Structure of PDB 3ryw Chain A Binding Site BS01

Receptor Information
>3ryw Chain A (length=358) Species: 126793 (Plasmodium vivax Sal-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LAFFRNMYDKYRDAFLSHLNEYSLEEEIKEHISKYYKLLFDYNCLGGKNN
RGILVILIYEYVKNRINSSEWEKAACLAWCIEILQAAFLVADDIMDKGEM
RRNKYCWYLLKDVETKNAVNDVLLLYNSIYKLIEIYLRNESCYVDVIATF
RDATLKTIIGQHLDTNIFSDKYSEIDVNNINVPEQPVIDINMINFGVYKN
IVIHKTAYYSFFLPIVCGMLLAGIAVDNLIYKKIEDISMLMGEYFQIHDD
YLDIFGDSTKTGKVGSDIQNNKLTWPLIKTFELCSEPDKIKIVKNYGKNN
LACVKVIDSLYEQYKIRKHYESYEKAQKAKILSAINELHHEGIEYVLKYL
LEILFTGV
Ligand information
Ligand IDK9H
InChIInChI=1S/C17H31NO7P2/c1-2-3-4-5-6-7-8-9-10-25-16-11-15(13-18-14-16)12-17(26(19,20)21)27(22,23)24/h11,13-14,17H,2-10,12H2,1H3,(H2,19,20,21)(H2,22,23,24)
InChIKeyCXNUSEYMNGPVLV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CCCCCCCCCCOc1cncc(CC([P](O)(O)=O)[P](O)(O)=O)c1
ACDLabs 12.01O=P(O)(O)C(P(=O)(O)O)Cc1cncc(OCCCCCCCCCC)c1
OpenEye OEToolkits 1.7.2CCCCCCCCCCOc1cc(cnc1)CC(P(=O)(O)O)P(=O)(O)O
FormulaC17 H31 N O7 P2
Name{2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)
ChEMBLCHEMBL492471
DrugBank
ZINCZINC000049878385
PDB chain3ryw Chain A Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3ryw Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
Resolution2.9 Å
Binding residue
(original residue number in PDB)		F122 A125 D126 R135 Q195 K243 D287 K301
Binding residue
(residue number reindexed from 1)		F88 A91 D92 R101 Q161 K205 D249 K263
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.24,Ki=570nM
Enzymatic activity
Catalytic site (original residue number in PDB) K81 A121 D126 D130 R135 D198 K243 F283 D287 D288
Catalytic site (residue number reindexed from 1) K48 A87 D92 D96 R101 D164 K205 F245 D249 D250
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004161 dimethylallyltranstransferase activity
GO:0004337 geranyltranstransferase activity
GO:0004659 prenyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0045337 farnesyl diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0016020 membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ryw, PDBe:3ryw, PDBj:3ryw
PDBsum3ryw
PubMed22392982
UniProtA5K4U6

[Back to BioLiP]