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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
2vk4 TPP Pyruvate decarboxylase 4.1.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vk4 TPPPyruvate decarboxylase 4.1.1.1 1.231
2w93 TPPPyruvate decarboxylase isozyme 1 / 1.197
2vk8 TPPPyruvate decarboxylase isozyme 1 / 1.158
1pvd TPPPyruvate decarboxylase isozyme 1 / 1.088
4cok TPPPyruvate decarboxylase / 1.079
1pyd TDPPyruvate decarboxylase isozyme 1 / 1.016
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.931
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.920
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.898
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.848
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.847
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.847
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.836
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.829
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.826
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.822
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.822
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.816
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.816
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.807
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.805
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.804
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.801
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.800
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.799
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.797
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.797
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.792
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.790
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.790
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.788
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.787
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.786
3ahj TPPProbable phosphoketolase / 0.786
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.783
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.782
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.778
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.775
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.774
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.769
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.766
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.764
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.763
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.757
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.754
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.752
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.751
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.751
1pox TPPPyruvate oxidase 1.2.3.3 0.750
2c3o TPPPyruvate synthase / 0.745
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.743
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.743
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.741
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.739
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.738
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.736
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.733
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.730
4qpz TPPBenzaldehyde lyase / 0.729
2c3y HTLPyruvate synthase / 0.727
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.726
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.726
2c42 TPPPyruvate synthase / 0.726
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.722
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.718
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.718
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.717
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.717
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.716
2c3u 2TPPyruvate synthase / 0.715
2ag0 TPPBenzaldehyde lyase / 0.714
3iae D7KBenzaldehyde lyase / 0.714
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.710
1tkc M6TTransketolase 1 2.2.1.1 0.708
2uz1 TPPBenzaldehyde lyase / 0.707
1y9d TPPPyruvate oxidase 1.2.3.3 0.705
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.704
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.703
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.701
2ez9 TDKPyruvate oxidase 1.2.3.3 0.700
3ahe THDProbable phosphoketolase / 0.700
1ay0 TPPTransketolase 1 2.2.1.1 0.695
2ag1 TPPBenzaldehyde lyase / 0.695
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.695
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.690
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.689
5c4i TPPOxalate oxidoreductase subunit alpha / 0.687
5c4i TPPOxalate oxidoreductase subunit beta / 0.687
2c3p 1TPPyruvate synthase / 0.683
3ahi HTLProbable phosphoketolase / 0.679
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.678
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.677
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.677
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.677
2pan TDPGlyoxylate carboligase 4.1.1.47 0.676
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.674
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.674
3d7k D7KBenzaldehyde lyase / 0.672
2uza HTLPyruvate synthase / 0.671
1kek HTLPyruvate synthase / 0.670
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.670
5exd TPPOxalate oxidoreductase subunit alpha / 0.670
5exd TPPOxalate oxidoreductase subunit beta / 0.670
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.669
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.668
3m34 TPPTransketolase / 0.667
5ahk TPPAcetolactate synthase II, large subunit / 0.667
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.663
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.663
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.663
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.662
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.662
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.662
2ezt TDMPyruvate oxidase 1.2.3.3 0.661
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.657
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.656
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.655
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.655
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.655
4c2u ANPDNA helicase / 0.654
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.651
3ruq ADPChaperonin / 0.650