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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
3zhr TPP Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.194
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.177
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.168
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.157
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.139
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.055
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.915
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.915
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.887
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.887
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.878
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.878
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.867
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.867
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.863
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.863
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.845
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.845
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.839
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.839
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.781
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.778
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.776
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.749
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.748
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.748
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.748
3ahi HTLProbable phosphoketolase / 0.747
5ahk TPPAcetolactate synthase II, large subunit / 0.742
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.740
3d7k D7KBenzaldehyde lyase / 0.736
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.735
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.730
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.730
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.730
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.729
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.728
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.728
2ezt TDMPyruvate oxidase 1.2.3.3 0.727
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.725
3ahe THDProbable phosphoketolase / 0.720
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.719
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.715
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.715
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.714
2r8o T5XTransketolase 1 / 0.714
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.714
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.710
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.709
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.709
1gpu THDTransketolase 1 2.2.1.1 0.707
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.706
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.706
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.706
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.705
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
3ahj TPPProbable phosphoketolase / 0.701
4qpz TPPBenzaldehyde lyase / 0.701
1y9d TPPPyruvate oxidase 1.2.3.3 0.700
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.699
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
2r5n TPPTransketolase 1 / 0.698
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.697
1trk TPPTransketolase 1 2.2.1.1 0.696
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.695
4cok TPPPyruvate decarboxylase / 0.695
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.694
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.693
2uz1 TPPBenzaldehyde lyase / 0.693
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.692
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.691
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.691
3upt TPPTransketolase / 0.690
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.689
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.688
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.688
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.687
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.685
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.684
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.684
4c7x TPPTransketolase / 0.683
3iae D7KBenzaldehyde lyase / 0.682
3m34 TPPTransketolase / 0.682
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.681
1tkc M6TTransketolase 1 2.2.1.1 0.680
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.678
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.678
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.677
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.676
5c4i TPPOxalate oxidoreductase subunit alpha / 0.676
5c4i TPPOxalate oxidoreductase subunit beta / 0.676
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.674
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.673
1uqt U2FTrehalose-6-phosphate synthase 2.4.1.15 0.673
3rim TPPTransketolase 2.2.1.1 0.673
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.673
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.673
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.673
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.672
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.672
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.671
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.671
3zfd ANPChromosome-associated kinesin KIF4 / 0.671
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.671
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.670
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.669
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.669
1pox TPPPyruvate oxidase 1.2.3.3 0.668
2ez9 TDKPyruvate oxidase 1.2.3.3 0.668
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.663
1pow TPPPyruvate oxidase 1.2.3.3 0.663
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.662
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.662
3m7i TPPTransketolase / 0.662
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.662
2pan TDPGlyoxylate carboligase 4.1.1.47 0.659
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.657
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.656
1uqu UPGTrehalose-6-phosphate synthase 2.4.1.15 0.656
1ay0 TPPTransketolase 1 2.2.1.1 0.654
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.654
1mdr APGMandelate racemase / 0.653
1ngs TPPTransketolase 1 2.2.1.1 0.653
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.652
3m6l TPPTransketolase / 0.650