9I0U: Human PD-L1

Structure of human PD-L1 in complex with clinically evaluated inhibitor. Determined by X-ray diffraction at 1.46 Å resolution. Released 18 Jun 2025.

Method: X-ray diffraction
Resolution: 1.46 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,376
Mol. weight: 30.78 kDa
Ligands: A1IZJ
Released: 18 Jun 2025

Explore 9I0U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I0U contains 11 α-helices and 20 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
β-strand	27-31	5	2
β-strand	36-41	6	1
α-helix	50-52	3
β-strand	54-59	6	2
β-strand	62-68	7	2
β-strand	71-72	2	2
α-helix	79-81	3
β-strand	85-87	3	1
α-helix	89-94	6
β-strand	96-101	6	1
α-helix	106-108	3
β-strand	110-118	9	2
β-strand	120-131	12	2
α-helix	134-142	9

Chain B: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	27-31	5	4
β-strand	36-41	6	3
α-helix	50-52	3
β-strand	54-59	6	4
β-strand	62-68	7	4
β-strand	71-72	2	4
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	3
α-helix	89-94	6
β-strand	96-101	6	3
α-helix	106-108	3
β-strand	110-118	9	4
β-strand	120-131	12	4
α-helix	134-142	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A, B	protein	131	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9I0U_1 Programmed cell death 1 ligand 1 (chains A, B)
MGSAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDL
KVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPY
AAALEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1IZJ	(5~{S})-5-[[[5-[2-chloranyl-3-[2-chloranyl-3-[6-methoxy-5-[[[(2~{S})-5-oxidanyl…	C34 H36 Cl2 N8 O4	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Characterization of Clinically Evaluated Small-Molecule Inhibitors of PD-L1 for Immunotherapy. Slota, A., Golebiowska-Mendroch, K., Kocik-Krol, J. et al. ACS Med Chem Lett (2025) 16:1359-1364. DOI 10.1021/acsmedchemlett.5c00245 · 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
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
5C3T 1.8 Å, PD-1 binding domain from human PD-L1

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