6TMQ

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures

• PDB DOI: https://doi.org/10.2210/pdb6TMQ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-12-05 Released: 2020-10-14 
• Deposition Author(s): Baker, L.M., Aimon, A., Murray, J.B., Surgenor, A.E., Matassova, N., Roughley, S.D., von Delft, F., Hubbard, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.234 
• R-Value Work: 0.176 

Literature

Rapid optimisation of fragments and hits to lead compounds from screening of crude reaction mixtures

Baker, L.M., Aimon, A., Murray, J.B., Surgenor, A.E., Matassova, N., Roughley, S.D., Collins, P.M., Krojer, T., von Delft, F., Hubbard, R.E.

(2020) Commun Chem 

• DOI: https://doi.org/10.1038/s42004-020-00367-0

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 45.49 kDa 
• Atom Count: 2,952 
• Modelled Residue Count: 340 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial	A [auth AAA]	394	Homo sapiens	Mutation(s): 0  Gene Names: PDK2, PDHK2 EC: 2.7.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15119 (Homo sapiens) Explore Q15119  Go to UniProtKB:  Q15119
PHAROS:  Q15119 GTEx:  ENSG00000005882

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NMW (Subject of Investigation/LOI)	C [auth AAA]	[2,4-bis(oxidanyl)phenyl]-[(1~{S})-6,7-dimethoxy-1-pyridin-3-yl-3,4-dihydro-1~{H}-isoquinolin-2-yl]methanone C23 H22 N2 O5 CLPZEFHDKKRVHY-JOCHJYFZSA-N
TF3	B [auth AAA]	N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE C20 H25 Cl N2 O2 DFXJYVQAAFOZDP-UHFFFAOYSA-N
DMS	D [auth AAA]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TF3	BindingDB:  6TMQ	IC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 0.234 
• R-Value Work: 0.176 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.368	α = 90
b = 110.368	β = 90
c = 83.863	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-10-14 
Deposition Author(s): Baker, L.M., Aimon, A., Murray, J.B., Surgenor, A.E., Matassova, N., Roughley, S.D., von Delft, F., Hubbard, R.E.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references, Derived calculations