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
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L2P (Subject of Investigation/LOI) Query on A1L2P Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth D]	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		Interactions Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth D]

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-02

Deposition Author(s):

Swaminathan, S.

Vaithilingam, K.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.