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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
1ni4 TPP Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 1.200
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 1.200
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 1.097
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 1.097
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.941
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.941
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.940
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.940
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.912
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.912
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.903
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.895
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.895
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.880
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.863
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.845
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.845
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.830
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.830
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.810
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.808
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.807
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.803
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.803
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.796
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.789
2pan TDPGlyoxylate carboligase 4.1.1.47 0.785
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.785
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.783
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.782
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.782
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.778
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.777
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.777
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.771
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.771
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.767
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.766
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.761
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.760
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.760
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.758
4qpz TPPBenzaldehyde lyase / 0.758
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.756
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.756
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.753
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.752
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.752
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.750
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.750
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.750
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.750
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.742
4cok TPPPyruvate decarboxylase / 0.741
3iae D7KBenzaldehyde lyase / 0.740
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.739
2uz1 TPPBenzaldehyde lyase / 0.737
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.736
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.732
2c3p 1TPPyruvate synthase / 0.731
2r8o T5XTransketolase 1 / 0.729
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.729
5ahk TPPAcetolactate synthase II, large subunit / 0.729
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.727
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.726
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.725
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.725
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.724
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.723
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.722
3d7k D7KBenzaldehyde lyase / 0.722
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.722
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.721
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.721
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.721
3ahe THDProbable phosphoketolase / 0.720
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.720
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.720
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.718
3ahj TPPProbable phosphoketolase / 0.717
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.717
3ahi HTLProbable phosphoketolase / 0.715
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.715
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.715
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.715
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.711
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.709
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.708
2ezt TDMPyruvate oxidase 1.2.3.3 0.707
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.707
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.706
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.705
5exd TPPOxalate oxidoreductase subunit alpha / 0.705
5exd TPPOxalate oxidoreductase subunit beta / 0.705
3upt TPPTransketolase / 0.703
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.702
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.701
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.701
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.700
5c4i TPPOxalate oxidoreductase subunit alpha / 0.699
5c4i TPPOxalate oxidoreductase subunit beta / 0.699
2ag0 TPPBenzaldehyde lyase / 0.697
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.695
2ez9 TDKPyruvate oxidase 1.2.3.3 0.694
3tgp GNPGTPase HRas / 0.693
1y9d TPPPyruvate oxidase 1.2.3.3 0.692
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.692
3rim TPPTransketolase 2.2.1.1 0.691
3m34 TPPTransketolase / 0.690
1tkc M6TTransketolase 1 2.2.1.1 0.689
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.687
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.684
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.682
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.681
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.681
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.680
1gpu THDTransketolase 1 2.2.1.1 0.679
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.678
3m7i TPPTransketolase / 0.678
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.677
1ay0 TPPTransketolase 1 2.2.1.1 0.675
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.675
3zfd ANPChromosome-associated kinesin KIF4 / 0.673
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.672
2r5n TPPTransketolase 1 / 0.670
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.667
4c7x TPPTransketolase / 0.666
1f5n GNPGuanylate-binding protein 1 / 0.665
1tu3 GNPRas-related protein Rab-5A / 0.665
1uqu UPGTrehalose-6-phosphate synthase 2.4.1.15 0.664
3oes GNPGTPase RhebL1 / 0.664
4xvq GNPGTPase HRas / 0.662
3k9l GNPGTPase HRas / 0.661
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.660
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.660
4idp GNPAtlastin-1 3.6.5 0.660
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.659
4gvz ADPArginine kinase 2.7.3.3 0.659
2c42 TPPPyruvate synthase / 0.658
2rgg GNPGTPase HRas / 0.658
1mmg AGSMyosin-2 heavy chain / 0.657
4xvr GNPGTPase HRas / 0.657
1ngs TPPTransketolase 1 2.2.1.1 0.656
1tka N3TTransketolase 1 2.2.1.1 0.656
1trk TPPTransketolase 1 2.2.1.1 0.656
3myk ANPMyosin-2 heavy chain / 0.656
4dwb 0M7Farnesyl pyrophosphate synthase / 0.655
2npi ATPmRNA cleavage and polyadenylation factor CLP1 / 0.654
1pow TPPPyruvate oxidase 1.2.3.3 0.653
3oee ANPATP synthase subunit alpha, mitochondrial / 0.653
3oee ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.653
1nhh ANPDNA mismatch repair protein MutL / 0.651
3qbt GNPRas-related protein Rab-8A / 0.650