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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
1x09 IPE Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.941
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.710
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.706
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.706
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.704
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.697
3krf DSTGeranyl diphosphate synthase large subunit / 0.690
3s87 DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.683
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.679
2idx ATPCob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrial 2.5.1.17 0.666
3mvw BHZNickel-binding periplasmic protein / 0.666
1pox TPPPyruvate oxidase 1.2.3.3 0.664
2zev B71Geranylgeranyl pyrophosphate synthase / 0.663
4dwb 0M7Farnesyl pyrophosphate synthase / 0.662
3zhq TPPMultifunctional 2-oxoglutarate metabolism enzyme 1.2.4.2 0.661
1d3g BREDihydroorotate dehydrogenase (quinone), mitochondrial 1.3.5.2 0.660
4w5j AP5Adenylate kinase / 0.659
1m9n AMZBifunctional purine biosynthesis protein PURH 2.1.2.3 0.657
3fce ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.656
1g3l TRHGlucose-1-phosphate thymidylyltransferase / 0.654
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.654
4pl0 ANPMicrocin-J25 export ATP-binding/permease protein McjD / 0.654
3m0e ATPTranscriptional regulator (NtrC family) / 0.652
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.651
1eqy ATPActin, alpha skeletal muscle / 0.650
2z08 ATPUniversal stress protein family / 0.650