4LB9

X-ray study of human serum albumin complexed with etoposide

• PDB DOI:  https://doi.org/10.2210/pdb4LB9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2013-07-24 
• Deposition Author(s): Wang, Z., Ho, J.X., Ruble, J., Rose, J.P., Carter, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Structural studies of several clinically important oncology drugs in complex with human serum albumin.

Wang, Z.M., Ho, J.X., Ruble, J.R., Rose, J., Ruker, F., Ellenburg, M., Murphy, R., Click, J., Soistman, E., Wilkerson, L., Carter, D.C.

(2013) Biochim Biophys Acta 1830: 5356-5374

• PubMed: 23838380 
• DOI: https://doi.org/10.1016/j.bbagen.2013.06.032
• Primary Citation of Related Structures:  
  4L8U, 4L9K, 4L9Q, 4LA0, 4LB2, 4LB9


• PubMed Abstract: 
  

Serum albumin is a major pharmacokinetic effector of drugs. To gain further insight into albumin binding chemistry, the crystal structures of six oncology agents were determined in complex with human serum albumin at resolutions of 2.8 to 2.0Å: camptothecin, 9-amino-camptothecin, etoposide, teniposide, bicalutamide and idarubicin.

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Related Citations: 

• Crystallographic survey of albumin drug interaction and preliminary applications in cancer chemotherapy
  Carter, D.C.
  (2010) Burgers Medicinal Chemistry Drug Design And Development, 7th Edition --: 437

• Structure of Serum Albumin
  Carter, D.C., Ho, J.X.
  (1994) Adv Protein Chem 45: 153

• Preliminary crystallographic studies of four crystal forms of serum albumin.
  Carter, D.C., Chang, B., Ho, J.X., Keeling, K., Krishnasami, Z.
  (1994) Eur J Biochem 226: 1049

• Erratum. Atomic Structure and Chemistry of Human Serum Albumin
  Ho, X.M., Carter, D.C.
  (1993) Nature 364: 362

• Atomic structure and chemistry of human serum albumin.
  He, X.M., Carter, D.C.
  (1992) Nature 358: 209

• Structure of Human Serum Albumin
  Carter, D.C., Ho, X.M.
  (1990) Science 249: 302

• Three-dimensional structure of human serum albumin.
  Carter, D.C., He, X.M., Munson, S.H., Twigg, P.D., Gernert, K.M., Broom, M.B., Miller, T.Y.
  (1989) Science 244: 1195

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Organizational Affiliation: 

New Century Pharmaceuticals, Inc., 895 Martin Road, Suite C, Huntsville, AL 35824, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 68.07 kDa 
• Atom Count: 4,809 
• Modelled Residue Count: 583 
• Deposited Residue Count: 585 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERUM ALBUMIN	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EVP	F [auth A]	(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside C29 H32 O13 VJJPUSNTGOMMGY-MRVIYFEKSA-N
MYR	B [auth A], C [auth A], D [auth A], E [auth A]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.249 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.543	α = 90
b = 38.677	β = 104.56
c = 99.221	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MERLOT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Wang, Z., Ho, J.X., Ruble, J., Rose, J.P., Carter, D.C.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2014-02-19
  Changes: Other