9IJT | pdb_00009ijt

Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10

• PDB DOI: https://doi.org/10.2210/pdb9IJT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-06-25 Released: 2025-07-02 
• Deposition Author(s): Swaminathan, S., Birudukota, S., Vaithilingam, K., Sadhu, N., Gosu, R., Rajagopal, S.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.236 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-20

Swaminathan, S., Birudukota, S., Vaithilingam, K., Sadhu, N., Gosu, R., Rajagopal, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 60.14 kDa 
• Atom Count: 4,302 
• Modeled Residue Count: 507 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B, C, D	129	Homo sapiens	Mutation(s): 0  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
A1L2P (Subject of Investigation/LOI)	E [auth B], F [auth D]	(2~{S})-1-[[4-methoxy-2-[(2-methyl-3-phenyl-phenyl)methoxy]pyrimidin-5-yl]methyl]piperidine-2-carboxylic acid C26 H29 N3 O4 ANUJMSZHAOMHOI-QHCPKHFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.260 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.236 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.717	α = 90
b = 85.206	β = 90
c = 161.157	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Swaminathan, S., Birudukota, S., Vaithilingam, K., Sadhu, N., Gosu, R., Rajagopal, S.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release