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Basic information

Entry
Database: PDB / ID: 7vun
TitleDesign, modification, evaluation and cocrystal studies of novel phthalimides regulating PD-1/PD-L1 interaction
ComponentsProgrammed cell death 1 ligand 1
KeywordsSTRUCTURAL PROTEIN / Dimer / Beta-sheet
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 / positive regulation of interleukin-10 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 / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / receptor ligand activity / positive regulation of cell migration / immune response / 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
Chem-8H7 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsCheng, Y. / Sun, C.L. / Chen, M.R. / Yang, P. / Xiao, Y.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharm Sin B / Year: 2022
Title: Novel phthalimides regulating PD-1/PD-L1 interaction as potential immunotherapy agents.
Authors: Sun, C. / Cheng, Y. / Liu, X. / Wang, G. / Min, W. / Wang, X. / Yuan, K. / Hou, Y. / Li, J. / Zhang, H. / Dong, H. / Wang, L. / Lou, C. / Sun, Y. / Yu, X. / Deng, H. / Xiao, Y. / Yang, P.
History
DepositionNov 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Programmed cell death 1 ligand 1
A: Programmed cell death 1 ligand 1
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
E: Programmed cell death 1 ligand 1
F: Programmed cell death 1 ligand 1
G: Programmed cell death 1 ligand 1
H: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,52212
Polymers115,2208
Non-polymers2,3024
Water79344
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)84.033, 97.864, 136.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14402.465 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9NZQ7
#2: Chemical
ChemComp-8H7 / (2~{S},3~{S})-2-[[6-[(3-cyanophenyl)methoxy]-2-(2-methyl-3-phenyl-phenyl)-1,3-bis(oxidanylidene)isoindol-5-yl]methylamino]-3-oxidanyl-butanoic acid


Mass: 575.611 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H29N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 1,4 - Dioxane, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.701→48.932 Å / Num. obs: 59381 / % possible obs: 99.76 % / Redundancy: 13.2 % / CC1/2: 0.998 / Net I/σ(I): 19.68
Reflection shellResolution: 2.701→2.798 Å / Num. unique obs: 59381 / CC1/2: 0.944

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2.701→48.932 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 3772 6.35 %
Rwork0.2345 55609 -
obs0.2379 59381 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.08 Å2 / Biso mean: 50.9795 Å2 / Biso min: 4.43 Å2
Refinement stepCycle: final / Resolution: 2.701→48.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7927 0 172 44 8143
Biso mean--52.04 24.38 -
Num. residues----1001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068281
X-RAY DIFFRACTIONf_angle_d0.9311232
X-RAY DIFFRACTIONf_chiral_restr0.0511238
X-RAY DIFFRACTIONf_plane_restr0.0041416
X-RAY DIFFRACTIONf_dihedral_angle_d13.3734868
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7015-2.73570.35121310.2774190594
2.7357-2.77170.28921410.26832070100
2.7717-2.80960.31911440.27982113100
2.8096-2.84980.37151330.2872027100
2.8498-2.89230.30361430.29192096100
2.8923-2.93750.36511370.30262070100
2.9375-2.98570.31041390.27462038100
2.9857-3.03710.31041420.26572067100
3.0371-3.09230.36661420.2682068100
3.0923-3.15180.33591380.28352060100
3.1518-3.21610.35761440.27292070100
3.2161-3.28610.31691330.27322070100
3.2861-3.36250.35991420.26992071100
3.3625-3.44650.31341400.25522021100
3.4465-3.53970.33561380.25662094100
3.5397-3.64380.26721410.23952072100
3.6438-3.76140.26741430.23492074100
3.7614-3.89580.2811430.23752067100
3.8958-4.05170.3261360.232041100
4.0517-4.2360.24531410.20622069100
4.236-4.45920.26141450.19582070100
4.4592-4.73840.22561360.18332047100
4.7384-5.10390.2551430.19352061100
5.1039-5.61680.23021430.18552080100
5.6168-6.4280.27081420.2032073100
6.428-8.09270.26371320.22722061100
8.0927-48.9320.2641400.21072054100
Refinement TLS params.Method: refined / Origin x: 28.4399 Å / Origin y: -28.9264 Å / Origin z: -11.3667 Å
111213212223313233
T0.0546 Å20.0039 Å20.0439 Å2-0.0173 Å2-0.0125 Å2---0.0103 Å2
L0.7336 °2-0.0633 °20.2 °2-0.0779 °20.0925 °2--0.2981 °2
S0.0656 Å °0.0136 Å °-0.1893 Å °0.0093 Å °-0.0581 Å °-0.0929 Å °-0.0705 Å °-0.0084 Å °0.0056 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB18 - 143
2X-RAY DIFFRACTION1allA18 - 142
3X-RAY DIFFRACTION1allC18 - 143
4X-RAY DIFFRACTION1allD18 - 143
5X-RAY DIFFRACTION1allE18 - 142
6X-RAY DIFFRACTION1allF18 - 143
7X-RAY DIFFRACTION1allG18 - 142
8X-RAY DIFFRACTION1allH18 - 139
9X-RAY DIFFRACTION1allI1
10X-RAY DIFFRACTION1allI2 - 4
11X-RAY DIFFRACTION1allS1 - 139

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