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- PDB-5n2d: Structure of PD-L1/small-molecule inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 5n2d
TitleStructure of PD-L1/small-molecule inhibitor complex
ComponentsProgrammed cell death 1 ligand 1
KeywordsCELL CYCLE / PD-L1 / PD-1 / small-molecule inhibitor
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / 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 / 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 ...positive regulation of tolerance induction to tumor cell / 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 / 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 / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-8J8 / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Programmed cell death 1 ligand 1
D: Programmed cell death 1 ligand 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8346
Polymers66,9374
Non-polymers8972
Water3,081171
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-19 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.201, 85.734, 161.126
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16734.254 Da / Num. of mol.: 4
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-8J8 / ~{N}-[2-[[2,6-dimethoxy-4-[(2-methyl-3-phenyl-phenyl)methoxy]phenyl]methylamino]ethyl]ethanamide


Mass: 448.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H32N2O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M magnesium chloride, 30% (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 PILATUS3 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: 2.35→42.87 Å / Num. all: 160996 / Num. obs: 23740 / % possible obs: 96.8 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.7
Reflection shellResolution: 2.35→2.434 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 5 / Num. unique obs: 16186 / CC1/2: 0.962 / % possible all: 95.98

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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: 5j89

5j89


Resolution: 2.35→42.87 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29
RfactorNum. reflection% reflection
Rfree0.2672 1149 4.84 %
Rwork0.2102 --
obs0.213 23740 96.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.35→42.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 66 171 4080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094009
X-RAY DIFFRACTIONf_angle_d1.1315451
X-RAY DIFFRACTIONf_dihedral_angle_d20.1562407
X-RAY DIFFRACTIONf_chiral_restr0.058611
X-RAY DIFFRACTIONf_plane_restr0.007741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4570.32651170.2542743X-RAY DIFFRACTION95
2.457-2.58650.34281500.25312749X-RAY DIFFRACTION95
2.5865-2.74850.30991440.25622826X-RAY DIFFRACTION98
2.7485-2.96070.31791420.24772847X-RAY DIFFRACTION98
2.9607-3.25860.32651450.24082705X-RAY DIFFRACTION94
3.2586-3.72990.26391580.21272901X-RAY DIFFRACTION99
3.7299-4.69850.22791460.17162833X-RAY DIFFRACTION96
4.6985-45.52350.2111470.18062987X-RAY DIFFRACTION95
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)
11.87480.5724-0.26193.2087-4.82678.13330.25940.1361-0.28-0.0015-0.1908-0.65470.24910.68520.01040.2080.01360.00190.327-0.14240.4002-4.958813.9179-34.7591
20.83580.4733-0.81592.7939-0.21041.4537-0.07350.0393-0.0476-0.01970.19550.6925-0.0048-0.1069-0.14790.1403-0.04030.00820.31850.02940.425-14.960416.1821-34.0695
31.00811.7727-0.41556.6945-2.37241.67050.3172-0.38820.28690.912-0.50050.3672-0.6189-0.4722-0.12050.3877-0.05240.17110.41550.05480.4264-18.299918.598-24.2382
41.4941-1.39070.99884.72270.19231.05370.19290.0007-0.19590.83060.45780.9214-0.3119-0.78090.06880.6381-0.0550.39520.53790.03040.9507-24.305814.3133-23.4631
51.6246-0.97710.58944.576-0.10682.5681-0.1193-0.03180.11770.02240.32691.0548-0.1318-0.5226-0.16890.2365-0.00980.00860.3268-0.00920.6323-21.01216.3575-34.5874
61.4102-0.42550.55543.80850.33592.27930.06270.05660.05890.19840.17770.99340.1408-0.2072-0.05510.11790.03850.04240.3427-0.00870.3365-14.989221.7594-30.1132
72.8587-3.65652.55778.1284-3.97353.524-0.3680.16030.41240.35090.3067-0.4411-0.03610.03680.16990.12720.00250.0630.275-0.00170.2283-8.38123.1604-31.6892
86.08961.15564.27167.623-1.48353.7050.4511-0.5889-0.22060.71150.35411.0924-0.1421-0.9607-0.18290.25040.04120.15640.37520.08280.6431-20.925743.6023-32.9468
92.84080.21530.52036.99352.35985.07530.2088-0.1580.08080.2046-0.30990.44120.2607-1.07420.03360.2722-0.15530.02970.48010.07880.2865-13.797413.8295-8.9164
102.11440.9212-0.17242.47990.5572.7685-0.23990.0438-0.2120.73140.20450.01470.4182-0.16180.16780.22010.02390.02280.28370.06180.2662-3.665615.0719-5.529
113.52450.58140.66421.74441.53743.0588-0.50850.7267-0.3852-0.5660.18450.2081-0.09790.43170.38060.4533-0.14190.03510.3722-0.10070.3261-1.405512.4293-17.7201
123.51642.22792.37467.3601-0.80012.50820.04440.2105-1.3146-0.63220.5465-0.59920.31740.26080.32710.5349-0.2690.25540.6324-0.24750.9165.78769.8872-19.0774
131.06770.6579-0.93681.1862-0.921.429-0.1240.3343-0.2283-0.30680.3316-0.25610.01850.14250.17810.0944-0.46810.4270.6494-0.30190.66148.941420.2698-13.6945
140.0795-0.66160.3468.4248-1.66486.98210.0258-0.1168-0.74710.90180.105-0.87080.82810.8247-0.01870.31470.0961-0.03420.2978-0.03530.3560.20156.683-6.5466
152.93671.77990.5114.5351.23533.0413-0.19330.4485-0.45940.21690.0955-0.57810.0650.25380.10570.2515-0.0874-0.01650.32850.03860.1454-1.698317.5675-11.3004
165.5115.59636.08755.6646.1616.7389-0.37380.21790.5796-0.0635-0.1040.6822-0.0533-0.33010.30050.2556-0.0725-0.01190.3236-0.06070.2023-8.153921.6022-11.3935
170.1847-0.0941-0.01130.05120.0019-0.00150.1711-0.62270.10570.5546-0.1416-0.9856-0.21590.67660.1927-0.125-0.4481-0.88180.42290.10990.42618.480338.3317-7.3996
181.70241.08121.32963.73070.67571.3699-0.0830.00820.2286-0.20030.23790.7696-0.5289-0.27-0.08020.31730.04960.11610.2230.08180.34-11.73953.0222-34.6738
191.62951.9488-0.0976.04792.21122.70910.2128-0.0360.21110.55280.0650.2997-0.2560.0174-0.19410.42640.05720.06870.2406-0.00130.2739-4.830163.9318-30.0625
204.3409-0.21090.64967.24210.83782.83970.46970.27910.16281.063-0.1152-1.70180.44841.14730.01560.49450.0148-0.17410.5925-0.02630.42783.928358.0381-28.5377
210.35840.3728-0.49740.3913-0.52840.7053-0.3459-0.81460.93960.8063-0.1133-1.4218-0.18870.8793-0.20020.88180.3625-0.17921.0364-0.46861.28456.656550.598-33.9954
220.27210.66170.01867.30820.76040.4358-0.0815-0.0321-0.01960.07940.3267-0.3982-0.4208-0.0498-0.15930.35070.04250.0850.3116-0.04480.2682-3.939657.3876-33.9055
230.177-0.0836-0.13655.73550.61131.3034-0.11260.03610.05120.19440.3486-0.4429-0.16990.2445-0.20620.23870.01190.07880.29120.01430.2794-5.640541.1165-34.3658
244.2863-1.0220.13592.47131.9361.7397-0.17170.3224-0.0910.64670.2619-0.8756-0.62760.86230.11880.7008-0.3026-0.10540.55210.05350.51257.723857.2927-12.1314
250.6984-0.16430.22331.03240.43270.2741-0.1263-0.05250.26310.761-0.2105-0.5361-0.740.2513-0.12271.2325-0.0718-0.22480.3305-0.00170.37281.789754.2723-3.4989
260.85940.09760.09245.135-0.45870.0575-0.02080.17370.62270.24340.08030.202-1.0802-0.3155-0.04841.2874-0.0828-0.02030.3570.08430.4768-5.088361.5628-11.6057
271.15741.96640.61593.3521.02970.33670.0311-0.25220.7660.1467-0.09560.9985-0.9139-0.3550.10771.21570.14270.11870.36770.00280.513-11.852658.4111-9.6968
283.33971.79294.35971.04432.34096.7723-0.018-0.18770.38680.95950.12420.5085-1.0035-0.56460.14951.4272-0.06040.43760.54430.04110.4786-14.019450.6388-3.5198
291.06370.24580.40620.56660.36820.29740.1491-0.84910.28581.2826-0.43870.014-0.4187-0.09310.00971.60980.1135-0.04810.4982-0.03220.4402-2.217863.1189-1.1986
300.57310.22250.29113.12461.17340.51440.02050.02060.25520.88710.05950.3028-1.1209-0.1428-0.04351.1963-0.082-0.14320.33530.05270.3228-3.377953.5208-7.4525
310.92320.9849-0.41823.0436-1.3751.4353-0.17250.0744-0.1820.5394-0.2459-0.5027-0.72780.32380.06950.6427-0.1552-0.13180.32940.03820.35331.405849.1626-11.8666
323.08272.3604-2.0045.26391.30915.8090.11181.17070.9388-0.4971-0.14651.5077-0.8705-0.99530.00210.32730.1036-0.08050.3979-0.02390.3735-10.574331.1645-0.6844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 78 )
5X-RAY DIFFRACTION5chain 'A' and (resid 79 through 101 )
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 131 )
8X-RAY DIFFRACTION8chain 'A' and (resid 132 through 142 )
9X-RAY DIFFRACTION9chain 'B' and (resid 18 through 26 )
10X-RAY DIFFRACTION10chain 'B' and (resid 27 through 49 )
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 68 )
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 78 )
13X-RAY DIFFRACTION13chain 'B' and (resid 79 through 84 )
14X-RAY DIFFRACTION14chain 'B' and (resid 85 through 94 )
15X-RAY DIFFRACTION15chain 'B' and (resid 95 through 120 )
16X-RAY DIFFRACTION16chain 'B' and (resid 121 through 131 )
17X-RAY DIFFRACTION17chain 'B' and (resid 132 through 141 )
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 35 )
19X-RAY DIFFRACTION19chain 'C' and (resid 36 through 59 )
20X-RAY DIFFRACTION20chain 'C' and (resid 60 through 73 )
21X-RAY DIFFRACTION21chain 'C' and (resid 74 through 84 )
22X-RAY DIFFRACTION22chain 'C' and (resid 85 through 120 )
23X-RAY DIFFRACTION23chain 'C' and (resid 121 through 144 )
24X-RAY DIFFRACTION24chain 'D' and (resid 18 through 26 )
25X-RAY DIFFRACTION25chain 'D' and (resid 27 through 49 )
26X-RAY DIFFRACTION26chain 'D' and (resid 50 through 59 )
27X-RAY DIFFRACTION27chain 'D' and (resid 60 through 78 )
28X-RAY DIFFRACTION28chain 'D' and (resid 79 through 84 )
29X-RAY DIFFRACTION29chain 'D' and (resid 85 through 94 )
30X-RAY DIFFRACTION30chain 'D' and (resid 95 through 120 )
31X-RAY DIFFRACTION31chain 'D' and (resid 121 through 131 )
32X-RAY DIFFRACTION32chain 'D' and (resid 132 through 141 )

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