9GJS | pdb_00009gjs

ERAP1 in complex with 1-[2-(6-bromo-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)acetamido]-4,4-difluorocyclohexane-1-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.203 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

Optimization of Potent and Selective Cyclohexyl Acid ERAP1 Inhibitors Using Structure- and Property-Based Drug Design.

Hryczanek, R.P.Hackett, A.S.Rowland, P.Chung, C.W.Convery, M.A.Holmes, D.S.Hutchinson, J.P.Kitchen, S.Korczynska, J.Law, R.P.Lea, J.D.Liddle, J.Lonsdale, R.Neu, M.Nickels, L.Phillipou, A.Rowedder, J.E.Schneck, J.L.Scott-Stevens, P.Sheehan, H.Tayler, C.L.Temponeras, I.Tinworth, C.P.Walker, A.L.Wojno-Picon, J.Young, R.J.Lindsay, D.M.Stratikos, E.

(2024) ACS Med Chem Lett 15: 2107-2114

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00401
  • Primary Citation of Related Structures:  
    9GJN, 9GJS, 9GK6, 9GKE

  • PubMed Abstract: 

    Endoplasmic reticulum aminopeptidase 1 (ERAP1) cleaves the N -terminal amino acids of peptides, which can then bind onto major histocompatibility class I (MHC-I) molecules for presentation onto the cell surface, driving the activation of adaptive immune responses. In cancer, overtrimming of mature antigenic peptides can reduce cytotoxic T-cell responses, and ERAP1 can generate self-antigenic peptides which contribute to autoimmune cellular responses. Therefore, modulation of ERAP1 activity has potential therapeutic indications for cancer immunotherapy and in autoimmune disease. Herein we describe the hit-to-lead optimization of a series of cyclohexyl acid ERAP1 inhibitors, found by X-ray crystallography to bind at an allosteric regulatory site. Structure-based drug design enabled a >1,000-fold increase in ERAP1 enzymatic and cellular activity, resulting in potent and selective tool molecules. For lead compound 7 , rat pharmacokinetic properties showed moderate unbound clearance and oral bioavailability, thus highlighting the promise of the series for further optimization.


  • Organizational Affiliation

    GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoplasmic reticulum aminopeptidase 1922Homo sapiensMutation(s): 0 
Gene Names: ERAP1APPILSARTS1KIAA0525UNQ584/PRO1154
EC: 3.4.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZ08 (Homo sapiens)
Explore Q9NZ08 
Go to UniProtKB:  Q9NZ08
PHAROS:  Q9NZ08
GTEx:  ENSG00000164307 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZ08
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IMJ (Subject of Investigation/LOI)
Query on A1IMJ

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
1-[2-(6-bromanyl-3-oxidanylidene-1,4-benzoxazin-4-yl)ethanoylamino]-4,4-bis(fluoranyl)cyclohexane-1-carboxylic acid
C17 H17 Br F2 N2 O5
YSUUSESRJZNQHW-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.203 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.693α = 90
b = 140.804β = 90
c = 57.71γ = 90
Software Package:
Software NamePurpose
autoPROCdata reduction
XDSdata reduction
autoPROCdata scaling
Aimlessdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted A1IMJClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-22 
  • Deposition Author(s): Rowland, P.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release