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 26RW | pdb_000026rw

Crystal structure of the C65A/M94W/M145W/C167A mutant of Human lipocalin-type Prostaglandin D Synthase in complex with 10-O-(3-fluoropropyl)-substituted SN-38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 
    0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Development of a drug delivery vehicle protein exhibiting high binding affinity and low leakage of the anti-cancer drug SN-38.

Nakatsuji, M., Muroya, H., Okubo, R., Teraoka, Y., Yamada, M., Nishide, K., Yoshida, H., Furuta, K., Koyama, R., Kida, T., Doi, H., Nishimura, S., Inui, T.

(2026) Int J Biol Macromol 381: 154313-154313

  • DOI: https://doi.org/10.1016/j.ijbiomac.2026.154313
  • Primary Citation Related Structures: 
    26JH, 26RW

  • PubMed Abstract: 

    Drug leakage from delivery vehicles is a major limitation of drug delivery systems (DDSs) for cancer chemotherapy because premature release of loaded drugs reduces therapeutic efficacy and increases off-target toxicity. We previously developed a DDS for the poorly water-soluble anti-cancer drug SN-38 using lipocalin-type prostaglandin D synthase (L-PGDS). To suppress drug leakage, in this study we generated an L-PGDS mutant (M94W-M145W) with enhanced binding affinity for SN-38 by introducing amino acid substitutions into the ligand-binding cavity. Docking simulations identified residues involved in SN-38 recognition, and selected residues were replaced with tryptophan to strengthen ligand binding. The dissociation constant of the M94W-M145W mutant for SN-38 was 2.7 ± 0.4 μM, approximately 4-fold lower than that of L-PGDS. In addition, 1 mM M94W-M145W enhanced the solubility of SN-38 by approximately 3.3-fold compared with 1 mM L-PGDS. In vitro release assays showed that the SN-38/M94W-M145W complex released SN-38 more slowly than the SN-38/L-PGDS complex. We also determined the crystal structure of the 10-O-(3-fluoropropyl)-substituted SN-38 derivative/M94W-M145W complex. The overall structure of M94W-M145W retained the typical lipocalin fold, indicating that these substitutions do not alter the global protein architecture. Two SN-38 derivative molecules were accommodated within the cavity through hydrogen bonding and hydrophobic interactions, including π-π stacking interactions introduced by the substituted tryptophan residues. These findings demonstrate that simple amino acid substitutions in L-PGDS can optimize drug binding, improve solubility, and suppress drug release, thus providing a basis for affinity-driven design of protein-based DDSs.


  • Organizational Affiliation: 
    • Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8531, Japan; Department of Pathobiochemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan.

Macromolecule Content 

  • Total Structure Weight: 19.81 kDa 
  • Atom Count: 1,394 
  • Modeled Residue Count: 155 
  • Deposited Residue Count: 170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Prostaglandin-H2 D-isomerase170Homo sapiensMutation(s): 6 
Gene Names: PTGDS, PDS
EC: 5.3.99.2
UniProt & NIH Common Fund Data Resources
Find proteins for P41222 (Homo sapiens)
Explore P41222 
Go to UniProtKB:  P41222
PHAROS:  P41222
GTEx:  ENSG00000107317 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41222
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1MG3
(Subject of Investigation/LOI)

Query on A1MG3



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
(4S)-4,11-diethyl-9-(3-fluoropropoxy)-4-hydroxy-1H-pyrano[3',4':6,7]indolizino[1,2-b]quinoline-3,14(4H,12H)-dione
C25 H25 F N2 O5
DDCVJVRBDJWVHJ-VWLOTQADSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free:  0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.011α = 90
b = 56.407β = 90
c = 71.416γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17K19329
Japan Society for the Promotion of Science (JSPS)Japan25242046

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release