6NNV

PD-L1 IgV domain complex with macro-cyclic peptide

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens, synthetic construct
  • Expression System: Escherichia coli K-12
  • Mutation(s): Yes 

  • Deposited: 2019-01-15 Released: 2019-02-20 
  • Deposition Author(s): Zhao, B., Perry, E.
  • Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Fragment-based screening of programmed death ligand 1 (PD-L1).

Perry, E., Mills, J.J., Zhao, B., Wang, F., Sun, Q., Christov, P.P., Tarr, J.C., Rietz, T.A., Olejniczak, E.T., Lee, T., Fesik, S.

(2019) Bioorg Med Chem Lett 29: 786-790

  • DOI: https://doi.org/10.1016/j.bmcl.2019.01.028
  • Primary Citation of Related Structures:  
    6NM7, 6NM8, 6NNV, 6NOJ, 6NOS, 6NP9

  • PubMed Abstract: 

    The PD-1 immune checkpoint pathway is a highly validated target for cancer immunotherapy. Despite the potential advantages of small molecule inhibitors over antibodies, the discovery of small molecule checkpoint inhibitors has lagged behind. To discover small molecule inhibitors of the PD-1 pathway, we have utilized a fragment-based approach. Small molecules were identified that bind to PD-L1 and crystal structures of these compounds bound to PD-L1 were obtained.

    • Organizational Affiliation: 

    Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Programmed cell death 1 ligand 1
A, B, C, D
127Homo sapiensMutation(s): 1 
Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens)
Explore Q9NZQ7 
Go to UniProtKB:  Q9NZQ7
PHAROS:  Q9NZQ7
GTEx:  ENSG00000120217 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZQ7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
macrocyclic peptideE [auth I],
F [auth J],
G [auth K],
H [auth L]		16synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA		E [auth I],
F [auth J],
G [auth K],
H [auth L]		L-PEPTIDE LINKINGC10 H13 N O2PHE
SAR
Query on SAR		E [auth I],
F [auth J],
G [auth K],
H [auth L]		PEPTIDE LINKINGC3 H7 N O2GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.84α = 90
b = 61.683β = 90.17
c = 80.895γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States5T32GM065086
National Science Foundation (NSF, United States)United States0922862
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR025677
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR026915
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description