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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
3ahi HTL Probable phosphoketolase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3ahi HTLProbable phosphoketolase / 1.156
3ahe THDProbable phosphoketolase / 1.143
3ahj TPPProbable phosphoketolase / 1.072
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.876
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.844
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.840
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.831
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.831
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.811
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.808
1y9d TPPPyruvate oxidase 1.2.3.3 0.787
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.777
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.776
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.774
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.772
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.771
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.760
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.760
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.757
2r8o T5XTransketolase 1 / 0.754
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.751
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.751
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.749
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.747
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.744
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.744
1pox TPPPyruvate oxidase 1.2.3.3 0.742
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.740
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.740
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.738
2ezt TDMPyruvate oxidase 1.2.3.3 0.734
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.734
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.732
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.730
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.729
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.727
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.723
2ez9 TDKPyruvate oxidase 1.2.3.3 0.722
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.721
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.718
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.718
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.716
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.715
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.715
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.714
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.713
5ahk TPPAcetolactate synthase II, large subunit / 0.712
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.710
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.705
2r8p T6FTransketolase 1 / 0.701
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.700
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.700
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.697
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.696
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.695
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.695
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.694
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.694
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.694
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.693
3upt TPPTransketolase / 0.692
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.691
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.691
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.690
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.689
3d7k D7KBenzaldehyde lyase / 0.689
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.688
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.688
3rim TPPTransketolase 2.2.1.1 0.684
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.682
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.681
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.681
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.679
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.679
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.678
2c3o TPPPyruvate synthase / 0.676
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.676
2jib TPPOxalyl-CoA decarboxylase 4.1.1.8 0.675
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.674
2c42 TPPPyruvate synthase / 0.672
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.671
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.670
1n2e APCPantothenate synthetase 6.3.2.1 0.669
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.669
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.669
1zm7 TTPDeoxynucleoside kinase / 0.668
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.666
2dwp ACP6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 2.7.1.105 0.665
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.665
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.663
3m6l TPPTransketolase / 0.663
4qpz TPPBenzaldehyde lyase / 0.663
1mdr APGMandelate racemase / 0.662
2r5n TPPTransketolase 1 / 0.662
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.660
1trk TPPTransketolase 1 2.2.1.1 0.659
2pan TDPGlyoxylate carboligase 4.1.1.47 0.659
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.658
2zcq B65Dehydrosqualene synthase / 0.657
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.657
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.657
4yj2 GTPTubulin alpha-1B chain / 0.657
1cjv DADAdenylate cyclase type 2 / 0.655
1cjv DADAdenylate cyclase type 5 / 0.655
2c3u 2TPPyruvate synthase / 0.655
4c7x TPPTransketolase / 0.653
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.653
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.652
3sbe GNPRas-related C3 botulinum toxin substrate 1 / 0.652
1mdl SMNMandelate racemase / 0.651
2ag0 TPPBenzaldehyde lyase / 0.651
4idp GNPAtlastin-1 3.6.5 0.650