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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
4mpr TPP Benzoylformate decarboxylase 4.1.1.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 1.138
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 1.117
4juf TPPBenzoylformate decarboxylase 4.1.1.7 1.111
4jub TPPBenzoylformate decarboxylase 4.1.1.7 1.107
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 1.096
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 1.095
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 1.093
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 1.091
4qel TZDBenzoylformate decarboxylase 4.1.1.7 1.091
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 1.090
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 1.089
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 1.089
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 1.082
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 1.068
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 1.060
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 1.057
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 1.056
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 1.053
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 1.033
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 1.025
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.999
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.993
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.989
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.985
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.982
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.965
4cok TPPPyruvate decarboxylase / 0.884
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.851
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.839
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.836
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.831
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.824
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.823
1y9d TPPPyruvate oxidase 1.2.3.3 0.820
1pox TPPPyruvate oxidase 1.2.3.3 0.819
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.817
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.815
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.809
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.809
1ovm TPPIndole-3-pyruvate decarboxylase 4.1.1.74 0.808
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.808
2ez9 TDKPyruvate oxidase 1.2.3.3 0.804
3lq2 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.803
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.801
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.801
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.796
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.796
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.787
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.786
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.785
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.780
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.778
2ezt TDMPyruvate oxidase 1.2.3.3 0.776
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.768
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.765
3iae D7KBenzaldehyde lyase / 0.763
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.759
2ji6 TPWOxalyl-CoA decarboxylase 4.1.1.8 0.759
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.758
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.758
2pan TDPGlyoxylate carboligase 4.1.1.47 0.757
1kek HTLPyruvate synthase / 0.755
1pow TPPPyruvate oxidase 1.2.3.3 0.753
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.752
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.748
2r8o T5XTransketolase 1 / 0.748
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.748
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.747
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.747
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.747
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.746
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.746
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.746
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.745
2uza HTLPyruvate synthase / 0.744
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.743
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.742
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.742
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.742
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.742
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.739
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.735
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.735
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.735
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.732
2ag0 TPPBenzaldehyde lyase / 0.730
3exh TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.730
3exh TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.730
3m7i TPPTransketolase / 0.724
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.723
5c4i TPPOxalate oxidoreductase subunit alpha / 0.723
5c4i TPPOxalate oxidoreductase subunit beta / 0.723
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.722
3ahe THDProbable phosphoketolase / 0.722
3d7k D7KBenzaldehyde lyase / 0.722
3m34 TPPTransketolase / 0.722
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.721
2c3p 1TPPyruvate synthase / 0.720
3m6l TPPTransketolase / 0.719
2uz1 TPPBenzaldehyde lyase / 0.718
3ahj TPPProbable phosphoketolase / 0.713
5ahk TPPAcetolactate synthase II, large subunit / 0.711
2c3y HTLPyruvate synthase / 0.709
1ay0 TPPTransketolase 1 2.2.1.1 0.708
2c42 TPPPyruvate synthase / 0.702
1gpu THDTransketolase 1 2.2.1.1 0.700
3upt TPPTransketolase / 0.700
3rim TPPTransketolase 2.2.1.1 0.699
3ahi HTLProbable phosphoketolase / 0.697
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.697
2r5n TPPTransketolase 1 / 0.695
1tkc M6TTransketolase 1 2.2.1.1 0.692
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.691
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.689
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.688
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.688
1tkb N1TTransketolase 1 2.2.1.1 0.687
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.683
4c7x TPPTransketolase / 0.682
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.681
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.676
1ngs TPPTransketolase 1 2.2.1.1 0.675
4qpz TPPBenzaldehyde lyase / 0.675
2r8p T6FTransketolase 1 / 0.673
2c3o TPPPyruvate synthase / 0.671
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.668
2ag1 TPPBenzaldehyde lyase / 0.665
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.665
2c3u 2TPPyruvate synthase / 0.663
3exf TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.663
3exf TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.663
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.661
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.659
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.659
1nhh ANPDNA mismatch repair protein MutL / 0.658
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.658
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.656
4rkf GNPRas-related protein Rab-3 / 0.654
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.653
3tgp GNPGTPase HRas / 0.652
2e8w IPEGeranylgeranyl pyrophosphate synthase / 0.651