9Q8L | pdb_00009q8l

Crystal Structure of 21A08Ap1-Fab in Complex with Human PD-1 at 1.85 angstrom Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.216 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.188 (DCC) 

Starting Models: experimental
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Literature

ANV600 is a novel PD-1 targeted IL-2R beta gamma agonist that selectively expands tumor antigen-specific T cells and potentiates PD-1 checkpoint inhibitor therapy.

Murer, P.Petersen, L.Egli, N.Salazar, U.Neubert, P.Zurbach, A.Rau, A.Stocker, C.Reichenstein, D.Katopodis, A.Huber, C.

(2025) J Immunother Cancer 13

  • DOI: https://doi.org/10.1136/jitc-2025-011905
  • Primary Citation of Related Structures:  
    9Q8L

  • PubMed Abstract: 

    Combining interleukin-2 (IL-2) agonism with programmed cell death protein 1 (PD-1) checkpoint inhibition has shown synergistic potential in reinvigorating antitumor T cell responses. However, integrating these two mechanisms within a single molecule has been challenging due to competing requirements for PD-1 engagement and IL-2 receptor signaling. ANV600 is a novel bispecific antibody-cytokine fusion protein that targets a non-blocking epitope on PD-1, enabling cis -targeted IL-2Rβγ agonism while preserving combinability with therapeutic PD-1 inhibitors. This design allows for selective expansion of tumor antigen-specific T cells while avoiding the systemic toxicity and regulatory T cell (Treg) expansion associated with conventional IL-2 therapies. The PD-1-targeting antibody used in ANV600 was generated by immunization of humanized mice and selected for its ability to bind PD-1 without blocking the binding epitope of PD-1 checkpoint blocking agents. ANV600 was evaluated in multiple syngeneic tumor models using human PD-1 transgenic mice. Tumor-infiltrating lymphocytes were analyzed to assess the selectivity of ANV600 for PD-1+ T cell subsets. Combination studies with pembrolizumab and nivolumab were performed to assess synergy with checkpoint inhibitors. ANV600 significantly inhibited tumor growth as monotherapy across multiple models, including the immune checkpoint-resistant B16F10 melanoma. By targeting PD-1, ANV600 selectively expanded tumor antigen-specific CD8+T cells, particularly progenitor exhausted (Tpex) and cytotoxic exhausted (Tcex) subsets, while sparing Tregs and NK cells. Combination with pembrolizumab and nivolumab resulted in additive effects, consistent with the complementary roles of PD-1 blockade in expanding Tpex cells and IL-2Rβγ signaling in reprogramming Tcex cells. ANV600's efficacy was dependent on CD8+T cells and primarily driven by tumor-resident T cells, as it remained effective despite blocked lymph node trafficking (FTY720) but was abrogated on CD8+ T cell depletion. ANV600 represents a novel approach to delivering IL-2Rβγ agonism specifically to PD-1+ cells while preserving the binding site for PD-1 checkpoint inhibitors. By targeting a non-blocking epitope on PD-1, ANV600 enables the selective expansion of tumor-reactive CD8+ T cells while allowing independent and optimized dosing of both agents. This design ensures combinability with PD-1 inhibitors at clinically relevant doses, including in patients previously treated with checkpoint blockade. These findings support the clinical development of ANV600 as both a monotherapy and a combination therapy in cancer immunotherapy.


  • Organizational Affiliation
    • ANAVEON AG, Basel, Switzerland.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of huIgG1-FabA [auth H]218Mus musculusMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of huIgG1-FabB [auth L]216Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death protein 1C [auth A]147Homo sapiensMutation(s): 0 
Gene Names: PDCD1PD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens)
Explore Q15116 
Go to UniProtKB:  Q15116
PHAROS:  Q15116
GTEx:  ENSG00000188389 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15116
Glycosylation
Glycosylation Sites: 3Go to GlyGen: Q15116-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth B],
E [auth C]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
J [auth L]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
DMS
Query on DMS

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I [auth H]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth H],
G [auth H],
H,
K [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.216 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.188 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.839α = 90
b = 70.241β = 90
c = 163.684γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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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: 2025-08-13
    Type: Initial release