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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
4dxj 0M9 Farnesyl pyrophosphate synthase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4dxj 0M9Farnesyl pyrophosphate synthase / 1.108
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.939
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.936
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.927
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.923
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.916
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.912
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.908
3dyh 721Farnesyl pyrophosphate synthase / 0.886
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.852
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.846
4dwb 0M7Farnesyl pyrophosphate synthase / 0.844
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.844
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.843
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.828
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.825
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.809
3egt 722Farnesyl pyrophosphate synthase / 0.807
3icz PB6Farnesyl pyrophosphate synthase / 0.806
2o1o RISPutative farnesyl pyrophosphate synthase / 0.800
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.783
2f94 BFQFarnesyl pyrophosphate synthase 2.5.1.10 0.770
3krf DSTGeranyl diphosphate synthase large subunit / 0.764
2zev B71Geranylgeranyl pyrophosphate synthase / 0.721
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.720
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.720
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.713
2i19 1BYFarnesyl pyrophosphate synthase / 0.709
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.701
1mx0 ANPType 2 DNA topoisomerase 6 subunit B / 0.701
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.695
3ai3 NDPNADPH-sorbose reductase / 0.685
2vp0 TTPDeoxynucleoside kinase / 0.680
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.680
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.676
1pnq NDPNAD(P) transhydrogenase subunit beta 1.6.1.2 0.674
3tb9 ANPRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.673
4tnq TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.671
3k0f ATPCircadian clock protein kinase KaiC 2.7.11.1 0.669
2y6p CTP3-deoxy-manno-octulosonate cytidylyltransferase 2.7.7.38 0.665
4tnr DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.664
4to0 DTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.664
4nke IPEFarnesyl pyrophosphate synthase 2.5.1.10 0.662
1yq7 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.661
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.661
3orl AGSSerine/threonine protein kinase / 0.660
1khb GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.659
3m0e ATPTranscriptional regulator (NtrC family) / 0.659
4bri UNPEctonucleoside triphosphate diphosphohydrolase I / 0.659
1p52 ADPArginine kinase 2.7.3.3 0.657
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.657
2q36 ATPActin, alpha skeletal muscle / 0.656
4fvr ATPTyrosine-protein kinase JAK2 / 0.656
4xjx ATPType I restriction enzyme EcoR124II R protein 3.1.21.3 0.656
5ero 210Fusicoccadiene synthase 2.5.1.29 0.656
1rqj IPEFarnesyl diphosphate synthase 2.5.1.10 0.655
1mdl SMNMandelate racemase / 0.654
1pno NAPNAD(P) transhydrogenase subunit beta 1.6.1.2 0.653
3q6j KPC2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.653
2cvx DGTRibonucleoside-diphosphate reductase large chain 1 1.17.4.1 0.652
1a5u ATPPyruvate kinase PKM 2.7.1.40 0.651
1qz5 ATPActin, alpha skeletal muscle / 0.651
1b38 ATPCyclin-dependent kinase 2 2.7.11.22 0.650
1til ATPAnti-sigma F factor / 0.650
3ai2 NDPNADPH-sorbose reductase / 0.650
4c0b ATPmRNA cleavage and polyadenylation factor CLP1 / 0.650
5bsm ATP4-coumarate--CoA ligase 2 6.2.1.12 0.650