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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
2j9f THV 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.464
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 1.464
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.048
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.005
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.992
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.992
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.965
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.965
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.940
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.940
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.936
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.936
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.907
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.892
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.891
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.891
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.880
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.878
5ahk TPPAcetolactate synthase II, large subunit / 0.878
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.871
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.868
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.864
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.864
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.863
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.837
2r8o T5XTransketolase 1 / 0.820
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.817
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.814
2ezt TDMPyruvate oxidase 1.2.3.3 0.809
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.808
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.805
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.803
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.801
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.797
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.797
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.794
3ahj TPPProbable phosphoketolase / 0.794
3upt TPPTransketolase / 0.794
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.791
1y9d TPPPyruvate oxidase 1.2.3.3 0.789
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.789
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.787
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.787
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.786
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.781
1trk TPPTransketolase 1 2.2.1.1 0.778
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.778
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.777
1gpu THDTransketolase 1 2.2.1.1 0.774
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.774
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.774
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.774
3ahe THDProbable phosphoketolase / 0.772
2r8p T6FTransketolase 1 / 0.771
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.769
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.768
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.766
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.763
2r5n TPPTransketolase 1 / 0.762
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.762
1tkc M6TTransketolase 1 2.2.1.1 0.760
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.757
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.757
3iae D7KBenzaldehyde lyase / 0.752
3ahi HTLProbable phosphoketolase / 0.751
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.748
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.748
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.747
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.745
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.742
3d7k D7KBenzaldehyde lyase / 0.740
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.740
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.739
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.739
1ngs TPPTransketolase 1 2.2.1.1 0.735
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.735
2ez9 TDKPyruvate oxidase 1.2.3.3 0.734
3rim TPPTransketolase 2.2.1.1 0.734
1kek HTLPyruvate synthase / 0.733
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.732
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.731
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.730
1pow TPPPyruvate oxidase 1.2.3.3 0.729
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.729
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.728
3m6l TPPTransketolase / 0.728
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.726
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.726
1pox TPPPyruvate oxidase 1.2.3.3 0.724
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.724
3m34 TPPTransketolase / 0.722
3m7i TPPTransketolase / 0.721
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.720
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.718
2uza HTLPyruvate synthase / 0.718
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.717
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.714
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.714
1tkb N1TTransketolase 1 2.2.1.1 0.712
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.712
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.710
5c4i TPPOxalate oxidoreductase subunit alpha / 0.710
5c4i TPPOxalate oxidoreductase subunit beta / 0.710
2c3u 2TPPyruvate synthase / 0.709
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.709
1ay0 TPPTransketolase 1 2.2.1.1 0.707
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.704
2pan TDPGlyoxylate carboligase 4.1.1.47 0.698
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.698
1uqt U2FTrehalose-6-phosphate synthase 2.4.1.15 0.695
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.695
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.695
2c3o TPPPyruvate synthase / 0.693
2c3p 1TPPyruvate synthase / 0.690
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.687
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.687
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.686
4c7x TPPTransketolase / 0.685
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.683
2c42 TPPPyruvate synthase / 0.682
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.680
1g4p FQPThiamine-phosphate synthase / 0.677
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.677
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.674
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.672
1nhh ANPDNA mismatch repair protein MutL / 0.669
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.669
4qpz TPPBenzaldehyde lyase / 0.668
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.666
1t9a YF4Acetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.664
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.662
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.660
2c3y HTLPyruvate synthase / 0.658
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.657
5ero 210Fusicoccadiene synthase 2.5.1.29 0.656
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.654
4gvz ADPArginine kinase 2.7.3.3 0.654
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.653
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.652
4cok TPPPyruvate decarboxylase / 0.652
3vth APCCarbamoyltransferase / 0.651
2jib ADPOxalyl-CoA decarboxylase 4.1.1.8 0.650