6NOJ

PD-L1 IgV domain V76T with fragment

• PDB DOI: https://doi.org/10.2210/pdb6NOJ/pdb

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


• Deposited: 2019-01-16 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.245 
• R-Value Work: 0.190 
• R-Value Observed: 0.196 

Starting Model: experimental

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

• PubMed: 30728114 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.34 kDa 
• Atom Count: 2,042 
• Modelled Residue Count: 251 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B	127	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KW7	C [auth A]	methyl 3-amino-4-(2-fluorophenyl)-1H-pyrrole-2-carboxylate C12 H11 F N2 O2 GWTUPBOJWRLEIN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 0.245 
• R-Value Work: 0.190 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.803	α = 90
b = 96.941	β = 90
c = 32.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Zhao, B., Perry, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	5T32GM065086
National Science Foundation (NSF, United States)	United States	0922862
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10 RR025677
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	S10 RR026915
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357

Revision History  

• 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
• Version 1.4: 2024-10-16
  Changes: Structure summary