9MHV | pdb_00009mhv

Monkey TLR7 ectodomain with small molecule agonist 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.244 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure-Based Design of Novel TLR7/8 Agonist Payloads Enabling an Immunomodulatory Conjugate Approach.

Poudel, Y.B.Lo, J.C.Norris, D.J.Cox, M.He, L.Johnson, W.L.A M Subbaiah, M.Mondal, S.Thangavel, S.Subramani, L.Reddy, M.Jain, S.Weiss, D.R.Sivaprakasam, P.Critton, D.Mulligan, D.Xie, C.Dhar, P.Li, Y.Sega, E.Yamazoe, S.Gavai, A.V.Mathur, A.Zapf, C.W.Chekler, E.P.

(2025) ACS Med Chem Lett 16: 80-88

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00463
  • Primary Citation of Related Structures:  
    9MHV, 9MHW, 9MHX, 9MHY

  • PubMed Abstract: 

    Dual activation of the TLR7 and TLR8 pathways leads to the production of type I interferon and proinflammatory cytokines, resulting in efficient antigen presentation by dendritic cells to promote T-cell priming and antitumor immunity. We developed a novel series of TLR7/8 dual agonists with varying ratios of TLR7 and TLR8 activity for use as payloads for an antibody-drug conjugate approach. The agonist-induced production of several cytokines in human whole blood confirmed their functional activity. Structure-activity relationship studies guided by structure-based drug design are described.


  • Organizational Affiliation

    Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 7
A, B
817Macaca mulattaMutation(s): 4 
Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta)
Explore B3Y653 
Go to UniProtKB:  B3Y653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB3Y653
Glycosylation
Glycosylation Sites: 9
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BLT (Subject of Investigation/LOI)
Query on A1BLT

Download Ideal Coordinates CCD File 
O [auth A],
Y [auth B]
(3S)-3-[(2-amino-5-{[2-methoxy-5-({[(3S)-oxolan-3-yl]amino}methyl)phenyl]methyl}-5H-pyrimido[5,4-b]indol-4-yl)amino]hexan-1-ol
C29 H38 N6 O3
IIFCCEWBZBDLAS-VXKWHMMOSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
P [auth A],
Z [auth B]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth A],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.244 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.265α = 90
b = 139.436β = 90
c = 149.415γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
BUSTERrefinement

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: 2025-03-05
    Type: Initial release