5YB1

Structure and function of human serum albumin-metal agent complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Developing an Anticancer Copper(II) Multitarget Pro-Drug Based on the His146 Residue in the IB Subdomain of Modified Human Serum Albumin.

Wang, J.Gou, Y.Zhang, Z.Yu, P.Qi, J.Qin, Q.Sun, H.Wu, X.Liang, H.Yang, F.

(2018) Mol Pharm 15: 2180-2193

  • DOI: https://doi.org/10.1021/acs.molpharmaceut.8b00045
  • Primary Citation of Related Structures:  
    5YB1

  • PubMed Abstract: 

    Designing a multitarget anticancer drug with improved delivery and therapeutic efficiency in vivo presents a great challenge. Thus, we proposed to design an anticancer multitarget metal pro-drug derived from thiosemicarbazone based on the His146 residue in the IB subdomain of palmitic acid (PA)-modified human serum albumin (HSA-PA). The structure-activity relationship of six Cu(II) compounds with 6-methyl-2-formylpyridine- 4 N-substituted thiosemicarbazones were investigated, and then the multitarget capability of 4b was confirmed in cancer cell DNA and proteins. The structure of the HSA-PA-4b complex (HSA-PA-4b) revealed that 4b is bound to the IB subdomain of modified HSA, and that His146 replaces the nitrate ligand in 4b, coordinating with Cu 2+ , whereas PA is complexed with the IIA subdomain by its carboxyl forming hydrogen bonds with Lys199 and His242. In vivo data showed that 4b and the HSA-PA-4b complex inhibit lung tumor growth, and the targeting ability and therapeutic efficacy of the PA-modified HSA complex was stronger than 4b alone.


  • Organizational Affiliation

    State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541003 , China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serum albumin
A, B
581Homo sapiensMutation(s): 0 
Gene Names: ALBGIG20GIG42PRO0903PRO1708PRO2044PRO2619PRO2675UNQ696/PRO1341
UniProt & NIH Common Fund Data Resources
Find proteins for P02768 (Homo sapiens)
Explore P02768 
Go to UniProtKB:  P02768
GTEx:  ENSG00000163631 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8ZR (Subject of Investigation/LOI)
Query on 8ZR

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B]
~{N},~{N},12-trimethyl-3$l^{3}-thia-1$l^{4},5,6$l^{4}-triaza-2$l^{3}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),3,6,9,11-pentaen-4-amine
C10 H14 Cu N4 S
ZYDBCACRMLYTBZ-RVDQCCQOSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.492α = 104.67
b = 95.653β = 101.43
c = 96.642γ = 89.97
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2019-03-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Data collection
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description