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
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Ligand Structure Quality Assessment 


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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 

  • DOI: https://doi.org/10.1158/0008-5472.CAN-25-0998
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
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  • 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