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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
4k9p TPP Benzoylformate decarboxylase 4.1.1.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 1.225
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 1.164
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 1.145
4juf TPPBenzoylformate decarboxylase 4.1.1.7 1.112
4juc TPPBenzoylformate decarboxylase 4.1.1.7 1.107
4jub TPPBenzoylformate decarboxylase 4.1.1.7 1.103
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 1.082
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 1.055
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 1.053
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 1.038
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 1.028
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 1.028
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 1.022
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 1.007
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.998
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.985
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.976
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.969
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.965
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.953
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.950
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.936
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.922
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.921
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.871
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.868
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.866
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.863
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.861
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.849
4cok TPPPyruvate decarboxylase / 0.839
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.822
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.822
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.814
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.811
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.805
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.799
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.794
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.791
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.791
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.790
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.790
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.789
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.789
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.783
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.783
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.781
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.779
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.779
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.777
1tkc M6TTransketolase 1 2.2.1.1 0.775
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.775
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.774
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.771
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.770
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.768
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.766
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.766
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.762
1pox TPPPyruvate oxidase 1.2.3.3 0.761
2ag0 TPPBenzaldehyde lyase / 0.760
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.760
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.760
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.757
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.757
2c42 TPPPyruvate synthase / 0.752
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.752
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.752
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.751
2ezt TDMPyruvate oxidase 1.2.3.3 0.750
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.750
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.749
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.749
1y9d TPPPyruvate oxidase 1.2.3.3 0.737
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.737
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.736
3iae D7KBenzaldehyde lyase / 0.734
2pan TDPGlyoxylate carboligase 4.1.1.47 0.730
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.729
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.729
3upt TPPTransketolase / 0.729
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.728
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.726
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.726
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.725
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.723
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.723
3rim TPPTransketolase 2.2.1.1 0.722
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.720
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.720
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.719
3ahj TPPProbable phosphoketolase / 0.718
1pow TPPPyruvate oxidase 1.2.3.3 0.716
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.714
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.711
2r5n TPPTransketolase 1 / 0.709
2r8o T5XTransketolase 1 / 0.709
3m7i TPPTransketolase / 0.708
1ay0 TPPTransketolase 1 2.2.1.1 0.707
3m34 TPPTransketolase / 0.707
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.707
4qpz TPPBenzaldehyde lyase / 0.707
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.706
3ahe THDProbable phosphoketolase / 0.706
5ahk TPPAcetolactate synthase II, large subunit / 0.706
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.705
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.703
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.702
2uz1 TPPBenzaldehyde lyase / 0.700
1ngs TPPTransketolase 1 2.2.1.1 0.698
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.697
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.696
2c3u 2TPPyruvate synthase / 0.694
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.694
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.692
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.692
1gpu THDTransketolase 1 2.2.1.1 0.688
3ahi HTLProbable phosphoketolase / 0.688
1tkb N1TTransketolase 1 2.2.1.1 0.686
2c3o TPPPyruvate synthase / 0.684
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.683
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.683
1trk TPPTransketolase 1 2.2.1.1 0.681
5c4i TPPOxalate oxidoreductase subunit alpha / 0.681
5c4i TPPOxalate oxidoreductase subunit beta / 0.681
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.680
2r8p T6FTransketolase 1 / 0.672
2uza HTLPyruvate synthase / 0.672
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.671
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.670
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.667
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.667
2ez9 TDKPyruvate oxidase 1.2.3.3 0.665
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.660
2pda TPPPyruvate synthase / 0.657
3d7k D7KBenzaldehyde lyase / 0.656
1t9a YF4Acetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.655
4c7x TPPTransketolase / 0.650