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- PDB-9ery: Co-crystal strucutre of PD-L1 with low molecular weight inhibitor -

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Basic information

Entry
Database: PDB / ID: 9ery
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 / 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
: / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPlewka, J. / Magiera-Mularz, K. / Zhang, W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877101 China
National Natural Science Foundation of China (NSFC)22177105 China
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Design, synthesis, and evaluation of antitumor activity of 2-arylmethoxy-4-(2-fluoromethyl-biphenyl-3-ylmethoxy) benzylamine derivatives as PD-1/PD-l1 inhibitors.
Authors: Zhang, F. / Zhang, H. / Zhou, S. / Plewka, J. / Wang, M. / Sun, S. / Wu, C. / Yu, Q. / Zhu, M. / Awadasseid, A. / Wu, Y. / Magiera-Mularz, K. / Zhang, W.
History
DepositionMar 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)30,5784
Polymers29,9082
Non-polymers6702
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-17 kcal/mol
Surface area11810 Å2
Unit cell
Length a, b, c (Å)74.534, 74.534, 95.392
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-201-

HOH

21B-206-

HOH

31B-207-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

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 asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 117 / Label seq-ID: 4 - 117

Dom-ID
1
2

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-VVH / 5-[[5-[[2-[bis(fluoranyl)methyl]-3-(2,3-dihydro-1,4-benzodioxin-6-yl)phenyl]methoxy]-2-[(2-hydroxyethylamino)methyl]phenoxy]methyl]pyridine-3-carbonitrile


Mass: 573.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H29F2N3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate and 0.1 M Sodium cacodylate pH 6.5

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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: 2.7→47.7 Å / Num. obs: 8822 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.028 / Rrim(I) all: 0.092 / Net I/σ(I): 17.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 20.4 % / Rmerge(I) obs: 3.835 / Num. unique obs: 1145 / CC1/2: 0.342 / Rpim(I) all: 1.226 / Rrim(I) all: 4.028

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
PDB-REDOrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→38.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.776 / SU ML: 0.363 / Cross valid method: FREE R-VALUE / ESU R: 0.951 / ESU R Free: 0.361
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2755 464 5.275 %
Rwork0.2217 8333 -
all0.225 --
obs-8797 99.943 %
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: 119.224 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.725 Å20 Å2
2--1.45 Å2-0 Å2
3----4.702 Å2
Refinement stepCycle: LAST / Resolution: 2.7→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 47 11 1889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121913
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161814
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.6472592
X-RAY DIFFRACTIONr_angle_other_deg0.8481.5734157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9795230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.757513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.21910326
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.9521085
X-RAY DIFFRACTIONr_chiral_restr0.0890.2292
X-RAY DIFFRACTIONr_chiral_restr_other0.2090.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022193
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02434
X-RAY DIFFRACTIONr_nbd_refined0.1230.2238
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1220.21557
X-RAY DIFFRACTIONr_nbtor_refined0.1470.2862
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.21045
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.23
X-RAY DIFFRACTIONr_nbd_other0.0930.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0670.25
X-RAY DIFFRACTIONr_mcbond_it10.52111.858926
X-RAY DIFFRACTIONr_mcbond_other10.51811.86926
X-RAY DIFFRACTIONr_mcangle_it14.55221.4691154
X-RAY DIFFRACTIONr_mcangle_other14.54821.471155
X-RAY DIFFRACTIONr_scbond_it11.74712.608987
X-RAY DIFFRACTIONr_scbond_other11.54512.6984
X-RAY DIFFRACTIONr_scangle_it17.6122.9351438
X-RAY DIFFRACTIONr_scangle_other17.26722.9281433
X-RAY DIFFRACTIONr_lrange_it21.357111.7481888
X-RAY DIFFRACTIONr_lrange_other21.367111.7831889
X-RAY DIFFRACTIONr_ncsr_local_group_10.1750.052950
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.175210.05006
12AX-RAY DIFFRACTIONLocal ncs0.175210.05006
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
2.7-2.770.456230.4176280.4186510.8610.791000.417
2.77-2.8460.315320.3635760.366080.8940.891000.353
2.846-2.9280.287380.3245580.3215960.9350.9341000.303
2.928-3.0170.349360.3215460.3235820.9060.9281000.3
3.017-3.1150.406390.3245370.3295760.8770.9221000.295
3.115-3.2240.371240.3065280.315520.9080.9351000.272
3.224-3.3450.37260.275070.2755330.920.9521000.241
3.345-3.480.366300.2614850.2665150.910.9581000.233
3.48-3.6340.235120.2334690.2334810.9610.9681000.215
3.634-3.8090.287200.2294600.2314800.9410.9671000.212
3.809-4.0130.262370.2214200.2244580.9570.96999.78170.214
4.013-4.2540.295240.2153920.2194160.9350.9721000.216
4.254-4.5430.335230.1863850.1934080.9450.9791000.196
4.543-4.9020.21990.1753780.1753870.9650.9821000.191
4.902-5.3610.169190.1873410.1853600.9870.981000.204
5.361-5.9790.313110.2023000.2053110.9590.9771000.22
5.979-6.8760.32160.2182790.2222950.960.9741000.233
6.876-8.3550.42100.2142380.2182490.940.97199.59840.236
8.355-11.5450.235200.1751860.182060.9610.9831000.205
11.545-38.360.233150.2931190.2861340.9760.9481000.358

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