6WUW

Crystal structure of Human Serum Albumin complex with JMS-053


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Literature

Structure of the Complex of an Iminopyridinedione Protein Tyrosine Phosphatase 4A3 Phosphatase Inhibitor with Human Serum Albumin.

Czub, M.P.Boulton, A.M.Rastelli, E.J.Tasker, N.R.Maskrey, T.S.Blanco, I.K.McQueeney, K.E.Bushweller, J.H.Minor, W.Wipf, P.Sharlow, E.R.Lazo, J.S.

(2020) Mol Pharmacol 98: 648-657

  • DOI: 10.1124/molpharm.120.000131
  • Primary Citation of Related Structures:  
    6WUW

  • PubMed Abstract: 
  • Protein tyrosine phosphatase (PTP) 4A3 is frequently overexpressed in human solid tumors and hematologic malignancies and is associated with tumor cell invasion, metastasis, and a poor patient prognosis. Several potent, selective, and allosteric small molecule inhibitors of PTP4A3 were recently identified ...

    Protein tyrosine phosphatase (PTP) 4A3 is frequently overexpressed in human solid tumors and hematologic malignancies and is associated with tumor cell invasion, metastasis, and a poor patient prognosis. Several potent, selective, and allosteric small molecule inhibitors of PTP4A3 were recently identified. A lead compound in the series, JMS-053 (7-imino-2-phenylthieno[3,2- c ]pyridine-4,6(5 H ,7 H )-dione), has a long plasma half-life (∼ 24 hours) in mice, suggesting possible binding to serum components. We confirmed by isothermal titration calorimetry that JMS-053 binds to human serum albumin. A single JMS-053 binding site was identified by X-ray crystallography in human serum albumin at drug site 3, which is also known as subdomain IB. The binding of JMS-053 to human serum albumin, however, did not markedly alter the overall albumin structure. In the presence of serum albumin, the potency of JMS-053 as an in vitro inhibitor of PTP4A3 and human A2780 ovarian cancer cell growth was reduced. The reversible binding of JMS-053 to serum albumin may serve to increase JMS-053's plasma half-life and thus extend the delivery of the compound to tumors. SIGNIFICANCE STATEMENT: X-ray crystallography revealed that a potent, reversible, first-in-class small molecule inhibitor of the oncogenic phosphatase protein tyrosine phosphatase 4A3 binds to at least one site on human serum albumin, which is likely to extend the compound's plasma half-life and thus assist in drug delivery into tumors.


    Organizational Affiliation

    Departments of Molecular Physiology and Biological Physics (M.P.C., A.M.B., J.H.B., W.M.) and Pharmacology (K.E.M., E.R.S., J.S.L.) and Center for Structural Genomics of Infectious Diseases (CSGID) (M.P.C., W.M.), University of Virginia, Charlottesville, Virginia; Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania (E.J.R., N.R.T., T.S.M., P.W.); and KeViRx, Inc., Charlottesville, Virginia (I.K.B., E.R.S., J.S.L.) lazo@virginia.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serum albuminA, B585Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UAY (Subject of Investigation/LOI)
Query on UAY

Download Ideal Coordinates CCD File 
D [auth A], O [auth B]7-imino-2-phenylthieno[3,2-c]pyridine-4,6(5H,7H)-dione
C13 H8 N2 O2 S
CQHAROORCYWRRH-UVTDQMKNSA-N
 Ligand Interaction
MYR (Subject of Investigation/LOI)
Query on MYR

Download Ideal Coordinates CCD File 
C [auth A] , G [auth A] , K [auth A] , L [auth A] , N [auth B] , P [auth B] , Q [auth B] , U [auth B] , 
C [auth A], G [auth A], K [auth A], L [auth A], N [auth B], P [auth B], Q [auth B], U [auth B], V [auth B]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A], R [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
OCA
Query on OCA

Download Ideal Coordinates CCD File 
F [auth A]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], M [auth B], T [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

Download Ideal Coordinates CCD File 
H [auth A], S [auth B]Unknown ligand
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.443α = 74.63
b = 93.44β = 89.63
c = 94.908γ = 80.44
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 2.0: 2020-08-05
    Type: Coordinate replacement
    Reason: Atomic clashes
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary
  • Version 2.1: 2020-11-25
    Changes: Database references