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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
5esd TDP 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
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.178
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.125
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.060
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.982
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.968
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.968
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.967
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.959
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.959
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.958
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.957
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.933
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.884
4cok TPPPyruvate decarboxylase / 0.866
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.866
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.848
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.830
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.827
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.826
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.822
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.822
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.815
2ezt TDMPyruvate oxidase 1.2.3.3 0.811
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.811
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.810
5ahk TPPAcetolactate synthase II, large subunit / 0.809
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.800
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.797
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.792
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.791
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.791
1y9d TPPPyruvate oxidase 1.2.3.3 0.788
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.784
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.784
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.784
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.783
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.783
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.782
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.782
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.782
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.782
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.780
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.779
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.776
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.775
3iae D7KBenzaldehyde lyase / 0.771
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.770
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.770
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.768
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.765
2ez9 TDKPyruvate oxidase 1.2.3.3 0.764
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.761
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.757
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.757
1pox TPPPyruvate oxidase 1.2.3.3 0.756
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.755
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.754
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.753
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.753
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.750
2ag0 TPPBenzaldehyde lyase / 0.749
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.746
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.746
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.745
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.744
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.740
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 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
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.737
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.736
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.735
2ag1 TPPBenzaldehyde lyase / 0.730
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.730
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.729
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.729
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.729
4qpz TPPBenzaldehyde lyase / 0.729
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.725
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.723
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.723
2pan TDPGlyoxylate carboligase 4.1.1.47 0.720
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.719
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.718
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.717
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.716
2r8o T5XTransketolase 1 / 0.714
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.710
2c42 TPPPyruvate synthase / 0.706
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.706
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.703
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.702
3ahj TPPProbable phosphoketolase / 0.701
5c4i TPPOxalate oxidoreductase subunit alpha / 0.701
5c4i TPPOxalate oxidoreductase subunit beta / 0.701
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.699
3ahi HTLProbable phosphoketolase / 0.696
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.696
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.693
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.690
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.690
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.690
1pow TPPPyruvate oxidase 1.2.3.3 0.689
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.686
2uz1 TPPBenzaldehyde lyase / 0.681
2c3p 1TPPyruvate synthase / 0.680
3ahe THDProbable phosphoketolase / 0.679
2c3o TPPPyruvate synthase / 0.678
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.675
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.675
3rim TPPTransketolase 2.2.1.1 0.673
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.671
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.671
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.666
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.666
3m34 TPPTransketolase / 0.665
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.665
1tkc M6TTransketolase 1 2.2.1.1 0.663
2c3y HTLPyruvate synthase / 0.663
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.660
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.656
1gpu THDTransketolase 1 2.2.1.1 0.650
3m7i TPPTransketolase / 0.650