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- PDB-8or1: Co-crystal strucutre of PD-L1 with low molecular weight inhibitor -

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Basic information

Entry
Database: PDB / ID: 8or1
TitleCo-crystal strucutre of PD-L1 with low molecular weight inhibitor
ComponentsProgrammed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / PD-L1 / inhibitor / immunotheraphy
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 / transcription coactivator activity / adaptive immune response / 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-VYC / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsZhang, H. / Zhou, S. / Wu, C. / Zhu, M. / Yu, Q. / Wang, X. / Awadasseid, A. / Plewka, J. / Magiera-Mularz, K. / Wu, Y. / Zhang, W.
Funding support China, Poland, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877101 China
Foundation for Polish ScienceTEAM TECH CORE FACILITY/2017-4/6 Poland
National Natural Science Foundation of China (NSFC)22177105 China
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design, Synthesis, and Antitumor Activity Evaluation of 2-Arylmethoxy-4-(2,2'-dihalogen-substituted biphenyl-3-ylmethoxy) Benzylamine Derivatives as Potent PD-1/PD-L1 Inhibitors.
Authors: Zhang, H. / Zhou, S. / Plewka, J. / Wu, C. / Zhu, M. / Yu, Q. / Musielak, B. / Wang, X. / Awadasseid, A. / Magiera-Mularz, K. / Wu, Y. / Zhang, W.
History
DepositionApr 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)26,9803
Polymers26,4622
Non-polymers5181
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-1 kcal/mol
Surface area12290 Å2
Unit cell
Length a, b, c (Å)73.459, 73.459, 95.156
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 13231.199 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-VYC / 5-[[5-[[2-chloranyl-3-(2-fluorophenyl)phenyl]methoxy]-2-[(~{E})-2-hydroxyethyliminomethyl]phenoxy]methyl]pyridine-3-carbonitrile


Mass: 517.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25ClFN3O3 / Feature type: SUBJECT OF INVESTIGATION
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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium acetate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 3.5→47.58 Å / Num. obs: 4021 / % possible obs: 99.9 % / Redundancy: 19.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.062 / Rrim(I) all: 0.201 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.57-47.58160.0653100.9990.0210.068
3.5-3.8320.51.8249370.8390.5731.912

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→38.13 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 122.631 / SU ML: 0.765 / Cross valid method: THROUGHOUT / ESU R Free: 0.781 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29624 385 9.7 %RANDOM
Rwork0.29228 ---
obs0.29265 3590 99.25 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.888 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å2-0 Å2
2---1.16 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 3.5→38.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 37 0 1895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0171930
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161797
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.8212609
X-RAY DIFFRACTIONr_angle_other_deg0.3281.5654180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875.208240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36510346
X-RAY DIFFRACTIONr_chiral_restr0.2640.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
LS refinement shellResolution: 3.501→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 22 -
Rwork0.424 258 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.63654.9011-1.37645.2904-0.79222.10250.3262-0.7768-0.30070.2815-0.279-0.9065-0.04480.0033-0.04720.42440.17030.03060.47040.15560.2648-35.14827.604-9.749
210.7473-1.1878-0.44455.8732-2.08584.34470.0365-0.551.23770.37240.12470.709-0.8914-1.0118-0.16120.47550.28830.21070.3361-0.07350.5354-38.1250.487-20.798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 119
2X-RAY DIFFRACTION2B4 - 119

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