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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
2w93 TPP Pyruvate decarboxylase isozyme 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2w93 TPPPyruvate decarboxylase isozyme 1 / 1.279
2vk8 TPPPyruvate decarboxylase isozyme 1 / 1.272
2vk4 TPPPyruvate decarboxylase 4.1.1.1 1.197
1pvd TPPPyruvate decarboxylase isozyme 1 / 1.144
1pyd TDPPyruvate decarboxylase isozyme 1 / 1.106
4cok TPPPyruvate decarboxylase / 1.084
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 1.055
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.980
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.954
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.900
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.890
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.885
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.864
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.863
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.863
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.862
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.862
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.862
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.861
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.853
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.852
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.848
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.848
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.842
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.839
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.837
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.837
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.835
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.835
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.832
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.832
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.829
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.827
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.826
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.826
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.823
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.823
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.821
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.820
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.819
1y9d TPPPyruvate oxidase 1.2.3.3 0.816
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.816
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.813
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.813
1pox TPPPyruvate oxidase 1.2.3.3 0.811
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.807
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.803
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.801
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.800
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.796
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.791
2ez9 TDKPyruvate oxidase 1.2.3.3 0.776
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.767
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.766
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.764
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.760
2pda TPPPyruvate synthase / 0.758
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.751
2c42 TPPPyruvate synthase / 0.750
2c3u 2TPPyruvate synthase / 0.749
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.749
5c4i TPPOxalate oxidoreductase subunit alpha / 0.744
5c4i TPPOxalate oxidoreductase subunit beta / 0.744
2c3p 1TPPyruvate synthase / 0.741
2c3o TPPPyruvate synthase / 0.739
2uza HTLPyruvate synthase / 0.728
2pan TDPGlyoxylate carboligase 4.1.1.47 0.726
2ezt TDMPyruvate oxidase 1.2.3.3 0.724
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.723
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.723
1tkc M6TTransketolase 1 2.2.1.1 0.722
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.720
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.718
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.718
2uz1 TPPBenzaldehyde lyase / 0.718
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.716
1pow TPPPyruvate oxidase 1.2.3.3 0.710
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.708
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.708
1kek HTLPyruvate synthase / 0.707
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.706
2c3y HTLPyruvate synthase / 0.704
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.704
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.704
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.703
2ag0 TPPBenzaldehyde lyase / 0.699
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.698
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.698
3iae D7KBenzaldehyde lyase / 0.698
3ahi HTLProbable phosphoketolase / 0.694
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.691
3ahe THDProbable phosphoketolase / 0.691
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.691
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.687
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.687
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.687
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.687
5ahk TPPAcetolactate synthase II, large subunit / 0.687
4qpz TPPBenzaldehyde lyase / 0.685
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.683
2r8o T5XTransketolase 1 / 0.681
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.677
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.677
3m34 TPPTransketolase / 0.677
5exd TPPOxalate oxidoreductase subunit alpha / 0.677
5exd TPPOxalate oxidoreductase subunit beta / 0.677
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.672
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.672
1ay0 TPPTransketolase 1 2.2.1.1 0.669
3d7k D7KBenzaldehyde lyase / 0.668
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.667
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.667
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.667
2r8p T6FTransketolase 1 / 0.667
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.667
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.667
2ag1 TPPBenzaldehyde lyase / 0.666
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.666
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.663
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.663
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.661
3ftq GNPSeptin-2 / 0.661
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.660
3wyf GTPGTP-binding nuclear protein / 0.660
3ahj TPPProbable phosphoketolase / 0.658
3myk ANPMyosin-2 heavy chain / 0.658