2YC5

Inhibitors of the herbicidal target IspD

PDB DOI: https://doi.org/10.2210/pdb2YC5/pdb

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.150
R-Value Observed: 0.152

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

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

Organizational Affiliation

BASF SE, Boschstrasse 14, 67056 Ludwigshafen, Germany. matthias.witschel@basf.com

Macromolecule Content

Total Structure Weight: 26.47 kDa
Atom Count: 1,969
Modelled Residue Count: 217
Deposited Residue Count: 228
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC	A	228	Arabidopsis thaliana	Mutation(s): 0 EC: 2.7.7.60
UniProt
Find proteins for P69834 (Arabidopsis thaliana) Explore P69834 Go to UniProtKB: P69834
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P69834
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6BC Query on 6BC Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	5-chloro-7-hydroxy-6-(phenylmethyl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile C₁₄ H₉ Cl N₄ O HOHNWEMSRSQMGQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A]	F [auth A], J [auth A], M [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain M [auth A] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain M [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], G [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A]	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
6BC	PDBBind: 2YC5	IC50: 35 (nM) from 1 assay(s)
	Binding MOAD: 2YC5	IC50: 35 (nM) from 1 assay(s)
	BindingDB: 2YC5	IC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.189
R-Value Work: 0.150
R-Value Observed: 0.152
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.9	α = 90
b = 74.9	β = 90
c = 220.06	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

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
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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Help and Resources

2YC5

Inhibitors of the herbicidal target IspD

Inhibitors of the Herbicidal Target Ispd: Allosteric Site Binding.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)