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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
4zp1 TPP Pyruvate decarboxylase 4.1.1.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4zp1 TPPPyruvate decarboxylase 4.1.1.1 1.139
4cok TPPPyruvate decarboxylase / 1.012
2vk8 TPPPyruvate decarboxylase isozyme 1 / 1.002
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.991
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.954
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.921
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.920
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.915
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.905
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.848
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.837
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.834
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.830
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.827
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.826
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.824
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.823
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.816
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.816
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.810
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.805
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.801
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.795
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.795
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.794
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.793
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.791
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.789
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.788
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.786
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.784
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.782
2pan TDPGlyoxylate carboligase 4.1.1.47 0.779
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.776
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.776
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.772
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.771
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.771
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.770
2ezt TDMPyruvate oxidase 1.2.3.3 0.763
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.763
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.758
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.754
2ez9 TDKPyruvate oxidase 1.2.3.3 0.751
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.750
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.744
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.741
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.740
1pox TPPPyruvate oxidase 1.2.3.3 0.735
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.734
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.733
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.733
5c4i TPPOxalate oxidoreductase subunit alpha / 0.733
5c4i TPPOxalate oxidoreductase subunit beta / 0.733
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.732
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.732
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.729
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.727
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.727
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.725
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.724
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.724
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.718
2c3p 1TPPyruvate synthase / 0.716
2pda TPPPyruvate synthase / 0.715
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.712
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.709
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.709
2c3o TPPPyruvate synthase / 0.707
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.705
2c3u 2TPPyruvate synthase / 0.702
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.702
4qpz TPPBenzaldehyde lyase / 0.702
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.701
5exd TPPOxalate oxidoreductase subunit alpha / 0.701
5exd TPPOxalate oxidoreductase subunit beta / 0.701
5ahk TPPAcetolactate synthase II, large subunit / 0.700
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.698
1pow TPPPyruvate oxidase 1.2.3.3 0.697
3iae D7KBenzaldehyde lyase / 0.696
1y9d TPPPyruvate oxidase 1.2.3.3 0.695
2uz1 TPPBenzaldehyde lyase / 0.695
2ag0 TPPBenzaldehyde lyase / 0.694
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.693
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.688
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.686
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.686
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.683
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.679
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.679
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.678
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.678
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.678
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
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.674
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.670
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.669
3ahj TPPProbable phosphoketolase / 0.669
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.666
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.666
2c42 TPPPyruvate synthase / 0.665
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.663
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.662
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.662
2uza HTLPyruvate synthase / 0.662
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.662
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.661
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.660
3m34 TPPTransketolase / 0.660
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.659
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.659
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.656
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.653
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.650