase / 0.714
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.713
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.713
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.711
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.709
3d7k D7KBenzaldehyde lyase / 0.709
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.709
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.708
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.708
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.707
4c7x TPPTransketolase / 0.703
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.703
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.696
1tkb N1TTransketolase 1 2.2.1.1 0.696
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.696
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.695
3iae D7KBenzaldehyde lyase / 0.695
4cok TPPPyruvate decarboxylase / 0.695
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.691
1kek HTLPyruvate synthase / 0.688
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.687
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.687
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.687
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.685
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.679
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.679
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.678
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.677
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.677
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.677
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.675
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.675
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.667
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.666
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.666
1pow TPPPyruvate oxidase 1.2.3.3 0.665
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.663
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.662
2pan TDPGlyoxylate carboligase 4.1.1.47 0.662
2ag1 TPPBenzaldehyde lyase / 0.660
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.657
1t9a YF4Acetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.653
5itz GTPTubulin alpha-1B chain / 0.653