8XR5: PD-L1

Crystal structure of PD-L1 complexed with small molecule inhibitor X18. Determined by X-ray diffraction at 1.95 Å resolution. Released 26 Feb 2025.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,141
Mol. weight: 29.61 kDa
Ligands: A1LV3
Released: 26 Feb 2025

Explore 8XR5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XR5 contains 10 α-helices and 24 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	9-13	5	2
β-strand	18-23	6	1
β-strand	26	1	3
β-strand	28	1	3
α-helix	32-34	3
β-strand	35-41	7	2
β-strand	44-50	7	2
β-strand	53-54	2	2
α-helix	61-63	3
β-strand	67-69	3	1
α-helix	71-76	6
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-100	9	2
β-strand	102-113	12	2
α-helix	116-125	10

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	4
β-strand	9-13	5	5
β-strand	18-20	3	6
β-strand	23	1	4
α-helix	32-34	3
β-strand	35-41	7	5
β-strand	44-50	7	5
β-strand	53-54	2	5
α-helix	61-63	3
β-strand	67-69	3	6
α-helix	72-76	5
β-strand	78	1	4
β-strand	81-83	3	6
α-helix	88-90	3
β-strand	92-100	9	5
β-strand	102-113	12	5
α-helix	116-120	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A, B	protein	126	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8XR5_1 Programmed cell death 1 ligand 1 (chains A, B)
FTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQH
SSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAHH
HHHHAA

Ligands and cofactors

ID	Name	Formula	Copies
A1LV3	(2~{R})-2-[[2-(2,1,3-benzoxadiazol-5-ylmethoxy)-5-chloranyl-4-[[2-fluoranyl-3-[…	C38 H40 Cl F N4 O8	1

Primary citation

Discovery of Novel PD-L1 Small-Molecular Inhibitors with Potent In Vivo Anti-tumor Immune Activity. Liu, L., Zhang, H., Hou, J. et al. J Med Chem (2024) 67:4977-4997. DOI 10.1021/acs.jmedchem.4c00102 · PubMed

Other PDB entries of the same protein (UniProt Q9NZQ7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5O45 0.99 Å, Structure of human PD-L1 in complex with inhibitor
8ALX 1.1 Å, Structure of human PD-L1 in complex with inhibitor
6NP9 1.27 Å, PD-L1 IgV domain V76T with fragment
9I0U 1.46 Å, Structure of human PD-L1 in complex with clinically evaluated inhibitor
6YCR 1.54 Å, Structure of human PD-L1 in complex with inhibitor
8AOK 1.6 Å, Complex of PD-L1 with VHH6
13DT 1.64 Å, Structure of FabS1CE2_P4a in complex with the N-terminal domain of PD-L1
7CZD 1.64 Å, Crystal structure of PD-L1 in complex with a VHH
5JDS 1.7 Å, Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution
5N2F 1.7 Å, Structure of PD-L1/small-molecule inhibitor complex
9QSM 1.75 Å, small molecule inhibitor in complex with PD-L1
8ZNL 1.77 Å, PD-L1 de novo designed binder with picomolar binding affinity

Browse structure collections

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