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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
1umc TDP 2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 1.283
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 1.283
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.993
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.992
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.992
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.961
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.946
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.946
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.941
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.941
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.922
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.922
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.904
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.904
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.870
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.867
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.863
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.863
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.858
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.853
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.834
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.832
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.831
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.830
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.829
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.829
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.825
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.825
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.823
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.822
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.822
3iae D7KBenzaldehyde lyase / 0.819
2uz1 TPPBenzaldehyde lyase / 0.814
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.813
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.811
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.808
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.807
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.804
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.804
5ahk TPPAcetolactate synthase II, large subunit / 0.801
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.794
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.793
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.791
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.788
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.785
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.784
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.781
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.778
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.774
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.774
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.773
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.772
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.772
1y9d TPPPyruvate oxidase 1.2.3.3 0.771
1kek HTLPyruvate synthase / 0.770
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.769
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.767
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.765
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.765
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.765
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.764
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.764
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.763
3d7k D7KBenzaldehyde lyase / 0.763
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.759
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.758
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.758
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.754
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.749
2r8o T5XTransketolase 1 / 0.749
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.749
2ag0 TPPBenzaldehyde lyase / 0.748
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.748
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.746
3ahi HTLProbable phosphoketolase / 0.744
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.739
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.738
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.735
2ag1 TPPBenzaldehyde lyase / 0.731
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.731
5c4i TPPOxalate oxidoreductase subunit alpha / 0.728
5c4i TPPOxalate oxidoreductase subunit beta / 0.728
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.727
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.723
1gpu THDTransketolase 1 2.2.1.1 0.722
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.720
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.720
1trk TPPTransketolase 1 2.2.1.1 0.718
4qpz TPPBenzaldehyde lyase / 0.718
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.717
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.717
2pan TDPGlyoxylate carboligase 4.1.1.47 0.714
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.713
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.713
3upt TPPTransketolase / 0.713
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.713
1pox TPPPyruvate oxidase 1.2.3.3 0.710
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.710
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.706
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.704
2ezt TDMPyruvate oxidase 1.2.3.3 0.701
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.698
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.696
2c3u 2TPPyruvate synthase / 0.696
1tkc M6TTransketolase 1 2.2.1.1 0.692
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.692
3ahe THDProbable phosphoketolase / 0.690
3rim TPPTransketolase 2.2.1.1 0.690
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.687
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.686
1pow TPPPyruvate oxidase 1.2.3.3 0.685
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.684
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.679
2ez9 TDKPyruvate oxidase 1.2.3.3 0.678
2r5n TPPTransketolase 1 / 0.677
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.677
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.676
3au2 DGTDNA polymerase beta family (X family) / 0.673
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.672
3m34 TPPTransketolase / 0.671
4c7x TPPTransketolase / 0.667
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.666
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.665
3ahj TPPProbable phosphoketolase / 0.665
5exd TPPOxalate oxidoreductase subunit alpha / 0.665
5exd TPPOxalate oxidoreductase subunit beta / 0.665
1ngs TPPTransketolase 1 2.2.1.1 0.663
2c42 TPPPyruvate synthase / 0.663
4cok TPPPyruvate decarboxylase / 0.659
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.658
1ay0 TPPTransketolase 1 2.2.1.1 0.657
1g4p FQPThiamine-phosphate synthase / 0.657
3nbz GTPGTP-binding nuclear protein Ran / 0.657
4dlx GNPGTPase HRas / 0.653
3vth APCCarbamoyltransferase / 0.651
4f9f GDPPutative glycosyltransferase / 0.650