5N2F: PD-L1/small-molecule inhibitor complex

Structure of PD-L1/small-molecule inhibitor complex. Determined by X-ray diffraction at 1.7 Å resolution. Released 28 Jun 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,307
Mol. weight: 29.03 kDa
Ligands: 8HW
Released: 28 Jun 2017

Explore 5N2F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5N2F contains 11 α-helices and 22 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	3
β-strand	27-31	5	4
β-strand	36-38	3	5
β-strand	41	1	3
α-helix	50-52	3
β-strand	54-59	6	4
β-strand	62-68	7	4
β-strand	71	1	4
α-helix	74-76	3
α-helix	79-81	3
β-strand	85-87	3	5
α-helix	89-94	6
β-strand	96	1	3
β-strand	99-101	3	5
α-helix	106-108	3
β-strand	110-117	8	4
β-strand	121-131	11	4
α-helix	134-139	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Programmed cell death 1 ligand 1	A	protein	126	Homo sapiens	Q9NZQ7 (AlphaFold model)
Programmed cell death 1 ligand 1	B	protein	124	Homo sapiens	Q9NZQ7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5N2F_1 Programmed cell death 1 ligand 1 (chains A)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAA
LEHHHH

Sequence of entity 2 (B), FASTA

>5N2F_2 Programmed cell death 1 ligand 1 (chains B)
AFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQ
HSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAPYAAA
LEHH

Ligands and cofactors

ID	Name	Formula	Copies
8HW	4-[[4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-2,5-bis(f…	C27 H25 F2 N O6	1

Primary citation

Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1. Guzik, K., Zak, K.M., Grudnik, P. et al. J Med Chem (2017) 60:5857-5867. DOI 10.1021/acs.jmedchem.7b00293 · 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
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

Browse structure collections

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