Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: gel filtration, homology

Macromolecule Content

• Total Structure Weight: 67.14 kDa 
• Atom Count: 4948 
• Modelled Residue Count: 580 
• Deposited Residue Count: 583 
• Unique protein chains: 1

6U4X

Crystal structure of Equine Serum Albumin complex with ibuprofen

• PDB DOI: 10.2210/pdb6U4X/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Equus caballus
• Mutation(s): Yes 


• Deposited: 2019-08-26 Released: 2019-09-04 
• Deposition Author(s): Czub, M.P., Handing, K.B., Venkataramany, B.S., Steen, E.H., Shabalin, I.G., Satchell, K.J., Joachimiak, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Albumin-Based Transport of Nonsteroidal Anti-Inflammatory Drugs in Mammalian Blood Plasma.

Czub, M.P., Handing, K.B., Venkataramany, B.S., Cooper, D.R., Shabalin, I.G., Minor, W.

(2020) J Med Chem 63: 6847-6862

• PubMed: 32469516 
• DOI: 10.1021/acs.jmedchem.0c00225
• Primary Citation of Related Structures:  
  5V0V, 6CI6, 6U4R, 6U4X, 6U5A


• PubMed Abstract: 
  

Every day, hundreds of millions of people worldwide take nonsteroidal anti-inflammatory drugs (NSAIDs), often in conjunction with multiple other medications. In the bloodstream, NSAIDs are mostly bound to serum albumin (SA). We report the crystal structures of equine serum albumin complexed with four NSAIDs (ibuprofen, ketoprofen, etodolac, and nabumetone) and the active metabolite of nabumetone (6-methoxy-2-naphthylacetic acid, 6-MNA). These compounds bind to seven drug-binding sites on SA. These sites are generally well-conserved between equine and human SAs, but ibuprofen binds to both SAs in two drug-binding sites, only one of which is common. We also compare the binding of ketoprofen by equine SA to binding of it by bovine and leporine SAs. Our comparative analysis of known SA complexes with FDA-approved drugs clearly shows that multiple medications compete for the same binding sites, indicating possibilities for undesirable physiological effects caused by drug-drug displacement or competition with common metabolites. We discuss the consequences of NSAID binding to SA in a broader scientific and medical context, particularly regarding achieving desired therapeutic effects based on an individual's drug regimen.

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Organizational Affiliation: 

Center for Structural Genomics of Infectious Diseases (CSGID), University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serum albumin	A	583	Equus caballus	Mutation(s): 1  Gene Names: ALB
UniProt
Find proteins for P35747 (Equus caballus) Explore P35747  Go to UniProtKB:  P35747

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IBP (Subject of Investigation/LOI)	L [auth A], M [auth A]	IBUPROFEN C13 H18 O2 HEFNNWSXXWATRW-JTQLQIEISA-N
SO4	N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	UNKNOWN ATOM OR ION X
UNL	B [auth A]	Unknown ligand

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.238 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 6₁
• Diffraction Data DOI: 10.18430/m36u4x Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.232	α = 90
b = 95.232	β = 90
c = 141.939	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data collection
Coot	model building
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-08-26 
• Released Date: 2019-09-04 
Deposition Author(s): Czub, M.P., Handing, K.B., Venkataramany, B.S., Steen, E.H., Shabalin, I.G., Satchell, K.J., Joachimiak, A., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)	United States	--

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2020-07-15
  Changes: Database references
• Version 1.3: 2020-07-22
  Changes: Database references