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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
3m7i TPP Transketolase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3m7i TPPTransketolase / 0.997
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.927
1ngs TPPTransketolase 1 2.2.1.1 0.914
3m34 TPPTransketolase / 0.914
2r8p T6FTransketolase 1 / 0.894
2r8o T5XTransketolase 1 / 0.891
3upt TPPTransketolase / 0.887
1gpu THDTransketolase 1 2.2.1.1 0.878
1trk TPPTransketolase 1 2.2.1.1 0.875
3rim TPPTransketolase 2.2.1.1 0.865
4c7x TPPTransketolase / 0.863
3m6l TPPTransketolase / 0.856
2r5n TPPTransketolase 1 / 0.851
1tkc M6TTransketolase 1 2.2.1.1 0.843
1ay0 TPPTransketolase 1 2.2.1.1 0.810
1tkb N1TTransketolase 1 2.2.1.1 0.747
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.745
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.741
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.741
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.740
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.740
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.728
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.724
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.721
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.721
1tka N3TTransketolase 1 2.2.1.1 0.715
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.709
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.708
5ahk TPPAcetolactate synthase II, large subunit / 0.708
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.705
3ahj TPPProbable phosphoketolase / 0.702
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.701
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.700
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.698
2ez9 TDKPyruvate oxidase 1.2.3.3 0.697
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.696
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.693
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.692
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.691
3ahe THDProbable phosphoketolase / 0.687
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.685
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.684
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.683
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.683
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.682
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.682
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.681
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.681
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.679
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.678
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.678
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.675
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.671
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.671
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.669
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.668
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.668
1pox TPPPyruvate oxidase 1.2.3.3 0.667
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.666
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.665
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.664
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.663
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.663
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.663
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.662
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.662
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.661
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.661
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.661
2ezt TDMPyruvate oxidase 1.2.3.3 0.659
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.659
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.657
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.657
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.657
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.657
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.654
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.653
1y9d TPPPyruvate oxidase 1.2.3.3 0.652
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.652
4cok TPPPyruvate decarboxylase / 0.651
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.650