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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
3rye UNR Farnesyl pyrophosphate synthase 2.5.1.10

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3rye UNRFarnesyl pyrophosphate synthase 2.5.1.10 1.040
4kqs RISFarnesyl pyrophosphate synthase 2.5.1.10 0.941
2f94 BFQFarnesyl pyrophosphate synthase 2.5.1.10 0.929
3ez3 ZOLFarnesyl pyrophosphate synthase, putative / 0.928
4q23 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.924
3ldw ZOLFarnesyl pyrophosphate synthase, putative / 0.923
4h5e YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.912
4nke RISFarnesyl pyrophosphate synthase 2.5.1.10 0.908
3dyh 721Farnesyl pyrophosphate synthase / 0.888
4h5c YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.876
4dwb 0M7Farnesyl pyrophosphate synthase / 0.869
1rqj RISFarnesyl diphosphate synthase 2.5.1.10 0.834
2o1o RISPutative farnesyl pyrophosphate synthase / 0.814
1zw5 ZOLFarnesyl pyrophosphate synthase 2.5.1.10 0.798
3rbm B73Farnesyl pyrophosphate synthase, putative / 0.794
4lfv YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.786
4ga3 4GAFarnesyl pyrophosphate synthase 2.5.1.10 0.781
2e95 B75Geranylgeranyl pyrophosphate synthase / 0.780
4dem YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.775
3krf DSTGeranyl diphosphate synthase large subunit / 0.756
1yq7 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.744
3ryw K9HFarnesyl pyrophosphate synthase, putative / 0.744
4h5d YS4Farnesyl pyrophosphate synthase 2.5.1.10 0.741
2z52 H23Geranylgeranyl pyrophosphate synthase / 0.737
4qm6 GTPMetallophosphoesterase / 0.726
2opm NI9Farnesyl pyrophosphate synthase 2.5.1.10 0.725
1yv5 RISFarnesyl pyrophosphate synthase 2.5.1.10 0.708
1x09 IPEDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) 2.5.1.31 0.706
4l2x YL2Farnesyl pyrophosphate synthase 2.5.1.10 0.703
2jiz ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.698
5erm 210Fusicoccadiene synthase 4.2.3.43 0.697
1khe GCPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.694
3oab DSTGeranyl diphosphate synthase large subunit / 0.693
2i19 1BYFarnesyl pyrophosphate synthase / 0.689
2jj2 ANPATP synthase subunit beta, mitochondrial 3.6.3.14 0.688
2py7 ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.684
3zcb ATPAdenosine monophosphate-protein transferase VbhT 2.7.7.n1 0.684
4qfx DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.683
2z4z SC0Geranylgeranyl pyrophosphate synthase / 0.682
4to2 DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.682
3ump ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.681
4qfy DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.680
4brd ANPEctonucleoside triphosphate diphosphohydrolase I / 0.678
3umo ATPATP-dependent 6-phosphofructokinase isozyme 2 2.7.1.11 0.675
4nu0 AP5Adenylate kinase / 0.675
1ytm ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.674
5ero 210Fusicoccadiene synthase 2.5.1.29 0.672
2olq ATPPhosphoenolpyruvate carboxykinase (ATP) / 0.670
3n0y APCAdenylate cyclase 2 / 0.670
4tl6 ANPCircadian clock protein kinase KaiC 2.7.11.1 0.666
3q9l ATPSeptum site-determining protein MinD / 0.665
2e8w IPEGeranylgeranyl pyrophosphate synthase / 0.662
2e91 ZOLGeranylgeranyl pyrophosphate synthase / 0.662
2hgs ADPGlutathione synthetase 6.3.2.3 0.662
1kqc FMNOxygen-insensitive NAD(P)H nitroreductase / 0.661
3dt4 GTPPhosphoenolpyruvate carboxykinase, cytosolic [GTP] 4.1.1.32 0.661
3mzb BHRNickel-binding periplasmic protein / 0.661
4a61 ANPPlasmid segregation protein ParM / 0.660
2z4w 749Geranylgeranyl pyrophosphate synthase / 0.659
3mw0 BHRNickel-binding periplasmic protein / 0.659
3uwq U5POrotidine 5'-phosphate decarboxylase / 0.658
4b1v ATPActin, alpha skeletal muscle / 0.658
4brg GNPEctonucleoside triphosphate diphosphohydrolase I / 0.658
4hut ATPCob(I)yrinic acid a,c-diamide adenosyltransferase 2.5.1.17 0.657
1kqd FMNOxygen-insensitive NAD(P)H nitroreductase / 0.655
4bzb DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.654
4cid ANPEH domain-containing protein 2 / 0.654
4tl7 ATPCircadian clock protein kinase KaiC 2.7.11.1 0.654
1g4p FQPThiamine-phosphate synthase / 0.653
1dej ATPMajor actin / 0.652
4hl2 ZZ7Metallo-beta-lactamase type 2 / 0.652
1ndc TYDNucleoside diphosphate kinase, cytosolic 2.7.4.6 0.651
3i5x ANPATP-dependent RNA helicase MSS116, mitochondrial 3.6.4.13 0.651
3m0e ATPTranscriptional regulator (NtrC family) / 0.650
4qfy DGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD1 3.1.5 0.650