6TMQ

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


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NMWClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


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 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrialA [auth AAA]394Homo sapiensMutation(s): 0 
Gene Names: PDK2PDHK2
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15119
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NMW (Subject of Investigation/LOI)
Query on NMW

Download Ideal Coordinates CCD File 
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
Query on TF3

Download Ideal Coordinates CCD File 
B [auth AAA]N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL)OXY]PHENYL} ACETAMIDE
C20 H25 Cl N2 O2
DFXJYVQAAFOZDP-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth AAA]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
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 = 110.368α = 90
b = 110.368β = 90
c = 83.863γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NMWClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

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