8QHE

Crystal structure IR-09


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Biocatalysis in Drug Design: Engineered Reductive Aminases (RedAms) Are Used to Access Chiral Building Blocks with Multiple Stereocenters.

Casamajo, A.R.Yu, Y.Schnepel, C.Morrill, C.Barker, R.Levy, C.W.Finnigan, J.Spelling, V.Westerlund, K.Petchey, M.Sheppard, R.J.Lewis, R.J.Falcioni, F.Hayes, M.A.Turner, N.J.

(2023) J Am Chem Soc 145: 22041-22046

  • DOI: https://doi.org/10.1021/jacs.3c07010
  • Primary Citation of Related Structures:  
    8QHE

  • PubMed Abstract: 

    Novel building blocks are in constant demand during the search for innovative bioactive small molecule therapeutics by enabling the construction of structure-activity-property-toxicology relationships. Complex chiral molecules containing multiple stereocenters are an important component in compound library expansion but can be difficult to access by traditional organic synthesis. Herein, we report a biocatalytic process to access a specific diastereomer of a chiral amine building block used in drug discovery. A reductive aminase (RedAm) was engineered following a structure-guided mutagenesis strategy to produce the desired isomer. The engineered RedAm (IR-09 W204R) was able to generate the ( S , S , S )-isomer 3 in 45% conversion and 95% ee from the racemic ketone 2 . Subsequent palladium-catalyzed deallylation of 3 yielded the target primary amine 4 in a 73% yield. This engineered biocatalyst was used at preparative scale and represents a potential starting point for further engineering and process development.


  • Organizational Affiliation

    Department of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase NADP-binding domain-containing protein305Aspergillus lentulusMutation(s): 0 
Gene Names: ALT_005006
UniProt
Find proteins for A0A0S7DXU4 (Aspergillus lentulus)
Explore A0A0S7DXU4 
Go to UniProtKB:  A0A0S7DXU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S7DXU4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
B [auth A]NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
VCU
Query on VCU

Download Ideal Coordinates CCD File 
C [auth A]~{N}-methylcyclohexanamine
C7 H15 N
XTUVJUMINZSXGF-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.255α = 90
b = 101.104β = 90
c = 36.388γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-10-11 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union742987
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomEP/S005226/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Database references