9R7A | pdb_00009r7a

Imine Reductase IR91 from Kribbella flavida with NADP+ and 5-methoxy-(S)-2-(N-methylamino)tetralin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.235 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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Literature

Structures of "Tyrosine-IRED" IR91 from Kribbella flavida in Complex with a Reductive Amination Substrate and Product.

Srinivas, K.Gilio, A.K.Sharma, M.Green, L.Ascham, A.Domenech, J.Pogranyi, B.Li, J.France, S.P.Lewis, R.D.Unsworth, W.P.Grogan, G.

(2025) Chembiochem 26: e202500450-e202500450

  • DOI: https://doi.org/10.1002/cbic.202500450
  • Primary Citation of Related Structures:  
    9R76, 9R79, 9R7A

  • PubMed Abstract: 

    Imine reductases with an (S)-preference for the reduction of the model substrate 2-methyl pyrroline typically contain tyrosine in the active site (Y-IREDs) instead of the aspartate present within (R)-selective enzymes (D-IREDs). As with D-IREDs, a subset of Y-IREDs is capable of enabling reductive amination reactions between some ketone and amine partners to give optically active amines with high optical purity. However, structures of Y-IREDs in complex with the substrates and products of the reductive amination have not been forthcoming. Herein, structures of the Y-IRED IR91 from Kribbella flavida in complex with 5-methoxy-2-tetralone, a synthetic precursor to the anti-Parkinson's treatment rotigotine, and also its reductive amination product with methylamine, 5-methoxy-(S)-2-(N-methylamino)-tetralin, are presented. The structures, in combination with mutation and kinetic studies, support a role for tryptophan residue W258 in the activity of the enzyme, possibly in binding of the ketone prior to reaction with methylamine.


  • Organizational Affiliation
    • Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphogluconate dehydrogenase NAD-binding protein
A, B
296Kribbella flavidaMutation(s): 0 
Gene Names: Kfla_3935
UniProt
Find proteins for D2PR38 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399))
Explore D2PR38 
Go to UniProtKB:  D2PR38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD2PR38
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
A1JDG (Subject of Investigation/LOI)
Query on A1JDG

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(2~{S})-5-methoxy-~{N}-methyl-1,2,3,4-tetrahydronaphthalen-2-amine
C12 H17 N O
VBJJOYHRWXQNFV-JTQLQIEISA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.235 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.8α = 90
b = 109.51β = 93.93
c = 53.75γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

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: 2025-11-05
    Type: Initial release