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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
3m34 TPP Transketolase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3m34 TPPTransketolase / 1.010
3upt TPPTransketolase / 0.915
3m7i TPPTransketolase / 0.914
3m6l TPPTransketolase / 0.907
1ngs TPPTransketolase 1 2.2.1.1 0.893
2r5n TPPTransketolase 1 / 0.879
3rim TPPTransketolase 2.2.1.1 0.853
1ay0 TPPTransketolase 1 2.2.1.1 0.851
1gpu THDTransketolase 1 2.2.1.1 0.851
2r8p T6FTransketolase 1 / 0.843
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.842
2r8o T5XTransketolase 1 / 0.828
4c7x TPPTransketolase / 0.827
1trk TPPTransketolase 1 2.2.1.1 0.796
1tkb N1TTransketolase 1 2.2.1.1 0.770
1tka N3TTransketolase 1 2.2.1.1 0.769
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.753
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.747
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.747
1tkc M6TTransketolase 1 2.2.1.1 0.734
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.733
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.733
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.729
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.727
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.724
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.724
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.722
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.722
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.722
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.722
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.718
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.716
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.715
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.715
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.715
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.714
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.708
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.707
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.707
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.704
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.704
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.703
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.701
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.701
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.700
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.700
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.699
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.698
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.696
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.693
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.692
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.691
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.690
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.690
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.684
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.683
5ahk TPPAcetolactate synthase II, large subunit / 0.683
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.682
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.682
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.680
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.678
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.678
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.678
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.678
1y9d TPPPyruvate oxidase 1.2.3.3 0.677
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.677
3ahe THDProbable phosphoketolase / 0.677
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.673
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.673
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.671
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.671
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.670
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.668
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.668
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.667
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.667
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.667
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.666
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.665
3ahj TPPProbable phosphoketolase / 0.665
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.665
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.662
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.661
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.660
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.660
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.660
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.659
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.658
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.654
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.653
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.653
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.653
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.650
2ezt TDMPyruvate oxidase 1.2.3.3 0.650