[English] 日本語
Yorodumi
- PDB-9ery: Co-crystal strucutre of PD-L1 with low molecular weight inhibitor -

+
Open data


ID or keywords:

Loading...

-
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


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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more