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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
5ej8 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
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.563
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.541
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.491
5eja 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 / 1.418
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.384
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.245
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.236
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.234
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.110
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.073
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.015
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.982
4cok TPPPyruvate decarboxylase / 0.881
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.864
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.843
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.829
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.825
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.815
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.810
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.808
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.808
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.805
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.804
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.795
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.789
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.789
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.784
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.782
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.775
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.772
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.772
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.770
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.769
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.768
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.767
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.765
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.762
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.761
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.760
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.760
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.760
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.758
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.758
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.757
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.754
5ahk TPPAcetolactate synthase II, large subunit / 0.754
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.753
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.751
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.751
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.751
2r8o T5XTransketolase 1 / 0.749
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.747
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.747
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.745
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.743
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.741
2ez9 TDKPyruvate oxidase 1.2.3.3 0.738
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.738
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.738
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.737
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.737
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.733
2ezt TDMPyruvate oxidase 1.2.3.3 0.732
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.730
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.730
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.727
2pan TDPGlyoxylate carboligase 4.1.1.47 0.726
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.725
3iae D7KBenzaldehyde lyase / 0.724
1y9d TPPPyruvate oxidase 1.2.3.3 0.723
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.722
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.721
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.718
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.718
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.717
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.714
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.712
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.711
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.710
3ahj TPPProbable phosphoketolase / 0.709
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.706
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.702
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.701
5c4i TPPOxalate oxidoreductase subunit alpha / 0.701
5c4i TPPOxalate oxidoreductase subunit beta / 0.701
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.698
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.697
1pox TPPPyruvate oxidase 1.2.3.3 0.694
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.692
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.691
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.687
2uz1 TPPBenzaldehyde lyase / 0.681
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.681
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.681
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.679
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.679
3ahi HTLProbable phosphoketolase / 0.678
1kek HTLPyruvate synthase / 0.677
4qpz TPPBenzaldehyde lyase / 0.677
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.676
2ag1 TPPBenzaldehyde lyase / 0.674
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.673
3ahe THDProbable phosphoketolase / 0.673
2pda TPPPyruvate synthase / 0.671
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.670
1toi HCIAspartate aminotransferase 2.6.1.1 0.669
2c3y HTLPyruvate synthase / 0.669
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.669
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.667
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.666
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.666
3rim TPPTransketolase 2.2.1.1 0.663
1trk TPPTransketolase 1 2.2.1.1 0.661
3h06 VBPGlutamate receptor 2 / 0.660
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.659
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.658
1tkc M6TTransketolase 1 2.2.1.1 0.657
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
2r5n TPPTransketolase 1 / 0.652
3upt TPPTransketolase / 0.652
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
2ag0 TPPBenzaldehyde lyase / 0.651