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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
2r5n TPP Transketolase 1

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2r5n TPPTransketolase 1 / 1.200
2r8p T6FTransketolase 1 / 1.085
3upt TPPTransketolase / 1.046
2r8o T5XTransketolase 1 / 0.943
1trk TPPTransketolase 1 2.2.1.1 0.933
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.930
3m6l TPPTransketolase / 0.924
1gpu THDTransketolase 1 2.2.1.1 0.917
1ngs TPPTransketolase 1 2.2.1.1 0.896
3rim TPPTransketolase 2.2.1.1 0.889
3m34 TPPTransketolase / 0.879
1tka N3TTransketolase 1 2.2.1.1 0.858
3m7i TPPTransketolase / 0.851
1ay0 TPPTransketolase 1 2.2.1.1 0.839
1tkb N1TTransketolase 1 2.2.1.1 0.834
4c7x TPPTransketolase / 0.791
1tkc M6TTransketolase 1 2.2.1.1 0.789
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.762
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.762
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.750
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.750
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.740
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.740
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.739
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.739
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.730
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.728
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.717
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.714
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.713
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.709
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.705
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.703
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.699
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.699
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.698
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.695
1y9d TPPPyruvate oxidase 1.2.3.3 0.694
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.691
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.688
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.686
5ahk TPPAcetolactate synthase II, large subunit / 0.686
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.685
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.685
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.684
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.683
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.682
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.681
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.681
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.681
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.680
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.678
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.678
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 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
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.677
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.676
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.676
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.676
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.674
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.674
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.672
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.671
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.670
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.670
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.670
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.669
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.668
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.667
4dsn GCPGTPase KRas / 0.666
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.664
2ezt TDMPyruvate oxidase 1.2.3.3 0.663
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.663
2uz1 TPPBenzaldehyde lyase / 0.662
3ahi HTLProbable phosphoketolase / 0.662
2ez9 TDKPyruvate oxidase 1.2.3.3 0.661
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.661
1z2c GNPRho-related GTP-binding protein RhoC / 0.660
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.660
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.660
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.659
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.657
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.654
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.654
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.652
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.651