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- PDB-5n2f: Structure of PD-L1/small-molecule inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5n2f
TitleStructure of PD-L1/small-molecule inhibitor complex
Components(Programmed cell death 1 ligand 1) x 2
KeywordsIMMUNE SYSTEM / PD-L1 / PD-1 / small-molecule inhibitor
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 ...: / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-8HW / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGuzik, K. / Zak, K.M. / Grudnik, P. / Dubin, G. / Holak, T.A.
Funding support Poland, 7items
OrganizationGrant numberCountry
National Science CenterUMO-2012/06/A/ST5/00224 Poland
National Science CenterUMO-2014/12/W/NZ1/00457 Poland
National Science CenterUMO-2011/01/D/NZ1/01169 Poland
National Science CenterUMO-2012/07/E/NZ1/01907 Poland
National Science CenterUMO-2015/19/N/ST5/00347 Poland
National Science CenterUMO-2016/20/T/NZ1/00519 Poland
National Science CenterUMO-2015/19/D/NZ1/02009 Poland
CitationJournal: J. Med. Chem. / Year: 2017
Title: Small-Molecule Inhibitors of the Programmed Cell Death-1/Programmed Death-Ligand 1 (PD-1/PD-L1) Interaction via Transiently Induced Protein States and Dimerization of PD-L1.
Authors: Guzik, K. / Zak, K.M. / Grudnik, P. / Magiera, K. / Musielak, B. / Torner, R. / Skalniak, L. / Domling, A. / Dubin, G. / Holak, T.A.
History
DepositionFeb 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)29,0263
Polymers28,5292
Non-polymers4971
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-4 kcal/mol
Surface area12840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.815, 52.379, 111.526
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 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 14402.465 Da / Num. of mol.: 1
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: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 14126.172 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-8HW / 4-[[4-[[3-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-methyl-phenyl]methoxy]-2,5-bis(fluoranyl)phenyl]methylamino]-3-oxidanylidene-butanoic acid


Mass: 497.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H25F2NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01 M Tris pH 8.4 , 0.28 M sodium chloride, 27% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.7→36.84 Å / Num. all: 222441 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 33.3
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 12071 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5c3t

5c3t


Resolution: 1.7→36.837 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2297 1664 4.87 %
Rwork0.1907 --
obs0.1925 34155 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→36.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 36 271 2254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092090
X-RAY DIFFRACTIONf_angle_d1.0252852
X-RAY DIFFRACTIONf_dihedral_angle_d20.4071264
X-RAY DIFFRACTIONf_chiral_restr0.059317
X-RAY DIFFRACTIONf_plane_restr0.006364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.34511030.28222719X-RAY DIFFRACTION100
1.75-1.80650.32671440.2492652X-RAY DIFFRACTION100
1.8065-1.87110.25681420.2262649X-RAY DIFFRACTION100
1.8711-1.9460.26561510.21342674X-RAY DIFFRACTION100
1.946-2.03460.23931330.20282659X-RAY DIFFRACTION100
2.0346-2.14180.25971300.21922681X-RAY DIFFRACTION100
2.1418-2.2760.25591520.21532702X-RAY DIFFRACTION100
2.276-2.45170.24881380.21242685X-RAY DIFFRACTION100
2.4517-2.69840.27691460.2162694X-RAY DIFFRACTION100
2.6984-3.08860.23441680.20262712X-RAY DIFFRACTION100
3.0886-3.89070.19331330.17052754X-RAY DIFFRACTION100
3.8907-36.84520.18821240.15722910X-RAY DIFFRACTION99
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)
11.75451.20830.81291.43311.30842.5330.1438-0.1335-0.12950.1598-0.0333-0.08940.0842-0.2512-0.14740.21870.0206-0.02040.1789-0.01050.220416.56497.178125.6869
22.4578-0.22810.46012.03431.01263.15710.1951-0.16510.10030.2078-0.05210.14510.214-0.0133-0.11110.28430.0350.0480.20310.01110.256817.966315.915135.5387
35.21681.91511.04884.69780.20333.1090.08170.56490.0069-0.10450.3948-0.6349-0.37780.6518-0.48340.25820.01670.00910.2296-0.04950.29825.585518.9991125.7383
47.59260.3154-0.49263.153.93475.0106-0.37770.73521.6766-0.20810.7689-0.4947-1.64970.2945-0.45051.0363-0.1045-0.07580.35160.06240.457624.574726.0349122.8329
56.90383.1498-2.78567.90790.22491.4705-0.07481.07590.7133-1.1907-0.01060.3309-1.00441.1334-0.03450.5523-0.0591-0.06730.71350.09080.256919.152719.9995114.0609
63.2556-0.3326-2.1451.02371.352.69910.22750.1046-0.01860.0516-0.04580.5034-1.3526-1.2466-0.00570.37250.0952-0.02260.3581-0.00410.349213.888220.6021130.7039
72.29691.3092.85390.99582.07484.4093-0.20190.11770.0393-0.10630.03010.0013-0.45120.20420.07220.23590.0197-0.0110.23780.00740.24815.68413.5789118.7482
82.01711.8222.90143.07515.0868.8998-0.05880.04820.05790.22910.1287-0.07250.05260.1899-0.27510.26620.0395-0.04060.2244-0.10710.289425.791313.3338129.1942
95.62893.46042.15373.58492.46841.6754-0.0190.3127-0.36050.18440.3495-0.31290.02320.4972-0.47640.23410.055-0.02740.1739-0.05190.232123.14726.5785125.326
103.91583.9089-0.63144.13320.00036.8108-0.26330.2980.2207-0.5817-0.0162-0.7314-0.67810.39450.28640.3458-0.02550.04490.32510.00510.35316.01785.6153101.2903
111.9417-0.3421-1.51881.5541.61752.37350.1176-0.06290.3504-0.08890.0556-0.2044-0.18450.0511-0.15090.2196-0.0103-0.00310.2253-0.02050.240448.438911.665122.5388
120.67050.03430.08373.37621.21793.6576-0.0417-0.38720.24340.8658-0.19-0.384-0.895-0.005-0.15380.6125-0.0095-0.1160.3264-0.14340.517345.56222.4687134.1875
135.5387-1.4107-1.47134.66121.80793.60580.06-0.4217-0.19940.44780.06170.13320.0566-0.53460.00830.2347-0.0072-0.01540.2836-0.00680.197438.94379.2192132.829
143.63080.63250.1695.4831-4.06813.1264-0.1497-0.4778-0.19120.6685-0.287-0.1089-0.2581-0.34030.38760.3199-0.0465-0.01330.27010.00640.365440.14363.0447137.3715
155.2527-3.940.26193.0235-0.63032.7903-0.1297-0.79-0.54860.89540.2962-0.65570.45750.31920.0730.33740.02750.00140.3587-0.01280.357348.59642.7592134.628
164.17634.3977-0.86964.7098-0.5142.2522-0.3787-1.0520.63541.0048-0.2397-2.0579-0.36990.26610.45440.4277-0.0227-0.20070.3869-0.15970.733549.902618.0865135.901
174.336-1.6995-0.17354.85731.54263.0398-0.015-0.2332-0.03110.2084-0.06790.0351-0.068-0.13970.08990.1508-0.01740.00290.2167-0.00760.139743.40818.0656127.0223
188.3733-5.8961-5.9254.4664.83656.16510.23970.33540.1833-0.0633-0.3653-0.0083-0.2307-0.46420.33740.2211-0.0005-0.00140.2267-0.0480.195941.452112.0207121.2676
191.73660.92522.11173.11233.67188.2831-0.0977-0.5735-0.23680.69750.54730.00060.8868-1.0313-0.33540.2788-0.02360.00430.27330.08540.282649.4161-10.8137114.2982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 35 )
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 84 )
6X-RAY DIFFRACTION6chain 'A' and (resid 85 through 94 )
7X-RAY DIFFRACTION7chain 'A' and (resid 95 through 109 )
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 119 )
9X-RAY DIFFRACTION9chain 'A' and (resid 120 through 131 )
10X-RAY DIFFRACTION10chain 'A' and (resid 132 through 143 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 38 )
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 49 )
13X-RAY DIFFRACTION13chain 'B' and (resid 50 through 68 )
14X-RAY DIFFRACTION14chain 'B' and (resid 69 through 81 )
15X-RAY DIFFRACTION15chain 'B' and (resid 82 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 98 )
17X-RAY DIFFRACTION17chain 'B' and (resid 99 through 119 )
18X-RAY DIFFRACTION18chain 'B' and (resid 120 through 131 )
19X-RAY DIFFRACTION19chain 'B' and (resid 132 through 141 )

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