PD-L1 Target DEMO

PD-L1 (CD274, B7-H1) is a membrane protein that binds PD-1 on T cells to drive immune evasion.
This campaign looks for a minibinder that blocks the GFCC′ face of the IgV domain.

Structure prep (stage B)

Binding only uses the extracellular IgV domain 19-127. The transmembrane and cytoplasmic parts are trimmed.
Reference structure: PD-L1/Structure/4ZQK — Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.
Resolution 2.45 Å, method X-RAY DIFFRACTION

Automatic check results

Seeded domain_range with the largest of 2 UniProt domains (Ig-like V-type 19-127). Check it is the ectodomain you actually mean to bind.
1 transmembrane span(s): 239-259. Trim to the ectodomain.

Epitope and hotspots (stage C)

Hotspots: A54, A56, A115, A121, A123. Solvent-exposed, within the PD-1 contact face, and spread as a small patch rather than concentrated at one point.

Confirmed in the structure that the glycan sites (N35, N192, N200, N219) don't mask the epitope.

Basic

Gene name	CD274
Aliases	B7H1PDCD1L1PDCD1LG1PDL1B7 homolog 1 ?
UniProt	Q9NZQ7
Organism	Homo sapiens
Indication	Non-small cell lung cancerMelanomaUrothelial carcinoma
Status	Active

Structure

PDB ID	4ZQK
Chain	A
Domain range	19-127 ?
Structure source	PDB
Epitope	The GFCC′ face of the IgV domain — where PD-1 binds, overlapping the atezolizumab epitope. Blocking this face is the campaign's goal. ?
Hotspot residues	A54A56A115A121A123 ?
N-glycan sites	N35N192N200N219 ?
Disulfide bonds	C40-C114C155-C209

Sequence

    1  MRIFAVFIFM TYWHLLNAFT VTVPKDLYVV EYGSNMTIEC KFPVEKQLDL AALIVYWEME
   61  DKNIIQFVHG EEDLKVQHSS YRQRARLLKD QLSLGNAALQ ITDVKLQDAG VYRCMISYGG
  121  ADYKRITVKV NAPYNKINQR ILVVDPVTSE HELTCQAEGY PKAEVIWTSS DHQVLSGKTT
  181  TTNSKREEKL FNVTSTLRIN TTTNEIFYCT FRRLDPEENH TAELVIPELP LAHPPNERTH
  241  LVILGAILLC LGVALTFIFR LRKGRMMDVK KCGIQDTNSK KQSDTHLEET

290 aa

Experimental

Expression system	HEK293
Cross-reactivity targets	Homo sapiensMus musculus

Aliases

CD274B7-H1PDL1PD-L1

Page info

Revision	r1
Last edited	2026-08-26 18:13:30
Editor	Demo seed
Summary	Demo seed

Structure — pick epitope & hotspots Step C

Loading structure…

Click a residue to select or deselect it. Once chosen, copy it, then on the edit screen, paste it into the hotspot field. RFdiffusion usually takes 3–6 — spread them as small patches rather than piling on one spot.

Category: Target Active

PD-L1 Target DEMO

Structure prep (stage B)

Automatic check results

Epitope and hotspots (stage C)

Structure — pick epitope & hotspots Step C

Pages linking here (3) All