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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
3zhu TD8 Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.472
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.076
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.076
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.055
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 1.039
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.985
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.907
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.907
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.901
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.901
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.898
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.898
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.869
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.864
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.864
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.863
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.863
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.832
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.832
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.824
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.813
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.813
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.795
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.782
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.780
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.777
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.776
3ahe THDProbable phosphoketolase / 0.774
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.772
3ahi HTLProbable phosphoketolase / 0.772
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.772
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.772
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.771
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.768
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.768
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.768
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.767
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.767
3ahj TPPProbable phosphoketolase / 0.766
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.762
5ahk TPPAcetolactate synthase II, large subunit / 0.759
2r8o T5XTransketolase 1 / 0.755
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.754
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.735
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.726
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.722
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.722
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.719
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.719
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.717
3upt TPPTransketolase / 0.715
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.714
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.710
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.709
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.704
5c4i TPPOxalate oxidoreductase subunit alpha / 0.704
5c4i TPPOxalate oxidoreductase subunit beta / 0.704
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.703
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.702
4qpz TPPBenzaldehyde lyase / 0.702
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.699
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.698
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.697
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.694
1kek HTLPyruvate synthase / 0.693
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.691
1gpu THDTransketolase 1 2.2.1.1 0.690
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.689
2r8p T6FTransketolase 1 / 0.688
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.686
2ezt TDMPyruvate oxidase 1.2.3.3 0.685
3rim TPPTransketolase 2.2.1.1 0.685
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.683
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.682
1trk TPPTransketolase 1 2.2.1.1 0.681
2c42 TPPPyruvate synthase / 0.680
3m34 TPPTransketolase / 0.680
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.680
1ay0 TPPTransketolase 1 2.2.1.1 0.678
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.676
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.675
1y9d TPPPyruvate oxidase 1.2.3.3 0.673
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.673
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.670
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.669
4cok TPPPyruvate decarboxylase / 0.669
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.667
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.667
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.665
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.665
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.664
3zfd ANPChromosome-associated kinesin KIF4 / 0.664
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.663
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.663
2r5n TPPTransketolase 1 / 0.663
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.663
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.662
2c3p 1TPPyruvate synthase / 0.660
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.658
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.657
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.657
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.657
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.656
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.655
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.655
1tkc M6TTransketolase 1 2.2.1.1 0.653
2c3y HTLPyruvate synthase / 0.653
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.651
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.650
4c7x TPPTransketolase / 0.650