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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
4gm1 TZD Benzoylformate decarboxylase 4.1.1.7

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4gm1 TZDBenzoylformate decarboxylase 4.1.1.7 1.095
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 1.068
1po7 TZDBenzoylformate decarboxylase 4.1.1.7 1.049
4juf TPPBenzoylformate decarboxylase 4.1.1.7 1.049
2fwn TDPBenzoylformate decarboxylase 4.1.1.7 1.043
4ju8 TZDBenzoylformate decarboxylase 4.1.1.7 1.034
4mq5 TPPBenzoylformate decarboxylase 4.1.1.7 1.034
4ju9 TZDBenzoylformate decarboxylase 4.1.1.7 1.031
3fsj D7KBenzoylformate decarboxylase 4.1.1.7 1.022
4jd5 TZDBenzoylformate decarboxylase 4.1.1.7 1.010
5dgt TZDBenzoylformate decarboxylase 4.1.1.7 1.000
1bfd TPPBenzoylformate decarboxylase 4.1.1.7 0.999
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.999
4mpp TZDBenzoylformate decarboxylase 4.1.1.7 0.999
4qel TZDBenzoylformate decarboxylase 4.1.1.7 0.997
4jub TPPBenzoylformate decarboxylase 4.1.1.7 0.995
3fzn D7KBenzoylformate decarboxylase 4.1.1.7 0.980
4gm0 TZDBenzoylformate decarboxylase 4.1.1.7 0.977
4k9n TZDBenzoylformate decarboxylase 4.1.1.7 0.976
4mzx TZDBenzoylformate decarboxylase 4.1.1.7 0.970
4gm4 TZDBenzoylformate decarboxylase 4.1.1.7 0.964
4k9p TPPBenzoylformate decarboxylase 4.1.1.7 0.953
1mcz TDPBenzoylformate decarboxylase 4.1.1.7 0.948
4k9o TPPBenzoylformate decarboxylase 4.1.1.7 0.937
4juc TPPBenzoylformate decarboxylase 4.1.1.7 0.913
2v3w TPPBenzoylformate decarboxylase 4.1.1.7 0.890
2q5q TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.877
4cok TPPPyruvate decarboxylase / 0.870
2q5o TPWIndole-3-pyruvate decarboxylase 4.1.1.74 0.865
2vk8 TPPPyruvate decarboxylase isozyme 1 / 0.850
3oe1 TDLPyruvate decarboxylase 4.1.1.1 0.848
2w93 TPPPyruvate decarboxylase isozyme 1 / 0.832
5c4i TPPOxalate oxidoreductase subunit alpha / 0.812
5c4i TPPOxalate oxidoreductase subunit beta / 0.812
2pan TDPGlyoxylate carboligase 4.1.1.47 0.807
1y9d TPPPyruvate oxidase 1.2.3.3 0.801
2ezt TDMPyruvate oxidase 1.2.3.3 0.794
4zp1 TPPPyruvate decarboxylase 4.1.1.1 0.793
1jsc TPPAcetolactate synthase catalytic subunit, mitochondrial 2.2.1.6 0.790
5ej7 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.788
2ez9 TDKPyruvate oxidase 1.2.3.3 0.787
2x7j TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.787
1pyd TDPPyruvate decarboxylase isozyme 1 / 0.786
5ej9 TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.786
1pvd TPPPyruvate decarboxylase isozyme 1 / 0.780
3hwx TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.775
5ej8 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.775
1umc TDP2-oxoisovalerate dehydrogenase subunit alpha 1.2.4.4 0.772
1umc TDP2-oxoisovalerate dehydrogenase subunit beta 1.2.4.4 0.772
1ols TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.769
5ej4 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.769
3iae D7KBenzaldehyde lyase / 0.768
5eso TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.768
2j9f THV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.766
2j9f THV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial 1.2.4.4 0.766
1pox TPPPyruvate oxidase 1.2.3.3 0.757
5esd TDP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.757
1ni4 TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial 1.2.4.1 0.756
1ni4 TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial 1.2.4.1 0.756
5ej5 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.755
2jlc TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.745
5ahk TPPAcetolactate synthase II, large subunit / 0.745
1v11 TDP2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial 1.2.4.4 0.744
2qta TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.743
1rp7 TZDPyruvate dehydrogenase E1 component 1.2.4.1 0.739
2vk4 TPPPyruvate decarboxylase 4.1.1.1 0.738
1qpb TPPPyruvate decarboxylase isozyme 1 / 0.729
1pow TPPPyruvate oxidase 1.2.3.3 0.728
2c3y HTLPyruvate synthase / 0.727
2ihu TP9N(2)-(2-carboxyethyl)arginine synthase / 0.726
3ey9 TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.726
2ji7 OXTOxalyl-CoA decarboxylase 4.1.1.8 0.724
2o1s TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.724
5eja TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.718
1upb TPPN(2)-(2-carboxyethyl)arginine synthase / 0.717
3d7k D7KBenzaldehyde lyase / 0.717
2uza HTLPyruvate synthase / 0.716
2qtc TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.715
1upc TPPN(2)-(2-carboxyethyl)arginine synthase / 0.714
1l8a TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.712
2g28 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.712
3ahj TPPProbable phosphoketolase / 0.708
1kek HTLPyruvate synthase / 0.707
2uz1 TPPBenzaldehyde lyase / 0.706
2jla TPP2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
5ej6 TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase / 0.705
3ahe THDProbable phosphoketolase / 0.704
3ahi HTLProbable phosphoketolase / 0.700
2r8o T5XTransketolase 1 / 0.696
3lq4 TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.696
3zhs TD6Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.692
2g25 TDKPyruvate dehydrogenase E1 component 1.2.4.1 0.687
1upa TPPN(2)-(2-carboxyethyl)arginine synthase / 0.683
1w88 TDPPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.681
1w88 TDPPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.681
1itz TPPTransketolase, chloroplastic 2.2.1.1 0.680
2iea TDPPyruvate dehydrogenase E1 component 1.2.4.1 0.677
3zht TD9Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.677
3zhv TDWMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.677
3zhr TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.673
3m7i TPPTransketolase / 0.671
1ozh HE3Acetolactate synthase, catabolic 2.2.1.6 0.667
2c31 TZDOxalyl-CoA decarboxylase 4.1.1.8 0.666
2bc9 GNPGuanylate-binding protein 1 / 0.664
3a0t ADPSensor histidine kinase / 0.664
1w1w AGSStructural maintenance of chromosomes protein 1 / 0.661
3b1x GNPFerrous iron transport protein B / 0.660
3ruq ADPChaperonin / 0.660
5exd TPPOxalate oxidoreductase subunit alpha / 0.660
5exd TPPOxalate oxidoreductase subunit beta / 0.660
3dv0 TPWPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.657
3dv0 TPWPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.657
3eya TDPPyruvate dehydrogenase [ubiquinone] 1.2.5.1 0.657
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.657
3zhu TD8Multifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.657
3duf R1TPyruvate dehydrogenase E1 component subunit alpha 1.2.4.1 0.656
3duf R1TPyruvate dehydrogenase E1 component subunit beta 1.2.4.1 0.656
2o1x TDP1-deoxy-D-xylulose-5-phosphate synthase 2.2.1.7 0.654
2ihv TPPN(2)-(2-carboxyethyl)arginine synthase / 0.653
1th8 ADPAnti-sigma F factor / 0.652
2iht TPPN(2)-(2-carboxyethyl)arginine synthase / 0.652
3tgp GNPGTPase HRas / 0.651
3wyg GTPGTP-binding nuclear protein GSP1/CNR1 / 0.651