9NTB | pdb_00009ntb

Crystal structure of human HDAC2 in complex with TNG260


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.161 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9NTB

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

TNG260 Is a Small-Molecule CoREST Inhibitor That Sensitizes STK11-Mutant Tumors to Anti-PD-1 Immunotherapy.

Ahronian, L.G.Sahu, S.Zhang, M.Patel, A.S.Geng, K.Bhattacharya, R.Falchook, G.S.Goldman, J.W.Spira, A.I.Punekar, S.R.Spigel, D.R.Wang, J.S.Skoulidis, F.Stephens, J.Meynardie, M.Powell, J.M.Lopez, A.Ranieri, M.Ploszaj, M.A.Tan, Y.J.Lee, Y.T.Yu, Y.Deng, J.Chen, T.McCarren, P.Tsai, A.Hussain, S.S.Doyon, B.Amemiya, K.Ermolieff, J.Shahagadkar, P.Das, N.M.Flynn, L.R.Shields, J.A.Danielczyk, L.McMillan, B.J.Mignault, A.Meier, S.R.Wu, H.J.Guerin, D.J.Whittington, D.A.Min, C.Sienczylo, I.Maxwell, J.P.DiBenedetto, H.J.Watanabe, H.Haines, B.B.Huang, A.Crystal, A.Andersen, J.N.Wu, X.Wong, K.K.

(2025) Cancer Res 85: 3966-3982

  • DOI: https://doi.org/10.1158/0008-5472.CAN-25-0998
  • Primary Citation Related Structures: 
    9NTB

  • PubMed Abstract: 

    Non-small cell lung cancer (NSCLC) patients with loss of the tumor suppressor gene STK11 are resistant to immune checkpoint therapies like anti-PD-1. Here, we conducted an in vivo CRISPR screen that identified HDAC1 as a target to reverse anti-PD-1 resistance driven by loss of STK11 and developed TNG260, a potent small-molecule inhibitor of the CoREST complex with selectivity exceeding previously generated inhibitors in this class in preclinical studies. Treatment with TNG260 led to increased expression of immunomodulatory genes in STK11-deficient cancer cells. When combined with anti-PD-1, TNG260 induced immune-mediated stasis and/or regression in STK11-deficient syngeneic tumor models and autochthonous NSCLC models. In the tumors of patients with STK11-deficient cancers on a clinical trial (NCT05887492), treatment with a combination of TNG260 and pembrolizumab increased intratumoral histone acetylation, PD-L1 tumor proportion scores, and T cell infiltration into the tumor microenvironment. This study illustrates a promising treatment strategy for addressing immune evasion in STK11-mutant NSCLC patients.


  • Organizational Affiliation
    • Tango Therapeutics (United States), Boston, MA, United States.

Macromolecule Content 

  • Total Structure Weight: 143 kDa 
  • Atom Count: 10,178 
  • Modeled Residue Count: 1,102 
  • Deposited Residue Count: 1,212 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone deacetylase 2
A, B, C
404Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98 (PDB Primary Data), 3.5.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens)
Explore Q92769 
Go to UniProtKB:  Q92769
PHAROS:  Q92769
GTEx:  ENSG00000196591 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92769
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1B1V
(Subject of Investigation/LOI)

Query on A1B1V



Download:Ideal Coordinates CCD File
D [auth A],
QA [auth C],
Y [auth B]
(R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide
C20 H18 F N3 O2 S
JPFMYSJUFUEHBI-HHHXNRCGSA-N
NHE

Query on NHE



Download:Ideal Coordinates CCD File
CA [auth B],
H [auth A]
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
OA [auth B],
PA [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
X [auth A],
ZA [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
DA [auth B]
IA [auth B]
LA [auth B]
MA [auth B]
NA [auth B]
DA [auth B],
IA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
S [auth A],
T [auth A],
U [auth A],
V [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
RA [auth C],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
I [auth A]
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
I [auth A],
J [auth A],
JA [auth B],
K [auth A],
KA [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
UA [auth C],
VA [auth C],
W [auth A],
WA [auth C],
XA [auth C],
YA [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth B]
F [auth A]
G [auth A]
SA [auth C]
AA [auth B],
BA [auth B],
F [auth A],
G [auth A],
SA [auth C],
TA [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.161 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.23α = 90
b = 97.31β = 90
c = 139.01γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Database references