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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
3zht TD9 Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.341
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.256
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.169
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.160
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.157
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.076
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.912
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.912
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.902
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.902
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.892
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.892
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.858
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.858
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.854
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.854
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.810
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.801
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.798
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.798
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.789
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.778
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.778
3ahi HTLProbable phosphoketolase / 0.771
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.770
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.768
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.768
5ahk TPPAcetolactate synthase II, large subunit / 0.766
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.759
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.751
3ahe THDProbable phosphoketolase / 0.747
2r8o T5XTransketolase 1 / 0.745
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.744
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.743
1y9d TPPPyruvate oxidase 1.2.3.3 0.740
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.738
3iae D7KBenzaldehyde lyase / 0.737
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.733
3ahj TPPProbable phosphoketolase / 0.726
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.725
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.725
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.723
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.722
3d7k D7KBenzaldehyde lyase / 0.717
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.716
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.715
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.714
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.711
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.711
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.710
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.709
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.708
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.706
2ezt TDMPyruvate oxidase 1.2.3.3 0.705
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.704
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.703
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.699
3upt TPPTransketolase / 0.698
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.698
1trk TPPTransketolase 1 2.2.1.1 0.697
1pox TPPPyruvate oxidase 1.2.3.3 0.696
2uz1 TPPBenzaldehyde lyase / 0.695
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.694
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.694
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.694
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.692
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.691
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.687
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.685
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.685
2r5n TPPTransketolase 1 / 0.680
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.679
2r8p T6FTransketolase 1 / 0.679
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.678
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.677
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.677
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.677
4cok TPPPyruvate decarboxylase / 0.675
5c4i TPPOxalate oxidoreductase subunit alpha / 0.675
5c4i TPPOxalate oxidoreductase subunit beta / 0.675
3m34 TPPTransketolase / 0.673
1uqt U2FTrehalose-6-phosphate synthase 2.4.1.15 0.672
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.671
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.671
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.670
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.669
2ez9 TDKPyruvate oxidase 1.2.3.3 0.668
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.668
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.667
1ngs TPPTransketolase 1 2.2.1.1 0.666
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.666
1ay0 TPPTransketolase 1 2.2.1.1 0.665
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.665
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.664
1gpu THDTransketolase 1 2.2.1.1 0.662
1kek HTLPyruvate synthase / 0.662
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.661
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.660
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.658
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.658
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.657
1pow TPPPyruvate oxidase 1.2.3.3 0.657
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.657
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.656
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.653
3rim TPPTransketolase 2.2.1.1 0.652
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.651