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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
1yv5 RIS Farnesyl pyrophosphate synthase 2.5.1.10

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.993
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.943
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.932
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.924
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.923
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.911
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.909
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.905
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.864
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.861
4dxj 0M9Farnesyl pyrophosphate synthase / 0.843
3dyh 721Farnesyl pyrophosphate synthase / 0.840
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.834
3icz PB6Farnesyl pyrophosphate synthase / 0.810
4dwb 0M7Farnesyl pyrophosphate synthase / 0.809
1yq7 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.798
2o1o RISPutative farnesyl pyrophosphate synthase / 0.798
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.797
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.766
3egt 722Farnesyl pyrophosphate synthase / 0.764
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.758
3krf DSTGeranyl diphosphate synthase large subunit / 0.757
2f94 BFQFarnesyl pyrophosphate synthase 2.5.1.10 0.753
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.748
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.745
5erm 210Fusicoccadiene synthase 4.2.3.43 0.739
3oab DSTGeranyl diphosphate synthase large subunit / 0.734
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.727
2opm NI9Farnesyl pyrophosphate synthase 2.5.1.10 0.714
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 0.708
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.702
1mb9 ATPCarboxyethyl-arginine beta-lactam-synthase 6.3.3.4 0.702
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.702
1g4p FQPThiamine-phosphate synthase / 0.694
4zwg DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.684
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.679
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.672
4qg1 DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.672
2q36 ATPActin, alpha skeletal muscle / 0.670
3h4l ANPDNA mismatch repair protein PMS1 / 0.669
3w2w ATPCRISPR system Cmr subunit Cmr2 / 0.668
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.668
2yww ATPAspartate carbamoyltransferase regulatory chain / 0.667
3mhy ATPNitrogen regulatory protein P-II 1 / 0.667
4jvj 1MVFarnesyl pyrophosphate synthase 2.5.1.10 0.667
1t44 ATPActin, alpha skeletal muscle / 0.666
1mdl SMNMandelate racemase / 0.664
3m1f ATPActin, alpha skeletal muscle / 0.663
4eht ADP2-hydroxyisocaproyl-CoA dehydratase activator / 0.661
2i19 1BYFarnesyl pyrophosphate synthase / 0.659
1dtn APGMandelate racemase / 0.656
1n2e APCPantothenate synthetase 6.3.2.1 0.655
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.654
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.652
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.652
1e1m NAPNADPH:adrenodoxin oxidoreductase, mitochondrial 1.18.1.6 0.651
2ogi GDPUncharacterized protein / 0.651
2xul ATPNitrogen regulatory protein P-II / 0.650