2YCM

Inhibitors of herbicidal target IspD

• PDB DOI: https://doi.org/10.2210/pdb2YCM/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-03-16 Released: 2011-08-24 
• Deposition Author(s): Hoeffken, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Inhibitors of the Herbicidal Target Ispd: Allosteric Site Binding.

Witschel, M.C., Hoeffken, H.W., Seet, M., Parra, L., Mietzner, T., Thater, F., Niggeweg, R., Rohl, F., Illarionov, B., Rohdich, F., Kaiser, J., Fischer, M., Bacher, A., Diederich, F.

(2011) Angew Chem Int Ed Engl 50: 7931

• PubMed: 21766403 
• DOI: https://doi.org/10.1002/anie.201102281
• Primary Citation of Related Structures:  
  2YC3, 2YC5, 2YCM

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Organizational Affiliation: 

BASF SE, Boschstrasse 14, 67056 Ludwigshafen, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.03 kDa 
• Atom Count: 1,775 
• Modelled Residue Count: 213 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC	A	227	Arabidopsis thaliana	Mutation(s): 0  EC: 2.7.7.60
UniProt
Find proteins for P69834 (Arabidopsis thaliana) Explore P69834  Go to UniProtKB:  P69834

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
30A	G [auth A]	6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXYLIC ACID C14 H10 Cl N3 O3 AMDMCXLZDLJCSY-UHFFFAOYSA-N
CD	B [auth A], C [auth A], D [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N
CU	F [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
30A	PDBBind:  2YCM	IC50: 2.74e+5 (nM) from 1 assay(s)
	Binding MOAD:  2YCM	IC50: 2.74e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.233 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.06	α = 90
b = 75.06	β = 90
c = 220.82	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Hoeffken, H.W.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description