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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
5erm 210 Fusicoccadiene synthase 4.2.3.43

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
5erm 210Fusicoccadiene synthase 4.2.3.43 0.983
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.762
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.762
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.760
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.760
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.757
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.756
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.739
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.736
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.733
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.730
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.724
3icz PB6Farnesyl pyrophosphate synthase / 0.716
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.716
4dwb 0M7Farnesyl pyrophosphate synthase / 0.713
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.704
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.702
2f94 BFQFarnesyl pyrophosphate synthase 2.5.1.10 0.700
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.699
3dyh 721Farnesyl pyrophosphate synthase / 0.699
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.697
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.697
3ruq ADPChaperonin / 0.688
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.687
4hnc 0UTMandelate racemase / 0.686
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.683
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.682
1mdl SMNMandelate racemase / 0.681
1ja0 NAPNADPH--cytochrome P450 reductase / 0.678
3egt 722Farnesyl pyrophosphate synthase / 0.673
4rzu ADPProbable thymidylate kinase 2.7.4.9 0.672
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.670
4bzc T8TDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.667
1n2e APCPantothenate synthetase 6.3.2.1 0.665
1lwx AZDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.664
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.664
1n75 ATPGlutamate--tRNA ligase 6.1.1.17 0.663
1jsz NDMCap-specific mRNA (nucleoside-2'-O-)-methyltransferase 2.1.1.57 0.660
1n2g APCPantothenate synthetase 6.3.2.1 0.660
2zev B71Geranylgeranyl pyrophosphate synthase / 0.659
2a84 ATPPantothenate synthetase 6.3.2.1 0.656
2e8w IPEGeranylgeranyl pyrophosphate synthase / 0.656
1wua ATPActin, alpha skeletal muscle / 0.652
4iok ADPFormate--tetrahydrofolate ligase / 0.652
3wt0 ATPCell division protein FtsA / 0.651
2vwi ANPSerine/threonine-protein kinase OSR1 2.7.11.1 0.650