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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
2o1s TDP 1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 1.144
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.801
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.789
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.786
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.779
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.778
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.775
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.771
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.771
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.771
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.771
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.767
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.767
3ahj TPPProbable phosphoketolase / 0.765
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.765
3ahe THDProbable phosphoketolase / 0.764
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.763
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.761
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.761
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.758
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.758
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.758
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.758
4cok TPPPyruvate decarboxylase / 0.757
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.748
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.748
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.748
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.745
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.745
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.737
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.737
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.734
3ahi HTLProbable phosphoketolase / 0.734
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.731
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.730
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.730
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.730
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.724
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.722
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.722
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.722
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.722
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.721
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.721
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.720
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.717
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.716
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.714
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.706
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.706
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.705
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.704
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.704
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.704
1gpu THDTransketolase 1 2.2.1.1 0.703
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.703
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.701
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.701
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.699
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.696
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.695
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.694
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.694
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.691
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.691
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.688
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.688
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.688
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.685
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.684
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.684
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.683
1tkc M6TTransketolase 1 2.2.1.1 0.682
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.679
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.679
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.678
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.677
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.675
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.675
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.674
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.674
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.674
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.673
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.673
2c3u 2TPPyruvate synthase / 0.671
2ag0 TPPBenzaldehyde lyase / 0.670
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.670
2ezt TDMPyruvate oxidase 1.2.3.3 0.669
5ahk TPPAcetolactate synthase II, large subunit / 0.669
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.669
1trk TPPTransketolase 1 2.2.1.1 0.668
3upt TPPTransketolase / 0.667
1tkb N1TTransketolase 1 2.2.1.1 0.666
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.666
3m6l TPPTransketolase / 0.665
3b05 IPEIsopentenyl-diphosphate delta-isomerase / 0.664
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.662
2r5n TPPTransketolase 1 / 0.661
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.659
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.657
1y9d TPPPyruvate oxidase 1.2.3.3 0.657
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.657
3iae D7KBenzaldehyde lyase / 0.657
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.657
1ay0 TPPTransketolase 1 2.2.1.1 0.654
2ez9 TDKPyruvate oxidase 1.2.3.3 0.654
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.651