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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
2e8w IPE Geranylgeranyl pyrophosphate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
2e8w IPEGeranylgeranyl pyrophosphate synthase / 1.034
2i19 1BYFarnesyl pyrophosphate synthase / 0.725
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.710
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.705
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.698
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.696
3krf DSTGeranyl diphosphate synthase large subunit / 0.696
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.687
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.685
4dwb 0M7Farnesyl pyrophosphate synthase / 0.678
2opm NI9Farnesyl pyrophosphate synthase 2.5.1.10 0.676
1sxj AGSReplication factor C subunit 1 / 0.675
3ryh GTPTubulin alpha chain / 0.667
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.662
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.662
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.662
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.660
3bgz VX3Serine/threonine-protein kinase pim-1 2.7.11.1 0.658
4qxa GTPRas-related protein Rab-9A / 0.658
1mb9 ATPCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.657
4zol GTPTubulin alpha-1B chain / 0.656
5erm 210Fusicoccadiene synthase 4.2.3.43 0.656
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.654
1m7b GTPRho-related GTP-binding protein RhoE / 0.651
4mpr TPPBenzoylformate decarboxylase 4.1.1.7 0.651
4qm6 GTPMetallophosphoesterase / 0.651
4gg1 TZDBenzoylformate decarboxylase 4.1.1.7 0.650