9PVF | pdb_00009pvf

KRAS complex with UM0152533 compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9PVF

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Targeting the H/KRAS alpha 4-beta 6-alpha 5 Allosteric Lobe with Macrocyclic Peptides.

Tran, K.Lavoie, H.Wahhab, A.Garrido, D.Jo, C.H.Poupart, M.A.Arya, T.Beautrait, A.Killoran, R.Dicaire-Leduc, C.Bonneil, E.Osborne, M.Schuetz, D.A.Shaikh, F.Thibault, P.Smith, M.J.Marinier, A.Therrien, M.

(2026) ACS Med Chem Lett 17: 1154-1162

  • DOI: https://doi.org/10.1021/acsmedchemlett.6c00078
  • Primary Citation Related Structures: 
    9PU1, 9PU3, 9PU8, 9PUL, 9PUN, 9PUQ, 9PUT, 9PUZ, 9PVE, 9PVF

  • PubMed Abstract: 

    Despite therapeutic advances against RAS mutations in cancer, acquired resistance frequently arises. Several secondary mutations at the binding sites effectively confer resistance to both Switch-II inhibitors and cyclophilin-A molecular glues. This underscores the need for RAS inhibitors that engage alternative binding pockets or operate through novel mechanisms. Here, we report the design of 10-mer macrocyclic peptides that mimic the FG-loop of the NS1 monobody, which targets the allosteric α4-α5-β6 surface of H/KRAS to disrupt RAS clustering and downstream signaling. These noncovalent inhibitors bind to H/KRAS with equivalent potencies, regardless of nucleotide state or the presence of oncogenic mutations (G12D, G12V, G13R, Q61K), and their binding site was confirmed by NMR and X-ray crystallography. Furthermore, covalent analogs targeting Cys118 were shown to label RAS in vitro and in complete cell lysates. Finally, we demonstrated that the key pharmacophores are connectable, providing a foundation for the development of smaller allosteric H/KRAS inhibitors.


  • Organizational Affiliation
    • Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada.

Macromolecule Content 

  • Total Structure Weight: 125.59 kDa 
  • Atom Count: 9,414 
  • Modeled Residue Count: 1,060 
  • Deposited Residue Count: 1,062 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTPase KRas
A, B, C, D, E
A, B, C, D, E, F
166Homo sapiensMutation(s): 0 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
UM015253311synthetic constructMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
EA [auth F]
M [auth A]
P [auth B]
U [auth C]
V [auth D]
EA [auth F],
M [auth A],
P [auth B],
U [auth C],
V [auth D],
Y [auth E]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
AA [auth E]
BA [auth F]
CA [auth F]
DA [auth F]
N [auth A]
AA [auth E],
BA [auth F],
CA [auth F],
DA [auth F],
N [auth A],
O [auth A],
Q [auth B],
R [auth B],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
A1CK7
Query on A1CK7
G [auth I]
H [auth J]
I [auth K]
J [auth L]
K [auth M]
G [auth I],
H [auth J],
I [auth K],
J [auth L],
K [auth M],
L [auth N]
PEPTIDE-LIKEC5 H11 N O2

--

DPR
Query on DPR
G [auth I]
H [auth J]
I [auth K]
J [auth L]
K [auth M]
G [auth I],
H [auth J],
I [auth K],
J [auth L],
K [auth M],
L [auth N]
D-PEPTIDE LINKINGC5 H9 N O2

--

DTR
Query on DTR
G [auth I]
H [auth J]
I [auth K]
J [auth L]
K [auth M]
G [auth I],
H [auth J],
I [auth K],
J [auth L],
K [auth M],
L [auth N]
D-PEPTIDE LINKINGC11 H12 N2 O2

--

IIL
Query on IIL
G [auth I]
H [auth J]
I [auth K]
J [auth L]
K [auth M]
G [auth I],
H [auth J],
I [auth K],
J [auth L],
K [auth M],
L [auth N]
L-PEPTIDE LINKINGC6 H13 N O2ILE

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.64α = 90
b = 99.64β = 90
c = 140.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-22
    Type: Initial release
  • Version 1.1: 2026-06-03
    Changes: Database references