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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
3upt TPP Transketolase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3upt TPPTransketolase / 1.167
1itz TPPTransketolase, chloroplastic 2.2.1.1 1.097
2r8p T6FTransketolase 1 / 1.068
1gpu THDTransketolase 1 2.2.1.1 1.052
2r5n TPPTransketolase 1 / 1.046
2r8o T5XTransketolase 1 / 1.003
1ngs TPPTransketolase 1 2.2.1.1 0.961
1tkc M6TTransketolase 1 2.2.1.1 0.928
3rim TPPTransketolase 2.2.1.1 0.926
1trk TPPTransketolase 1 2.2.1.1 0.921
4c7x TPPTransketolase / 0.916
3m34 TPPTransketolase / 0.915
1tkb N1TTransketolase 1 2.2.1.1 0.908
3m7i TPPTransketolase / 0.887
3m6l TPPTransketolase / 0.861
1tka N3TTransketolase 1 2.2.1.1 0.846
1ay0 TPPTransketolase 1 2.2.1.1 0.844
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.799
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.799
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.794
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.794
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.784
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.760
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.760
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.756
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.756
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.756
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.751
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.739
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.739
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.738
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.734
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.732
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.730
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.729
5ahk TPPAcetolactate synthase II, large subunit / 0.729
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.725
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.720
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.720
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.715
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.714
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.714
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.713
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.713
1y9d TPPPyruvate oxidase 1.2.3.3 0.711
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.710
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.709
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.709
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.709
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.706
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.705
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.704
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.703
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.703
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.701
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.701
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.700
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.700
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.698
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.697
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.695
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.695
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.694
3ahi HTLProbable phosphoketolase / 0.692
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.690
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.690
2ezt TDMPyruvate oxidase 1.2.3.3 0.688
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.688
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.688
3ahe THDProbable phosphoketolase / 0.686
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.683
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.683
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.682
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.681
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.681
1pox TPPPyruvate oxidase 1.2.3.3 0.676
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.675
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.675
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.675
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.674
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.672
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.671
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.671
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.671
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.670
3ahj TPPProbable phosphoketolase / 0.669
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.669
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.668
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.667
1pow TPPPyruvate oxidase 1.2.3.3 0.666
2uz1 TPPBenzaldehyde lyase / 0.666
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.666
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.665
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.665
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.664
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.659
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.659
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.659
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.659
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.658
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.658
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.657
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.656
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.655
4cok TPPPyruvate decarboxylase / 0.655
2ez9 TDKPyruvate oxidase 1.2.3.3 0.654
3d7k D7KBenzaldehyde lyase / 0.653
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.652
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.652