2YC3

Inhibitors of the herbicidal target IspD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTICA228Arabidopsis thalianaMutation(s): 0 
Gene Names: ISPDMCTMECTMEPCTAt2g02500T8K22.20
EC: 2.7.7.60
UniProt
Find proteins for P69834 (Arabidopsis thaliana)
Explore P69834 
Go to UniProtKB:  P69834
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69834
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MW5
Query on MW5

Download Ideal Coordinates CCD File 
B [auth A]6-benzyl-5-chloro[1,2,4]triazolo[1,5-a]pyrimidin-7(3H)-one
C12 H9 Cl N4 O
MQEBPOLOTAZMKF-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MW5 Binding MOAD:  2YC3 IC50: 140 (nM) from 1 assay(s)
PDBBind:  2YC3 IC50: 140 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.6α = 90
b = 74.6β = 90
c = 220.5γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2011-03-11 
  • Released Date: 2011-08-24 
  • Deposition Author(s): Hoeffken, H.W.

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release