9VW7 | pdb_00009vw7

NAD(P)-dependent oxidoreductase from Kutzneria albida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.168 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Engineering an Imine Reductase for Enantioselective Synthesis of Atropisomeric Amides.

Yao, Z.Meng, R.Zhou, Z.Yu, L.Wu, Z.Tang, L.Qiao, T.Li, K.Huang, L.Song, D.Fu, H.

(2025) J Am Chem Soc 147: 40616-40625

  • DOI: https://doi.org/10.1021/jacs.5c12724
  • Primary Citation of Related Structures:  
    9VVS, 9VW7

  • PubMed Abstract: 

    Atropisomeric amides possess unique axial chirality arising from the rotation-restricted C aryl -C amide bond and find broad application in bioactive molecules and asymmetric catalysis. However, catalytic asymmetric methods for their synthesis remain underdeveloped, with no biocatalytic approaches reported. Herein, we report the first efficient biocatalytic strategy for the atroposelective synthesis of atropisomeric amides via dynamic kinetic resolution using engineered imine reductases (IREDs). Structure-guided engineering of an IRED from Kutzneria albida provided a quadruple mutant (IRED-68-M4) capable of catalyzing the stereoconvergent synthesis of diverse napthamides and benzamides in high yields and excellent enantioselectivities (up to 98% yield, >99:1 er). Gram-scale synthesis of an axially chiral napthamide was also demonstrated. Moreover, protein X-ray crystallography and molecular modeling studies revealed the structural basis of the enhanced catalytic performance of the IRED-68-M4 variant.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrogenase
A, B
309Kutzneria albida DSM 43870Mutation(s): 0 
Gene Names: KALB_1124
UniProt
Find proteins for W5W0Y1 (Kutzneria albida DSM 43870)
Explore W5W0Y1 
Go to UniProtKB:  W5W0Y1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW5W0Y1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
PE8
Query on PE8

Download Ideal Coordinates CCD File 
E [auth B]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NA
Query on NA

Download Ideal Coordinates CCD File 
H [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.168 (DCC) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.395α = 90
b = 117.395β = 90
c = 99.569γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references
  • Version 1.2: 2025-11-19
    Changes: Database references