6O5Y

Structure of Human Cytochrome P450 1A1 with 5-amino-N-(5-((4R,5R)-4-amino-5-fluoroazepan-1-yl)-1-methyl-1H-pyrazol-4-yl)-2-(2,6-difluorophenyl)thiazole-4-carboxamide)

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-03-04 Released: 2019-12-04 
  • Deposition Author(s): Bart, A.G., Scott, E.E.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Human Cytochrome P450 1A1 Adapts Active Site for Atypical Nonplanar Substrate.

Bart, A.G.Takahashi, R.H.Wang, X.Scott, E.E.

(2020) Drug Metab Dispos 48: 86-92

  • DOI: https://doi.org/10.1124/dmd.119.089607
  • Primary Citation of Related Structures:  
    6O5Y

  • PubMed Abstract: 

    The human cytochrome P450 1A1 (CYP1A1) is well known for chemical activation of procarcinogens and often has a substrate scope of small and highly planar compounds. Substrates deviating from these characteristics are certainly known, but how these larger and nonplanar substrates are accommodated and oriented within the CYP1A1 active site is not understood. Herein a new X-ray structure of CYP1A1 bound to the pan-Pim kinase inhibitor GDC-0339 reveals how the CYP1A1 active site cavity is reconfigured to bind larger and nonplanar compounds. The shape and size of the cavity are controlled by structural elements in the active site roof, with major changes in the conformation of the F helix break and relocation of Phe224 from the active site to the protein surface. This altered CYP1A1 active site architecture is consistent with the proposed mechanism for CYP1A1 generation of an unusual aminoazepane-rearranged metabolite for this substrate. SIGNIFICANCE STATEMENT: Cytochrome P450 1A1 metabolizes drugs, procarcinogens, and toxins and although previous structures have revealed how its stereotypical planar, aromatic compounds are accommodated in the CYP1A1 active site, this is not the case for flexible and nonplanar compounds. The current work determines the X-ray structure of CYP1A1 with such a flexible, nonplanar Pim kinase inhibitor, revealing significant modification of the CYP1A1 roof that accommodate this preclinical candidate and support an unusual intramolecular rearrangement reaction.


  • Organizational Affiliation

    Program in Biophysics (A.G.B., E.E.S.) and Departments of Medicinal Chemistry and Pharmacology (E.E.S.), University of Michigan, Ann Arbor, Michigan; and Department of Drug Metabolism and Pharmacokinetics (R.H.T.) and Department of Discovery Chemistry (X.W.), Genentech Inc., South San Francisco, California.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450 1A1
A, B, C, D
491Homo sapiensMutation(s): 0 
Gene Names: CYP1A1
EC: 1.14.14.1 (PDB Primary Data), 4.2.1.152 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04798 (Homo sapiens)
Explore P04798 
Go to UniProtKB:  P04798
PHAROS:  P04798
GTEx:  ENSG00000140465 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04798
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
J [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KUV
Query on KUV

Download Ideal Coordinates CCD File 
F [auth A]5-amino-N-{5-[(4R,5R)-4-amino-5-fluoroazepan-1-yl]-1-methyl-1H-pyrazol-4-yl}-2-(2,6-difluorophenyl)-1,3-thiazole-4-carboxamide
C20 H22 F3 N7 O S
NHXVGMQFCYBLTL-ZWNOBZJWSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
H [auth B]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.147α = 90
b = 195.897β = 90
c = 236.976γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM076343

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description