7GT0

PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOMB000275a

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2024-01-03 Released: 2024-01-24 
  • Deposition Author(s): Mehlman, T., Ginn, H.M., Keedy, D.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Helmholtz Association

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 


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Literature

An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data.

Mehlman, T.S.Ginn, H.M.Keedy, D.A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.01.05.574428
  • Primary Citation of Related Structures:  
    7GS7, 7GS8, 7GS9, 7GSA, 7GSB, 7GSC, 7GSD, 7GSE, 7GSF, 7GSG, 7GSH, 7GSI, 7GSJ, 7GSK, 7GSL, 7GSM, 7GSN, 7GSO, 7GSQ, 7GSR, 7GST, 7GSU, 7GSV, 7GSW, 7GSX, 7GSY, 7GSZ, 7GT0, 7GT1, 7GT2, 7GT3, 7GT4, 7GT5, 7GT6, 7GT7, 7GT8, 7GT9, 7GTA, 7GTB, 7GTC, 7GTD, 7GTE, 7GTF, 7GTG, 7GTH, 7GTI, 7GTJ, 7GTK, 7GTL, 7GTM

  • PubMed Abstract: 

    The recent advent of crystallographic small-molecule fragment screening presents the opportunity to obtain unprecedented numbers of ligand-bound protein crystal structures from a single high-throughput experiment, mapping ligandability across protein surfaces and identifying useful chemical footholds for structure-based drug design. However, due to the low binding affinities of most fragments, detecting bound fragments from crystallographic datasets has been a challenge. Here we report a trove of 65 new fragment hits across 59 new liganded crystal structures for PTP1B, an "undruggable" therapeutic target enzyme for diabetes and cancer. These structures were obtained from computational analysis of data from a large crystallographic screen, demonstrating the power of this approach to elucidate many (~50% more) "hidden" ligand-bound states of proteins. Our new structures include a fragment hit found in a novel binding site in PTP1B with a unique location relative to the active site, one that validates another new binding site recently identified by simulations, one that links adjacent allosteric sites, and, perhaps most strikingly, a fragment that induces long-range allosteric protein conformational responses via a previously unreported intramolecular conduit. Altogether, our research highlights the utility of computational analysis of crystallographic data, makes publicly available dozens of new ligand-bound structures of a high-value drug target, and identifies novel aspects of ligandability and allostery in PTP1B.


  • Organizational Affiliation

    Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 1321Homo sapiensMutation(s): 2 
Gene Names: PTPN1PTP1B
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens)
Explore P18031 
Go to UniProtKB:  P18031
PHAROS:  P18031
GTEx:  ENSG00000196396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18031
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ABG (Subject of Investigation/LOI)
Query on A1ABG

Download Ideal Coordinates CCD File 
C [auth A]N-benzyl-N'-methyl-N-[(pyridin-3-yl)methyl]thiourea
C15 H17 N3 S
DSMRJWBOXYJVMG-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.715α = 90
b = 89.715β = 90
c = 106.496γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM133769
Helmholtz AssociationGermanyVH-NG-19-02

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references