Structure of PDB 5jnl Chain A Binding Site BS01

Receptor Information
>5jnl Chain A (length=410) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAR
EFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDK
IVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAK
IIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQN
LTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVD
YNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKT
NLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIA
NNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKD
KATDIYNKHN
Ligand information
Ligand IDL54
InChIInChI=1S/C15H21F3NO5P/c1-19(21)14(20)9-12(10-25(22,23)24)4-2-3-11-5-7-13(8-6-11)15(16,17)18/h5-8,12,21H,2-4,9-10H2,1H3,(H2,22,23,24)/t12-/m1/s1
InChIKeyQJHOMBPUEUGKSC-GFCCVEGCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CN(C(=O)CC(CCCc1ccc(cc1)C(F)(F)F)CP(=O)(O)O)O
CACTVS 3.385CN(O)C(=O)C[CH](CCCc1ccc(cc1)C(F)(F)F)C[P](O)(O)=O
OpenEye OEToolkits 2.0.4CN(C(=O)C[C@@H](CCCc1ccc(cc1)C(F)(F)F)CP(=O)(O)O)O
CACTVS 3.385CN(O)C(=O)C[C@@H](CCCc1ccc(cc1)C(F)(F)F)C[P](O)(O)=O
ACDLabs 12.01O=C(CC(CP(O)(O)=O)CCCc1ccc(cc1)C(F)(F)F)N(O)C
FormulaC15 H21 F3 N O5 P
Name{(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-[4-(trifluoromethyl)phenyl]pentyl}phosphonic acid
ChEMBL
DrugBank
ZINCZINC000584905594
PDB chain5jnl Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jnl Targeting an Aromatic Hotspot in Plasmodium falciparum 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase with beta-Arylpropyl Analogues of Fosmidomycin.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		S232 S269 S270 W296 S306 N311 K312 H341 P358 D359 M360
Binding residue
(residue number reindexed from 1)		S156 S193 S194 W220 S230 N235 K236 H265 P282 D283 M284
Annotation score1
Binding affinityMOAD: ic50=0.27uM
PDBbind-CN: -logKd/Ki=6.57,IC50=0.27uM
Enzymatic activity
Enzyme Commision number 1.1.1.267: 1-deoxy-D-xylulose-5-phosphate reductoisomerase.
Gene Ontology
Molecular Function
GO:0030604 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
GO:0046872 metal ion binding
GO:0070402 NADPH binding
Biological Process
GO:0008299 isoprenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5jnl, PDBe:5jnl, PDBj:5jnl
PDBsum5jnl
PubMed27487410
UniProtQ8IKG4|DXR_PLAF7 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic (Gene Name=DXR)

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