9UPD | pdb_00009upd

Crystal structure of human serum albumin complex with nateglinide

• PDB DOI: https://doi.org/10.2210/pdb9UPD/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2025-04-28 Released: 2025-07-16 
• Deposition Author(s): Kawai, A., Nishi, K., Yamasaki, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Insights into Dual Binding Modes of Nateglinide to Human Serum Albumin

Kawai, A., Nishi, K., Tokuno, M., Otagiri, M., Yamasaki, K.

(2025) ACS Med Chem Lett 

• DOI: https://doi.org/10.1021/acsmedchemlett.5c00277

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 133.97 kDa 
• Atom Count: 8,471 
• Modeled Residue Count: 1,118 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A, B	585	Homo sapiens	Mutation(s): 0  Gene Names: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens) Explore P02768  Go to UniProtKB:  P02768
PHAROS:  P02768 GTEx:  ENSG00000163631

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1L9H (Subject of Investigation/LOI)	C [auth A], E [auth B]	(2R)-3-phenyl-2-[(4-propan-2-ylcyclohexyl)carbonylamino]propanoic acid C19 H27 N O3 OELFLUMRDSZNSF-BBWFWOEESA-N
PO4	D [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.287 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.45	α = 90
b = 180.8	β = 105.64
c = 60.29	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Kawai, A., Nishi, K., Yamasaki, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release