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- PDB-9inu: Novel PD-L1/VISTA dual inhibitor as potential immunotherapy agents -

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Basic information

Entry
Database: PDB / ID: 9inu
TitleNovel PD-L1/VISTA dual inhibitor as potential immunotherapy agents
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Immune checkpoint / Small molecular inhibitor / Dimer
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: 2.7 Å
AuthorsCheng, Y. / Xiao, Y.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Novel PD-L1/VISTA Dual Inhibitor as Potential Immunotherapy Agents.
Authors: Sun, C. / Cheng, Y. / Dong, J. / Hu, L. / Zhang, Y. / Shen, H. / Zhang, G. / Jiang, B. / Adam Youssouf, S. / Min, W. / Shen, Y. / Wang, L. / Deng, H. / Xiao, Y. / Yang, P.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 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)29,7663
Polymers29,3582
Non-polymers4081
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.096, 83.603, 96.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 14678.759 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-A1D9R / (2~{S})-2-[[6-methoxy-2-[(2-methyl-3-phenyl-phenyl)amino]pyrimidin-4-yl]methylamino]-3-oxidanyl-propanoic acid


Mass: 408.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: Tris, potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→48.42 Å / Num. obs: 94058 / % possible obs: 99.86 % / Redundancy: 12.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2223 / Net I/σ(I): 17
Reflection shellResolution: 2.7→2.797 Å / Rmerge(I) obs: 0.9106 / Num. unique obs: 9235 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.7→48.42 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 1377 9.99 %
Rwork0.244 --
obs0.2483 13782 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 30 1 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042022
X-RAY DIFFRACTIONf_angle_d0.7212752
X-RAY DIFFRACTIONf_dihedral_angle_d19.277702
X-RAY DIFFRACTIONf_chiral_restr0.053311
X-RAY DIFFRACTIONf_plane_restr0.004352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80.39311300.35921217X-RAY DIFFRACTION100
2.8-2.910.39141350.33821274X-RAY DIFFRACTION100
2.91-3.040.38251390.33061207X-RAY DIFFRACTION100
3.04-3.20.41621400.30151271X-RAY DIFFRACTION100
3.2-3.40.32431360.28311220X-RAY DIFFRACTION100
3.4-3.660.30371420.24261237X-RAY DIFFRACTION100
3.66-4.030.28371410.23231258X-RAY DIFFRACTION100
4.03-4.620.20451400.1891240X-RAY DIFFRACTION100
4.62-5.810.25661330.19681232X-RAY DIFFRACTION100
5.82-48.420.22941410.22641249X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.2073 Å / Origin y: 17.8986 Å / Origin z: 3.3648 Å
111213212223313233
T0.3933 Å2-0.0138 Å20.0262 Å2-0.3806 Å2-0.0323 Å2--0.6319 Å2
L0.4072 °2-0.0658 °2-0.0128 °2-0.7373 °20.2402 °2--2.0496 °2
S0.0663 Å °-0.0198 Å °0.1812 Å °0.0152 Å °0.0801 Å °-0.0435 Å °-0.104 Å °0.0413 Å °-0.1875 Å °
Refinement TLS groupSelection details: all

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