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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
5ej4 TD6 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.582
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.535
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.502
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.491
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.419
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.413
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.260
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.234
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.220
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.119
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.099
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.086
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.967
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.884
4cok TPPPyruvate decarboxylase / 0.875
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.863
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.858
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.848
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.826
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.825
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.824
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.822
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.816
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.812
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.804
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.804
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.800
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.798
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.793
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.790
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.785
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.783
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.783
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.782
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.781
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.779
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.778
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.777
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.777
2pan TDPGlyoxylate carboligase 4.1.1.47 0.776
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.776
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.775
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.775
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.772
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.771
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.769
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.767
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.767
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.766
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.765
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.762
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.762
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.761
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.760
5c4i TPPOxalate oxidoreductase subunit alpha / 0.756
5c4i TPPOxalate oxidoreductase subunit beta / 0.756
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.756
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.753
3iae D7KBenzaldehyde lyase / 0.752
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.749
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.747
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.746
5ahk TPPAcetolactate synthase II, large subunit / 0.746
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.745
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.744
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.744
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.744
2r8o T5XTransketolase 1 / 0.743
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.742
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.742
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.740
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.739
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.737
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.737
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.733
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.728
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.721
3ahj TPPProbable phosphoketolase / 0.719
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.718
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.718
2ezt TDMPyruvate oxidase 1.2.3.3 0.715
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.711
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.709
1kek HTLPyruvate synthase / 0.706
2ez9 TDKPyruvate oxidase 1.2.3.3 0.706
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.706
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.706
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.700
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.700
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.699
1pox TPPPyruvate oxidase 1.2.3.3 0.696
2c3y HTLPyruvate synthase / 0.696
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.694
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.693
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.692
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.691
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.691
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.690
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.689
2uz1 TPPBenzaldehyde lyase / 0.689
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.686
3rim TPPTransketolase 2.2.1.1 0.682
1y9d TPPPyruvate oxidase 1.2.3.3 0.681
3ahi HTLProbable phosphoketolase / 0.681
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.678
2pda TPPPyruvate synthase / 0.672
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.671
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.671
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.666
3ahe THDProbable phosphoketolase / 0.662
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.660
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.659
3upt TPPTransketolase / 0.657
4qpz TPPBenzaldehyde lyase / 0.657
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.653
1gpu THDTransketolase 1 2.2.1.1 0.652
1tkc M6TTransketolase 1 2.2.1.1 0.652