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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
3d7k D7K Benzaldehyde lyase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3d7k D7KBenzaldehyde lyase / 1.456
3iae D7KBenzaldehyde lyase / 1.275
2uz1 TPPBenzaldehyde lyase / 1.105
2ag1 TPPBenzaldehyde lyase / 0.996
2ag0 TPPBenzaldehyde lyase / 0.985
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.840
3iaf TPPBenzaldehyde lyase / 0.822
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.814
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.812
5ahk TPPAcetolactate synthase II, large subunit / 0.807
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 0.782
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 0.779
1y9d TPPPyruvate oxidase 1.2.3.3 0.775
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 0.773
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.770
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.765
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.764
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.763
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.763
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.760
5exd TPPOxalate oxidoreductase subunit alpha / 0.759
5exd TPPOxalate oxidoreductase subunit beta / 0.759
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.756
1kek HTLPyruvate synthase / 0.753
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.753
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.753
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 0.750
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.749
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.745
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 0.745
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.744
2ez9 TDKPyruvate oxidase 1.2.3.3 0.742
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.742
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.740
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.740
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.740
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.740
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.739
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 0.738
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.737
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.736
4juf TPPBenzoylformate decarboxylase 4.1.1.7 0.736
1pox TPPPyruvate oxidase 1.2.3.3 0.734
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.733
2ezt TDMPyruvate oxidase 1.2.3.3 0.732
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.732
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.728
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.726
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.724
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 0.724
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.722
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.722
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.722
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.720
1pow TPPPyruvate oxidase 1.2.3.3 0.719
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.717
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 0.717
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.716
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.716
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.716
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.712
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.709
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.709
5c4i TPPOxalate oxidoreductase subunit alpha / 0.709
5c4i TPPOxalate oxidoreductase subunit beta / 0.709
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.704
3dva TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.699
3dva TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.699
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.697
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 0.696
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.695
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.695
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.695
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.695
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.694
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.693
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.692
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.691
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.690
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.690
3ahi HTLProbable phosphoketolase / 0.689
2pan TDPGlyoxylate carboligase 4.1.1.47 0.681
3ahj TPPProbable phosphoketolase / 0.678
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.678
2pda TPPPyruvate synthase / 0.674
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.673
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.673
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.672
4mkf AP5Adenylate kinase / 0.672
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.671
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.670
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.668
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.667
3law GNPRas-related protein Rab-7a / 0.662
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.662
1trk TPPTransketolase 1 2.2.1.1 0.661
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.660
2eu8 AP5Adenylate kinase / 0.658
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.656
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.656
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.656
1tkc M6TTransketolase 1 2.2.1.1 0.653
3upt TPPTransketolase / 0.653
3zfd ANPChromosome-associated kinesin KIF4 / 0.650