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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
2o1x 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
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 1.085
3d7k D7KBenzaldehyde lyase / 0.765
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.760
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.760
1y9d TPPPyruvate oxidase 1.2.3.3 0.757
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.757
2ezt TDMPyruvate oxidase 1.2.3.3 0.748
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.748
2ez9 TDKPyruvate oxidase 1.2.3.3 0.747
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.747
2uz1 TPPBenzaldehyde lyase / 0.734
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.731
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.731
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.720
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.720
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.709
4cok TPPPyruvate decarboxylase / 0.708
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.707
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.705
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.703
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.702
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.697
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.695
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.695
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
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.693
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.693
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.693
5ahk TPPAcetolactate synthase II, large subunit / 0.693
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.692
1gpu THDTransketolase 1 2.2.1.1 0.691
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.691
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.690
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.689
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.688
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.688
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.687
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.686
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.686
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.686
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.686
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.685
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.683
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.682
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.682
1ay0 TPPTransketolase 1 2.2.1.1 0.679
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.679
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.677
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.674
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.674
3upt TPPTransketolase / 0.674
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.673
1pox TPPPyruvate oxidase 1.2.3.3 0.672
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.672
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.670
1trk TPPTransketolase 1 2.2.1.1 0.669
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.668
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.668
3rim TPPTransketolase 2.2.1.1 0.668
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.668
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.667
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.666
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.663
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.660
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.660
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.659
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.659
3ahe THDProbable phosphoketolase / 0.659
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.658
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.658
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.657
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.655
3ahj TPPProbable phosphoketolase / 0.655
2r5n TPPTransketolase 1 / 0.654
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.654
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.653
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.653
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.650