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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
5eja TD6 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.530
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.507
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.502
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.491
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.428
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.415
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.236
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.219
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.207
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.157
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.095
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 1.081
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.968
4cok TPPPyruvate decarboxylase / 0.884
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.860
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.852
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.852
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.848
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.848
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.847
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.846
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.837
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.835
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.827
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.823
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.808
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.808
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.807
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.803
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.796
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.792
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.791
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.788
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.788
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.787
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.780
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.779
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.778
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.778
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.775
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.774
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.773
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.771
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.770
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.769
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.767
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.767
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.766
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.763
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.757
5c4i TPPOxalate oxidoreductase subunit alpha / 0.757
5c4i TPPOxalate oxidoreductase subunit beta / 0.757
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.756
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.752
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.752
2r8o T5XTransketolase 1 / 0.750
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.750
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.749
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.749
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.744
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.744
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.742
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.742
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.741
2ag0 TPPBenzaldehyde lyase / 0.740
2pan TDPGlyoxylate carboligase 4.1.1.47 0.739
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.737
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.733
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.733
5ahk TPPAcetolactate synthase II, large subunit / 0.728
1pow TPPPyruvate oxidase 1.2.3.3 0.727
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.726
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.726
3iae D7KBenzaldehyde lyase / 0.724
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.723
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.723
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.723
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.720
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.720
1pox TPPPyruvate oxidase 1.2.3.3 0.718
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.718
1y9d TPPPyruvate oxidase 1.2.3.3 0.717
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.714
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.714
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.712
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.710
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.706
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.698
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.697
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.696
1kek HTLPyruvate synthase / 0.695
2ez9 TDKPyruvate oxidase 1.2.3.3 0.691
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.688
2ezt TDMPyruvate oxidase 1.2.3.3 0.687
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.687
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.687
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.685
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.685
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.684
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.684
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.684
2ji9 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.680
2pda TPPPyruvate synthase / 0.678
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.677
2r5n TPPTransketolase 1 / 0.676
2uz1 TPPBenzaldehyde lyase / 0.674
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.674
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.671
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.671
1gpu THDTransketolase 1 2.2.1.1 0.669
3rim TPPTransketolase 2.2.1.1 0.668
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.659
3upt TPPTransketolase / 0.659
3zlm ANPAdenosine monophosphate-protein transferase NmFic 2.7.7.n1 0.659
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.657
3l06 SN0N-acetylornithine carbamoyltransferase 2.1.3.9 0.654
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.651