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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
2x7j TPP 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
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.296
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.119
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.095
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.073
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.065
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.060
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.050
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.047
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.035
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.002
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.993
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.983
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.938
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.877
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.852
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.847
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.845
5ahk TPPAcetolactate synthase II, large subunit / 0.845
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.833
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.833
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.826
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.825
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.815
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.807
2ezt TDMPyruvate oxidase 1.2.3.3 0.804
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.802
4cok TPPPyruvate decarboxylase / 0.802
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.802
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.800
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.800
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.799
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.796
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.796
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.796
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.790
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.788
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.788
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.787
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.786
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.784
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.784
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.783
2ez9 TDKPyruvate oxidase 1.2.3.3 0.783
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.782
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.782
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.780
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.780
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.775
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.771
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.769
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.766
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.766
1y9d TPPPyruvate oxidase 1.2.3.3 0.763
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.763
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.762
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.761
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.761
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.755
2pan TDPGlyoxylate carboligase 4.1.1.47 0.753
2r8o T5XTransketolase 1 / 0.751
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.749
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.749
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.746
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.746
2ag0 TPPBenzaldehyde lyase / 0.745
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.745
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.740
1pow TPPPyruvate oxidase 1.2.3.3 0.739
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.738
1kek HTLPyruvate synthase / 0.736
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.736
5c4i TPPOxalate oxidoreductase subunit alpha / 0.736
5c4i TPPOxalate oxidoreductase subunit beta / 0.736
1pox TPPPyruvate oxidase 1.2.3.3 0.735
2uza HTLPyruvate synthase / 0.729
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.729
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.728
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.727
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.724
3ahj TPPProbable phosphoketolase / 0.722
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.719
2c3o TPPPyruvate synthase / 0.716
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.716
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.714
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.713
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.709
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.709
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.709
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.707
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.706
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.704
2c42 TPPPyruvate synthase / 0.703
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.703
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.701
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.701
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.700
2uz1 TPPBenzaldehyde lyase / 0.699
3upt TPPTransketolase / 0.699
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.699
2c3u 2TPPyruvate synthase / 0.698
3iae D7KBenzaldehyde lyase / 0.698
3m7i TPPTransketolase / 0.692
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.690
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.688
2r5n TPPTransketolase 1 / 0.685
2ag1 TPPBenzaldehyde lyase / 0.681
3ahi HTLProbable phosphoketolase / 0.681
1gpu THDTransketolase 1 2.2.1.1 0.677
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.677
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.677
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.673
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.673
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.673
4yj2 GTPTubulin alpha-1B chain / 0.673
3rim TPPTransketolase 2.2.1.1 0.671
3hiy UTPUncharacterized protein / 0.670
3m34 TPPTransketolase / 0.668
5la6 GTPTubulin alpha-1B chain / 0.667
1ngs TPPTransketolase 1 2.2.1.1 0.663
2c5l GTPGTPase HRas / 0.662
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.661
4qpz TPPBenzaldehyde lyase / 0.659
4qm6 GTPMetallophosphoesterase / 0.658
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.657
3d7k D7KBenzaldehyde lyase / 0.656
4mkg AP5Adenylate kinase / 0.655
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.652
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.652
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
3fvq ATPFe(3+) ions import ATP-binding protein FbpC / 0.650