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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
1ols TDP 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
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.129
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.097
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 1.048
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 1.048
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.993
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.993
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.903
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.903
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.875
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.875
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.869
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.858
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.854
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.854
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.851
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.851
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.828
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.825
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.817
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.816
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.813
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.813
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.813
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.809
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.805
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.804
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.803
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.803
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.799
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.798
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.798
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.796
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.796
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.795
3ahj TPPProbable phosphoketolase / 0.795
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.791
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.789
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.788
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.786
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.785
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.779
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.777
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.774
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.773
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.771
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.770
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.769
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.768
3iae D7KBenzaldehyde lyase / 0.764
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.764
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.761
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.761
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.760
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.760
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.758
3upt TPPTransketolase / 0.756
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.756
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.755
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.753
3m34 TPPTransketolase / 0.753
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.749
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.748
1tkc M6TTransketolase 1 2.2.1.1 0.748
2r8o T5XTransketolase 1 / 0.747
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.747
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.746
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.745
3m7i TPPTransketolase / 0.745
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.744
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.743
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.740
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.740
3ahi HTLProbable phosphoketolase / 0.732
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.732
4cok TPPPyruvate decarboxylase / 0.732
1pox TPPPyruvate oxidase 1.2.3.3 0.731
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.730
2ezt TDMPyruvate oxidase 1.2.3.3 0.729
2r5n TPPTransketolase 1 / 0.728
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.727
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.725
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.723
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.723
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.721
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.721
3m6l TPPTransketolase / 0.721
1gpu THDTransketolase 1 2.2.1.1 0.720
3rim TPPTransketolase 2.2.1.1 0.720
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.719
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.718
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.716
1y9d TPPPyruvate oxidase 1.2.3.3 0.715
3ahe THDProbable phosphoketolase / 0.714
5ahk TPPAcetolactate synthase II, large subunit / 0.713
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.710
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.710
4c7x TPPTransketolase / 0.710
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.708
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.708
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.707
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.706
1tkb N1TTransketolase 1 2.2.1.1 0.705
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
2pan TDPGlyoxylate carboligase 4.1.1.47 0.704
1ngs TPPTransketolase 1 2.2.1.1 0.703
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.700
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.698
1trk TPPTransketolase 1 2.2.1.1 0.698
4qfy DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.698
4qpz TPPBenzaldehyde lyase / 0.690
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.688
2c42 TPPPyruvate synthase / 0.688
1pow TPPPyruvate oxidase 1.2.3.3 0.687
1kek HTLPyruvate synthase / 0.684
1ay0 TPPTransketolase 1 2.2.1.1 0.681
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.679
2r8p T6FTransketolase 1 / 0.679
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.676
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.676
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.675
3d7k D7KBenzaldehyde lyase / 0.673
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.672
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.668
5exd TPPOxalate oxidoreductase subunit alpha / 0.668
5exd TPPOxalate oxidoreductase subunit beta / 0.668
2c3o TPPPyruvate synthase / 0.665
3k9l GNPGTPase HRas / 0.664
3tgp GNPGTPase HRas / 0.664
2rgg GNPGTPase HRas / 0.662
2c3u 2TPPyruvate synthase / 0.659
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.657
2xtn GTPGTPase IMAP family member 2 / 0.653
1zc3 GNPRas-related protein Ral-A / 0.652
3rep ATPIntegrin-linked protein kinase 2.7.11.1 0.652
2q3f GNPRas-related GTP-binding protein D / 0.650
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.650