8FDA

Human Cytochrome P450 17A1 in complex with steroidal isonitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Selective steroidogenic cytochrome P450 haem iron ligation by steroid-derived isonitriles.

Richard, A.M.Wong, N.R.Harris, K.Sundar, R.Scott, E.E.Pochapsky, T.C.

(2023) Commun Chem 6: 183-183

  • DOI: https://doi.org/10.1038/s42004-023-00994-3
  • Primary Citation of Related Structures:  
    8FDA

  • PubMed Abstract: 

    Alkyl isonitriles, R-NC, have previously been shown to ligate the heme (haem) iron of cytochromes P450 in both accessible oxidation states (ferrous, Fe 2+ , and ferric, Fe 3+ ). Herein, the preparation of four steroid-derived isonitriles and their interactions with several P450s, including the steroidogenic CYP17A1 and CYP106A2, as well as the more promiscuous drug metabolizers CYP3A4 and CYP2D6, is described. It was found that successful ligation of the heme iron by the isonitrile functionality for a given P450 depends on both the position and stereochemistry of the isonitrile on the steroid skeleton. Spectral studies indicate that isonitrile ligation of the ferric heme is stable upon reduction to the ferrous form, with reoxidation resulting in the original complex. A crystallographic structure of CYP17A1 with an isonitrile derived from pregnanalone further confirmed the interaction and identified the absolute stereochemistry of the bound species.


  • Organizational Affiliation

    Chemical Biology Program, University of Michigan, Ann Arbor, 48109, MI, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid 17-alpha-hydroxylase/17,20 lyase
A, B, C, D
494Homo sapiensMutation(s): 0 
Gene Names: CYP17A1CYP17S17AH
EC: 1.14.14.19 (PDB Primary Data), 1.14.14.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P05093 (Homo sapiens)
Explore P05093 
Go to UniProtKB:  P05093
PHAROS:  P05093
GTEx:  ENSG00000148795 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05093
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 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],
L [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XPK (Subject of Investigation/LOI)
Query on XPK

Download Ideal Coordinates CCD File 
F [auth A]
H [auth B]
J [auth C]
K [auth C]
M [auth D]
F [auth A],
H [auth B],
J [auth C],
K [auth C],
M [auth D],
N [auth D]
[(1~{R})-1-[(3~{S},5~{S},8~{R},9~{S},10~{S},13~{S},17~{R})-3-methanoyloxy-10,13-dimethyl-1,2,3,4,5,6,7,8,9,11,12,13,14,15,16,17-hexadecahydrocyclopenta[a]phenanthren-17-yl]ethyl]-methylidyne-azanium
C23 H35 N O2
YWSGHBLCVWYPMV-GNHYYDODSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.13α = 90
b = 152.275β = 90
c = 171.587γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
SCALAdata 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 StatesR01 GM130997

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references