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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
2vk8 TPP Pyruvate decarboxylase isozyme 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2vk8 TPPPyruvate decarboxylase isozyme 1 / 1.303
2w93 TPPPyruvate decarboxylase isozyme 1 / 1.272
1pvd TPPPyruvate decarboxylase isozyme 1 / 1.171
2vk4 TPPPyruvate decarboxylase 4.1.1.1 1.158
4cok TPPPyruvate decarboxylase / 1.141
1pyd TDPPyruvate decarboxylase isozyme 1 / 1.133
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 1.063
3oe1 TDLPyruvate decarboxylase 4.1.1.1 1.032
4zp1 TPPPyruvate decarboxylase 4.1.1.1 1.002
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.895
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.892
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.891
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.884
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.879
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.870
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.869
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.864
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.863
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.863
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.861
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.860
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.860
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.856
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.850
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.848
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.846
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.846
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.845
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.844
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.841
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.841
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.837
1pox TPPPyruvate oxidase 1.2.3.3 0.834
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.831
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.830
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.830
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.827
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.820
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.817
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.815
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.809
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.808
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.808
2ez9 TDKPyruvate oxidase 1.2.3.3 0.807
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.805
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.802
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.798
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.796
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.795
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.792
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.792
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.783
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.777
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.774
1y9d TPPPyruvate oxidase 1.2.3.3 0.771
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.765
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.762
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.760
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.758
2c3p 1TPPyruvate synthase / 0.751
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.750
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.750
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.750
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.750
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.748
2c3o TPPPyruvate synthase / 0.747
2uz1 TPPBenzaldehyde lyase / 0.741
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.731
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.727
2ezt TDMPyruvate oxidase 1.2.3.3 0.726
5c4i TPPOxalate oxidoreductase subunit alpha / 0.725
5c4i TPPOxalate oxidoreductase subunit beta / 0.725
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.724
2c3u 2TPPyruvate synthase / 0.721
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.720
2ag0 TPPBenzaldehyde lyase / 0.718
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.717
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.717
4qpz TPPBenzaldehyde lyase / 0.715
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.714
1kek HTLPyruvate synthase / 0.711
3ahe THDProbable phosphoketolase / 0.711
2pda TPPPyruvate synthase / 0.710
1tkc M6TTransketolase 1 2.2.1.1 0.709
2pan TDPGlyoxylate carboligase 4.1.1.47 0.709
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.706
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.706
5exd TPPOxalate oxidoreductase subunit alpha / 0.705
5exd TPPOxalate oxidoreductase subunit beta / 0.705
2c42 TPPPyruvate synthase / 0.704
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.703
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.703
2ag1 TPPBenzaldehyde lyase / 0.702
2c3y HTLPyruvate synthase / 0.699
2r8o T5XTransketolase 1 / 0.696
5ahk TPPAcetolactate synthase II, large subunit / 0.696
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.690
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.688
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.687
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.686
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.686
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.685
1pow TPPPyruvate oxidase 1.2.3.3 0.683
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.681
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.680
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.679
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.679
3iae D7KBenzaldehyde lyase / 0.678
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.677
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.677
3rim TPPTransketolase 2.2.1.1 0.676
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.675
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.675
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.672
1ay0 TPPTransketolase 1 2.2.1.1 0.667
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.667
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.664
3ahj TPPProbable phosphoketolase / 0.664
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.663
3ftq GNPSeptin-2 / 0.662
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.661
3upt TPPTransketolase / 0.659
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.658
4js0 GNPCell division control protein 42 homolog / 0.657
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.656
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.655
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.654
1tkb N1TTransketolase 1 2.2.1.1 0.653
1trk TPPTransketolase 1 2.2.1.1 0.653
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.652
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.652
4kvg GTPRas-related protein Rap-1A / 0.652
2pz8 APCNH(3)-dependent NAD(+) synthetase / 0.651
3eg5 GNPCell division control protein 42 homolog / 0.650