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- PDB-9i0w: Structure of human PD-L1 in complex with clinically evaluated inh... -

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Basic information

Entry
Database: PDB / ID: 9i0w
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 / T cell costimulation / negative regulation of T cell proliferation / response to cytokine / positive regulation of T cell proliferation / 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 / 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: 2.1 Å
AuthorsPlewka, J. / Golebiowska-Mendroch, K. / Slota, A. / 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
DepositionJan 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)30,6043
Polymers29,9082
Non-polymers6961
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-1 kcal/mol
Surface area11530 Å2
Unit cell
Length a, b, c (Å)72.066, 72.066, 89.048
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 18 - 131 / Label seq-ID: 4 - 117

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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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-A1IZP / (3~{R})-1-[[7-(iminomethyl)-2-[2-methyl-3-[2-methyl-3-[[3-[[(3~{R})-3-oxidanylpyrrolidin-1-yl]methyl]-1,7-naphthyridin-8-yl]amino]phenyl]phenyl]-1,3-benzoxazol-5-yl]methyl]pyrrolidine-3-carboxylic acid


Mass: 695.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H41N7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.1→62.41 Å / Num. obs: 15292 / % possible obs: 94.9 % / Redundancy: 5.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.118 / Rrim(I) all: 0.218 / Χ2: 1.03 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-62.415.10.04619.32490.9970.0310.0550.6198.6
2.1-2.166.31.6441.113120.1461.0631.9660.9100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
REFMAC5.8.0430 (refmacat 0.4.88)refinement
Aimlessdata scaling
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.246 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.518 / SU ML: 0.248 / Cross valid method: FREE R-VALUE / ESU R: 0.263 / ESU R Free: 0.234 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2995 750 4.914 %
Rwork0.2338 14514 -
all0.237 --
obs-15264 94.89 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 50.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0.54 Å20 Å2
2---1.08 Å20 Å2
3---3.504 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 52 3 1880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121917
X-RAY DIFFRACTIONr_angle_refined_deg2.721.8322603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4215229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.194516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15910329
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5581084
X-RAY DIFFRACTIONr_chiral_restr0.1790.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021444
X-RAY DIFFRACTIONr_nbd_refined0.1960.2685
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.21
X-RAY DIFFRACTIONr_mcbond_it7.5564.768922
X-RAY DIFFRACTIONr_mcangle_it10.8228.5561149
X-RAY DIFFRACTIONr_scbond_it9.5675.08995
X-RAY DIFFRACTIONr_scangle_it13.2929.0871454
X-RAY DIFFRACTIONr_lrange_it16.93752.2442670
X-RAY DIFFRACTIONr_ncsr_local_group_10.1390.053036
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.139270.05007
12BX-RAY DIFFRACTIONLocal ncs0.139270.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1550.436500.41411110.41411610.8380.8581000.411
2.155-2.2130.304510.38810760.38311270.9140.8661000.383
2.213-2.2770.481410.389300.38511050.7930.86787.87330.373
2.277-2.3470.379570.3510410.35110980.8780.8891000.341
2.347-2.4240.285350.31510010.31410360.9450.9071000.297
2.424-2.5080.364500.3219610.32310110.8820.9131000.304
2.508-2.6030.389510.2949400.2999910.9010.9251000.273
2.603-2.7080.345430.2726120.2779190.9120.94271.27310.25
2.708-2.8280.27470.2418630.2439110.9560.95699.89020.218
2.828-2.9650.349500.2268190.2338710.9350.96499.77040.201
2.965-3.1240.336420.2187890.2238320.9320.96699.87980.192
3.124-3.3120.317400.2167470.227890.9450.96599.74650.196
3.312-3.5390.365410.2255460.2357260.9170.96480.8540.204
3.539-3.8190.22310.1925200.1947070.9660.97577.93490.177
3.819-4.1790.221240.1694990.1726400.9810.98381.71880.166
4.179-4.6650.158210.1295610.135830.9860.9999.82850.13
4.665-5.3720.221190.1635010.1655200.9740.9831000.168
5.372-6.5430.29340.2134320.2184660.9410.9681000.22
6.543-9.1060.366140.2613440.2653590.9250.95199.72150.27
9.106-36.2460.36190.2592210.2622310.8760.95599.56710.294

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