9J4P | pdb_00009j4p

Regulatory domain and kinase domain of ALPK1 protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9J4P

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of a selective alpha-kinase 1 inhibitor for the rare genetic disease ROSAH syndrome.

Fan, J.Liu, D.Ming, Z.Yan, C.Dang, H.Pan, Y.Wei, X.Zhao, Z.Wang, W.Zhang, S.Chen, L.Cai, S.Ke, J.Luo, Y.Rao, L.Chen, J.Chen, Z.Zhou, J.Chen, F.Duan, X.Ren, B.Li, T.R.Melvin, L.Yogaratnam, J.Mahajan, V.B.Song, H.Lichenstein, H.Xu, T.Xu, C.

(2025) Nat Commun 16: 8251-8251

  • DOI: https://doi.org/10.1038/s41467-025-63731-5
  • Primary Citation Related Structures: 
    9J4P

  • PubMed Abstract: 

    ROSAH (retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and headache) syndrome is a rare genetic disease caused by variants in alpha-kinase 1 (ALPK1) resulting in downstream pro-inflammatory signaling mediated by the TIFA/TRAF6/NF-κB pathway. Here, we report the design of an ALPK1 inhibitor, DF-003, with pharmacokinetic properties suitable for daily oral dosing. In biochemical assays, DF-003 potently inhibits human ALPK1 (IC 50  = 1.5 nM) and the ROSAH disease-causing mutant ALPK1[T237M] (IC 50  = 16 nM). When tested against a panel of 394 human kinases, DF-003 exhibits ≥860-fold selectivity over the closest kinase. In cell-based assays, DF-003 suppresses inflammatory cytokine signaling mediated both by wild-type ALPK1 and the disease-causing ALPK1[T237M] mutant. Using mice heterozygous for wild-type human ALPK1 and ALPK1 T237M established to model ROSAH syndrome that exhibit retinal microglial infiltration, astrocyte activation, and inflammatory cytokine upregulation in the retina, optic nerve, and cortex, we show that orally administered DF-003 is sufficient to inhibit these inflammatory phenotypes.


  • Organizational Affiliation
    • Shanghai Yao Yuan Biotechnology Ltd (Drug Farm), Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 82.38 kDa 
  • Atom Count: 5,697 
  • Modeled Residue Count: 682 
  • Deposited Residue Count: 721 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-protein kinase 1A [auth B]446Homo sapiensMutation(s): 0 
Gene Names: ALPK1KIAA1527LAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens)
Explore Q96QP1 
Go to UniProtKB:  Q96QP1
GTEx:  ENSG00000073331 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QP1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-protein kinase 1B [auth A]275Mus musculusMutation(s): 0 
Gene Names: Alpk1Kiaa1527
EC: 2.7.11.1
UniProt
Find proteins for Q9CXB8 (Mus musculus)
Explore Q9CXB8 
Go to UniProtKB:  Q9CXB8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CXB8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DY0
(Subject of Investigation/LOI)

Query on DY0



Download:Ideal Coordinates CCD File
C [auth B][[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2S,3S,4S,5S,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
C17 H27 N5 O16 P2
KMSFWBYFWSKGGR-FQBROAFUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.383α = 90
b = 93.383β = 90
c = 172.27γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
BUCCANEERmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-07-30 
  • Deposition Author(s): Xu, C., Xu, T.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references