6L4K | pdb_00006l4k

Human serum albumin-Palmitic acid-Cu compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.290 (Depositor), 0.283 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Novel Brain-Tumor-Inhibiting Copper(II) Compound Based on a Human Serum Albumin (HSA)-Cell Penetrating Peptide Conjugate.

Zhang, Z.Yu, P.Gou, Y.Zhang, J.Li, S.Cai, M.Sun, H.Yang, F.Liang, H.

(2019) J Med Chem 62: 10630-10644

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00939
  • Primary Citation Related Structures: 
    6L4K

  • PubMed Abstract: 

    It is a great challenge to design drugs that penetrate the blood-brain barrier to inhibit brain tumor growth by acting against multiple targets and also improve their delivery efficacy and targeting ability to cancer cells. To overcome the above problems, we designed a multitarget metal agent for treating brain tumors based on an human serum albumin (HSA)-cell penetrating peptide conjugate. Thus, we rationally screened copper (Cu) and 2-acetyl-3-ethylpyrazine thiosemicarbazones to synthesize six compounds, and we investigated their structure-activity relationships and confirmed multiple mechanisms for brain glioma cells. The HSA- 6b complex structure indicated that 6b binds to the IIA subdomain of HSA and His242 replaces the Br ligand in 6b in coordination with Cu 2+ . In vivo data suggested that both 6b and the HSA- 6b -peptide conjugate penetrate the blood-brain barrier and inhibit brain tumor growth with few side effects. Furthermore, the HSA-peptide conjugate also improved the delivery efficacy and targeting ability of 6b in vivo.


  • Organizational Affiliation
    • State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources , Guangxi Normal University , Guilin , Guangxi 541004 , P. R. China.

Macromolecule Content 

  • Total Structure Weight: 135.9 kDa 
  • Atom Count: 9,106 
  • Modeled Residue Count: 1,162 
  • Deposited Residue Count: 1,162 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serum albuminA,
B [auth I]
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
PHAROS:  P02768
GTEx:  ENSG00000163631 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02768
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E5O
(Subject of Investigation/LOI)

Query on E5O



Download:Ideal Coordinates CCD File
I [auth A]2-bromanyl-9-ethyl-~{N},~{N},7-trimethyl-3-thia-1$l^{4},5,6$l^{4},10-tetraza-2$l^{4}-cupratricyclo[6.4.0.0^{2,6}]dodeca-1(8),4,6,9,11-pentaen-4-amine
C11 H16 Br Cu N5 S
NRJWSXGYYTZDRJ-JPMXUBAOSA-L
PLM

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],
J [auth I],
K [auth I],
L [auth I],
M [auth I],
N [auth I],
O [auth I]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.290 (Depositor), 0.283 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.356α = 74.89
b = 93.523β = 89.68
c = 96.359γ = 80.04
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-10-21 
  • Deposition Author(s): Zhang, Z.L.

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-09-25
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Structure summary