Structure of PDB 5mrp Chain A Binding Site BS01

Receptor Information
>5mrp Chain A (length=209) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKSVSVILLAGPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRD
IFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLV
NTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLWEMQTPQVI
KPELLKKGFELVKSEGLAVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDD
LLLAERILS
Ligand information
Ligand ID6BC
InChIInChI=1S/C14H9ClN4O/c15-12-11(6-9-4-2-1-3-5-9)14(20)19-13(18-12)10(7-16)8-17-19/h1-5,8,20H,6H2
InChIKeyHOHNWEMSRSQMGQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1c1ccc(cc1)Cc2c(nc3c(cnn3c2O)C#N)Cl
CACTVS 3.352Oc1n2ncc(C#N)c2nc(Cl)c1Cc3ccccc3
FormulaC14 H9 Cl N4 O
Name5-chloro-7-hydroxy-6-(phenylmethyl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile
ChEMBLCHEMBL2289489
DrugBank
ZINCZINC000095920851
PDB chain5mrp Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5mrp Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R157 Q158 I177 A203 Q238 V239 D262 V263 I265 V266 V273
Binding residue
(residue number reindexed from 1)		R72 Q73 I92 A118 Q148 V149 D172 V173 I175 V176 V183
Annotation score1
Binding affinityMOAD: ic50=3uM
PDBbind-CN: -logKd/Ki=5.52,Kd=3.0uM
BindingDB: IC50=35nM
Enzymatic activity
Enzyme Commision number 2.7.7.60: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0050518 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
GO:0070567 cytidylyltransferase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5mrp, PDBe:5mrp, PDBj:5mrp
PDBsum5mrp
PubMed28686408
UniProtP69834|ISPD_ARATH 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic (Gene Name=ISPD)

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