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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
1l8a TDP Pyruvate dehydrogenase E1 component 1.2.4.1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 1.234
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 1.050
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 1.019
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 1.015
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 1.009
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.952
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.896
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.828
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.817
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.810
3ahe THDProbable phosphoketolase / 0.801
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.799
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.786
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.786
3ahj TPPProbable phosphoketolase / 0.782
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.780
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.780
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.778
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.778
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.777
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.777
3ahi HTLProbable phosphoketolase / 0.776
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.775
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.773
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.773
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.773
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.772
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.769
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.768
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.767
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.767
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.765
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.765
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.765
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.764
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.756
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.752
2r8o T5XTransketolase 1 / 0.748
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.748
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.748
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.747
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.745
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.741
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.741
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.740
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.739
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.737
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.734
5ahk TPPAcetolactate synthase II, large subunit / 0.732
1tkc M6TTransketolase 1 2.2.1.1 0.725
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.724
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.721
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.720
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.719
1pow TPPPyruvate oxidase 1.2.3.3 0.718
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.718
3m34 TPPTransketolase / 0.718
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.717
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.717
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.717
4cok TPPPyruvate decarboxylase / 0.714
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.714
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.712
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.712
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.710
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.710
3upt TPPTransketolase / 0.710
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.709
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.709
3m7i TPPTransketolase / 0.709
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.708
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.708
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.706
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.706
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.705
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.703
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.702
1ngs TPPTransketolase 1 2.2.1.1 0.701
1pox TPPPyruvate oxidase 1.2.3.3 0.700
1y9d TPPPyruvate oxidase 1.2.3.3 0.700
2uz1 TPPBenzaldehyde lyase / 0.700
3kmw ATPIntegrin-linked protein kinase 2.7.11.1 0.698
2ezt TDMPyruvate oxidase 1.2.3.3 0.696
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.695
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.694
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.694
1nhh ANPDNA mismatch repair protein MutL / 0.692
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.691
3d7k D7KBenzaldehyde lyase / 0.691
3iae D7KBenzaldehyde lyase / 0.689
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.688
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.688
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.687
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.687
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.687
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.687
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.687
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.686
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.684
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.684
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.683
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.683
2pan TDPGlyoxylate carboligase 4.1.1.47 0.681
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.681
1ay0 TPPTransketolase 1 2.2.1.1 0.680
3zfd ANPChromosome-associated kinesin KIF4 / 0.680
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.678
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.678
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.677
4qpz TPPBenzaldehyde lyase / 0.677
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.675
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.672
3ftq GNPSeptin-2 / 0.672
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.671
3qbt GNPRas-related protein Rab-8A / 0.670
4goj GNPADP-ribosylation factor-like protein 3 / 0.670
2ez9 TDKPyruvate oxidase 1.2.3.3 0.669
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.669
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.668
3pcr GTPADP-ribosylation factor 6 / 0.668
1tkb N1TTransketolase 1 2.2.1.1 0.663
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.661
4idp GNPAtlastin-1 3.6.5 0.660
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.659
4fvq ATPTyrosine-protein kinase JAK2 / 0.659
1gpu THDTransketolase 1 2.2.1.1 0.658
4mit GTPRho-related protein racC / 0.658
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.657
2ag1 TPPBenzaldehyde lyase / 0.656
2r8p T6FTransketolase 1 / 0.655
2r5n TPPTransketolase 1 / 0.654
3mle ADPATP-dependent dethiobiotin synthetase BioD 6.3.3.3 0.654
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.651