9QSM: Small molecule inhibitor

small molecule inhibitor in complex with PD-L1. Determined by X-ray diffraction at 1.75 Å resolution. Released 18 Feb 2026.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,806
Mol. weight: 90.22 kDa
Ligands: A1JAE
Released: 18 Feb 2026

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

Secondary structure: helices and β-sheets

9QSM contains 25 α-helices and 60 β-strands across 6 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.

Chains A, B and C: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	1
β-strand	13-17	5	2
β-strand	22-27	6	1
α-helix	36-38	3
β-strand	40-45	6	2
β-strand	48-54	7	2
β-strand	57-58	2	2
α-helix	65-67	3
β-strand	71-73	3	1
α-helix	75-78	4
β-strand	82-87	6	1
α-helix	92-94	3
β-strand	96-103	8	2
β-strand	107-117	11	2

Chain D: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	7
β-strand	13-17	5	8
β-strand	22-27	6	7
α-helix	36-38	3
β-strand	40-45	6	8
β-strand	48-54	7	8
β-strand	57-58	2	8
α-helix	65-67	3
β-strand	71-73	3	7
α-helix	75-78	4
β-strand	82-87	6	7
α-helix	92-94	3
β-strand	96-104	9	8
β-strand	106-117	12	8

Chain E: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	9
β-strand	13-17	5	10
β-strand	22-27	6	9
α-helix	36-38	3
β-strand	40-45	6	10
β-strand	48-54	7	10
β-strand	57-58	2	10
α-helix	65-67	3
β-strand	71-73	3	9
α-helix	75-78	4
β-strand	82-87	6	9
α-helix	92-94	3
β-strand	96-103	8	10
β-strand	107-117	11	10
α-helix	118-119	2

Chain F: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	11
β-strand	13-17	5	12
β-strand	22-27	6	11
α-helix	36-38	3
β-strand	40-45	6	12
β-strand	48-54	7	12
β-strand	57-58	2	12
α-helix	65-67	3
β-strand	71-73	3	11
β-strand	82-87	6	11
α-helix	92-94	3
β-strand	96-103	8	12
β-strand	107-117	11	12
α-helix	118-120	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A, B, C, D, E, F	protein	128	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9QSM_1 Programmed cell death 1 ligand 1 (chains A, B, C, D, E, F)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAA
LEHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
A1JAE	~{N}-[2-chloranyl-3-[2-chloranyl-3-[4-[[[2-(hydroxymethyl)-1,3-bis(oxidanyl)pro…	C35 H40 Cl2 N4 O8	3

Primary citation

N-terphenylpicolinamide derivatives designed to target PD-L1 increase activation and proliferation of T cells, and their cytotoxic properties toward cancer cells. Muszak, D., Kocik-Krol, J., Zaber, J. et al. Eur J Med Chem (2026) 307:118652-118652. DOI 10.1016/j.ejmech.2026.118652 · 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
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

Browse structure collections

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