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- PDB-9hrt: Structure of human PD-L1 in complex with clinically evaluated inh... -

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Basic information

Entry
Database: PDB / ID: 9hrt
TitleStructure of human PD-L1 in complex with clinically evaluated inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / small-molecule inhibitor / PD-1 pathway / Programmed death-ligand 1
Function / homology
Function and homology information


negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of T cell mediated immune response to tumor cell / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / positive regulation of T cell proliferation / negative regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / positive regulation of cell migration / receptor ligand activity / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSlota, A. / Golebiowska-Mendroch, K. / Plewka, J. / Magiera-Mularz, K.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2021/43/B/NZ7/03170 Poland
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Characterization of Clinically Evaluated Small-Molecule Inhibitors of PD-L1 for Immunotherapy
Authors: Slota, A. / Golebiowska-Mendroch, K. / Kocik-Krol, J. / Musielak, B. / Stec, M. / Weglarczyk, K. / Siedlar, M. / Skalniak, L. / Plewka, J. / Magiera-Mularz, K.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4363
Polymers29,9082
Non-polymers5281
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-4 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.859, 52.030, 111.318
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-308-

HOH

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Components

#1: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14954.085 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Chemical ChemComp-A1IXH / (2~{R})-2-[[3-[(~{E})-2-[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]ethenyl]-4-(trifluoromethyl)phenyl]methylamino]-2-methyl-3-oxidanyl-propanoic acid


Mass: 527.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H28F3NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium sulfate; 0.1 soudium cacodylate; 6.53% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.3→47.18 Å / Num. obs: 13321 / % possible obs: 97.7 % / Redundancy: 5.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.89 / Num. unique obs: 1308 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
REFMACv5.5.0110refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.18 Å / SU B: 11.902 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26324 631 4.7 %RANDOM
Rwork0.20667 ---
obs0.20945 12665 96.9 %-
Displacement parametersBiso mean: 54.039 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å2-0 Å20 Å2
2---5.25 Å20 Å2
3---2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2026 0 38 38 2102

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