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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
3exh 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
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 1.331
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 1.331
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 1.097
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 1.097
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.987
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.987
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.965
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.965
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.922
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.922
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.913
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.913
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.901
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.867
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.867
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.854
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.848
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.839
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.833
3ahi HTLProbable phosphoketolase / 0.831
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.818
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.818
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.814
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.813
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.813
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.810
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.809
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.804
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.801
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.800
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.798
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.797
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.791
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.783
4qpz TPPBenzaldehyde lyase / 0.783
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.771
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.767
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.764
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.762
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.759
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.756
3upt TPPTransketolase / 0.756
2uz1 TPPBenzaldehyde lyase / 0.755
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.754
3d7k D7KBenzaldehyde lyase / 0.753
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.751
3ahe THDProbable phosphoketolase / 0.751
4cok TPPPyruvate decarboxylase / 0.751
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.750
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.748
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.746
1tkc M6TTransketolase 1 2.2.1.1 0.742
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.735
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.733
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.730
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.730
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.729
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.726
2ag0 TPPBenzaldehyde lyase / 0.725
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.723
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.720
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.720
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.720
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.720
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.716
2r8o T5XTransketolase 1 / 0.716
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.714
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.711
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.709
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.709
1pox TPPPyruvate oxidase 1.2.3.3 0.707
5ahk TPPAcetolactate synthase II, large subunit / 0.707
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.706
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.706
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.704
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.703
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.700
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.700
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
2ezt TDMPyruvate oxidase 1.2.3.3 0.698
2pan TDPGlyoxylate carboligase 4.1.1.47 0.696
4gvz ADPArginine kinase 2.7.3.3 0.696
3ahj TPPProbable phosphoketolase / 0.695
1wdt GTPElongation factor G (EF-G-2) / 0.693
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.693
1ngs TPPTransketolase 1 2.2.1.1 0.691
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.689
4tlc AGSCircadian clock protein kinase KaiC 2.7.11.1 0.689
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.688
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.687
4tld AGSCircadian clock protein kinase KaiC 2.7.11.1 0.687
1y9d TPPPyruvate oxidase 1.2.3.3 0.685
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.685
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.684
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.683
3rim TPPTransketolase 2.2.1.1 0.682
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.681
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.680
1trk TPPTransketolase 1 2.2.1.1 0.678
2r5n TPPTransketolase 1 / 0.678
3m34 TPPTransketolase / 0.678
1gpu THDTransketolase 1 2.2.1.1 0.673
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.672
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.671
5c46 GSPRas-related protein Rab-11A / 0.671
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.671
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.669
2rgg GNPGTPase HRas / 0.669
1ay0 TPPTransketolase 1 2.2.1.1 0.668
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.668
3k9l GNPGTPase HRas / 0.668
4ihj GTPTubulin alpha-1B chain / 0.668
1mmg AGSMyosin-2 heavy chain / 0.666
1nhh ANPDNA mismatch repair protein MutL / 0.666
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.666
1h8h ATPATP synthase subunit alpha, mitochondrial / 0.665
1h8h ATPATP synthase subunit beta, mitochondrial 3.6.3.14 0.665
3tgp GNPGTPase HRas / 0.665
4c7x TPPTransketolase / 0.663
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.663
5exd TPPOxalate oxidoreductase subunit alpha / 0.663
5exd TPPOxalate oxidoreductase subunit beta / 0.663
4tyq AP5Adenylate kinase / 0.662
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.661
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.660
4to4 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.659
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.658
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.657
4tl9 AGSCircadian clock protein kinase KaiC 2.7.11.1 0.656
2c3o TPPPyruvate synthase / 0.654
1os1 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.653
3m6l TPPTransketolase / 0.653
4fvq ATPTyrosine-protein kinase JAK2 / 0.653
4xvr GNPGTPase HRas / 0.653
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.653
1p3j AP5Adenylate kinase / 0.652
2c3u 2TPPyruvate synthase / 0.652
4tuy GTPTubulin alpha-1B chain / 0.652
4wbn GTPTubulin alpha-1B chain / 0.652
2cje DUNDUTPase / 0.651
2olr ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.651
3dt2 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.650