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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
3iae D7K Benzaldehyde lyase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3iae D7KBenzaldehyde lyase / 1.461
3d7k D7KBenzaldehyde lyase / 1.275
2uz1 TPPBenzaldehyde lyase / 1.140
2ag0 TPPBenzaldehyde lyase / 0.983
5ahk TPPAcetolactate synthase II, large subunit / 0.870
4qpz TPPBenzaldehyde lyase / 0.829
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.819
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.819
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.814
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.813
2ag1 TPPBenzaldehyde lyase / 0.796
1y9d TPPPyruvate oxidase 1.2.3.3 0.791
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.785
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.784
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.784
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.784
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.783
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.780
3iaf TPPBenzaldehyde lyase / 0.777
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.773
5c4i TPPOxalate oxidoreductase subunit alpha / 0.772
5c4i TPPOxalate oxidoreductase subunit beta / 0.772
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.771
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.771
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.769
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.768
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.767
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.764
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.764
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.763
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.757
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.753
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.753
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.753
2ez9 TDKPyruvate oxidase 1.2.3.3 0.752
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.752
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.752
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.752
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.749
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.748
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.748
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.746
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.746
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.743
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.740
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.740
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.740
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.737
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.737
1pox TPPPyruvate oxidase 1.2.3.3 0.736
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.734
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.734
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.733
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.730
2c3y HTLPyruvate synthase / 0.728
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.727
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.725
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.724
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.724
2ezt TDMPyruvate oxidase 1.2.3.3 0.720
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.719
1kek HTLPyruvate synthase / 0.718
4cok TPPPyruvate decarboxylase / 0.717
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.716
5exd TPPOxalate oxidoreductase subunit alpha / 0.715
5exd TPPOxalate oxidoreductase subunit beta / 0.715
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.714
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.713
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.711
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.707
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.703
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.701
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.698
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.698
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.698
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.696
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.696
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.696
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.696
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.695
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.695
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.694
1pow TPPPyruvate oxidase 1.2.3.3 0.690
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.689
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.689
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.685
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.685
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.685
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.684
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.684
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.682
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.678
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.673
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.671
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.670
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.668
2pan TDPGlyoxylate carboligase 4.1.1.47 0.667
3ahj TPPProbable phosphoketolase / 0.667
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.666
1gpu THDTransketolase 1 2.2.1.1 0.661
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.661
2r8o T5XTransketolase 1 / 0.659
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.657
3ahe THDProbable phosphoketolase / 0.654
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.651
3d2r ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial 2.7.11.2 0.651
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.650