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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
3m6l TPP Transketolase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3m6l TPPTransketolase / 0.996
2r5n TPPTransketolase 1 / 0.924
3m34 TPPTransketolase / 0.907
1ngs TPPTransketolase 1 2.2.1.1 0.867
3upt TPPTransketolase / 0.861
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.859
3m7i TPPTransketolase / 0.856
1tkb N1TTransketolase 1 2.2.1.1 0.835
3rim TPPTransketolase 2.2.1.1 0.831
1trk TPPTransketolase 1 2.2.1.1 0.829
4c7x TPPTransketolase / 0.806
2r8p T6FTransketolase 1 / 0.799
1ay0 TPPTransketolase 1 2.2.1.1 0.791
2r8o T5XTransketolase 1 / 0.785
1tka N3TTransketolase 1 2.2.1.1 0.779
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.740
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.740
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.737
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.737
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.736
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.728
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.728
1gpu THDTransketolase 1 2.2.1.1 0.727
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.727
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.725
1tkc M6TTransketolase 1 2.2.1.1 0.722
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.721
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.719
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.719
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.718
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.718
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.712
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.708
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.707
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.704
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.696
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.692
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.691
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.688
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.688
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.684
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.683
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.682
1y9d TPPPyruvate oxidase 1.2.3.3 0.681
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.681
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.678
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.677
2ezt TDMPyruvate oxidase 1.2.3.3 0.676
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.676
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.672
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.668
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.665
3ahi HTLProbable phosphoketolase / 0.663
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.663
2ez9 TDKPyruvate oxidase 1.2.3.3 0.662
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.662
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.661
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.659
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.657
3ahe THDProbable phosphoketolase / 0.656
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.653
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.653
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.650
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.650
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.650