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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
4gm4 TZD Benzoylformate decarboxylase 4.1.1.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 1.105
4juf TPPBenzoylformate decarboxylase 4.1.1.7 1.069
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 1.062
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 1.057
4qel TZDBenzoylformate decarboxylase 4.1.1.7 1.057
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 1.052
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 1.045
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 1.031
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 1.030
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 1.026
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 1.025
4jub TPPBenzoylformate decarboxylase 4.1.1.7 1.023
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 1.020
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 1.013
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 1.012
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.998
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.994
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.989
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.983
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.967
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.964
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.959
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.952
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.921
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.916
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.873
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.841
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.837
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.835
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.818
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.816
4cok TPPPyruvate decarboxylase / 0.807
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.804
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.803
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.802
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.801
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.799
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.794
5c4i TPPOxalate oxidoreductase subunit alpha / 0.794
5c4i TPPOxalate oxidoreductase subunit beta / 0.794
2ezt TDMPyruvate oxidase 1.2.3.3 0.789
1y9d TPPPyruvate oxidase 1.2.3.3 0.788
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.787
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.781
1pox TPPPyruvate oxidase 1.2.3.3 0.777
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.774
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.774
2pan TDPGlyoxylate carboligase 4.1.1.47 0.772
1kek HTLPyruvate synthase / 0.770
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.770
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.766
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.764
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.764
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.763
1pow TPPPyruvate oxidase 1.2.3.3 0.762
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.758
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.750
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.750
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.749
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.744
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.742
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.742
2c3p 1TPPyruvate synthase / 0.739
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.739
3iae D7KBenzaldehyde lyase / 0.737
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.729
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.724
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.723
2uza HTLPyruvate synthase / 0.722
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.721
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.720
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.720
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.717
2ez9 TDKPyruvate oxidase 1.2.3.3 0.716
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.716
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.712
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.712
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.711
2c3u 2TPPyruvate synthase / 0.711
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.710
2c42 TPPPyruvate synthase / 0.709
3ahe THDProbable phosphoketolase / 0.708
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.706
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.705
3m7i TPPTransketolase / 0.705
3m34 TPPTransketolase / 0.704
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.703
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.703
5ahk TPPAcetolactate synthase II, large subunit / 0.699
4c7x TPPTransketolase / 0.696
3d7k D7KBenzaldehyde lyase / 0.695
3ahi HTLProbable phosphoketolase / 0.694
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.694
2uz1 TPPBenzaldehyde lyase / 0.693
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.687
3upt TPPTransketolase / 0.682
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.678
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.678
3m6l TPPTransketolase / 0.678
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.674
1ay0 TPPTransketolase 1 2.2.1.1 0.673
3rim TPPTransketolase 2.2.1.1 0.672
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.671
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.671
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.671
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.670
1gpu THDTransketolase 1 2.2.1.1 0.668
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.668
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.667
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.667
2ag1 TPPBenzaldehyde lyase / 0.665
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.665
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.664
1ngs TPPTransketolase 1 2.2.1.1 0.663
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.662
3a0t ADPSensor histidine kinase / 0.662
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.662
1tkc M6TTransketolase 1 2.2.1.1 0.660
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.660
3b1x GNPFerrous iron transport protein B / 0.660
1nhh ANPDNA mismatch repair protein MutL / 0.659
1th8 ADPAnti-sigma F factor / 0.659
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.659
2r5n TPPTransketolase 1 / 0.659
2ag0 TPPBenzaldehyde lyase / 0.658
4qpz TPPBenzaldehyde lyase / 0.658
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.657
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.657
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.656
2r8o T5XTransketolase 1 / 0.653
2r8p T6FTransketolase 1 / 0.653
3tgp GNPGTPase HRas / 0.652