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- PDB-9h4d: Crystal structure of IL-17A in complex with compound 18 -

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Basic information

Entry
Database: PDB / ID: 9h4d
TitleCrystal structure of IL-17A in complex with compound 18
ComponentsInterleukin-17A
KeywordsCYTOKINE / Inhibitor / Complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.117 Å
AuthorsRondeau, J.M. / Lehmann, S. / Scheufler, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2025
Title: Thiazole-Based IL-17 Inhibitors Discovered by Scaffold Morphing.
Authors: Velcicky, J. / Ngo, E. / Bauer, M.R. / Meyer, A. / Schlapbach, A. / Racine, S. / Orain, D. / Pflieger, D. / Teixeira-Fouchard, S. / Dubois, C. / Goetz, A. / Steiner, R. / Palmieri, M. / ...Authors: Velcicky, J. / Ngo, E. / Bauer, M.R. / Meyer, A. / Schlapbach, A. / Racine, S. / Orain, D. / Pflieger, D. / Teixeira-Fouchard, S. / Dubois, C. / Goetz, A. / Steiner, R. / Palmieri, M. / Bussenault, A. / Stringer, R. / Larger, P. / Riek, S. / Schmutz, P. / Lehmann, S. / Scheufler, C. / Rondeau, J.M. / Burkhart, C. / Knoepfel, T. / Gommermann, N.
History
DepositionOct 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _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: Interleukin-17A
B: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0363
Polymers28,5022
Non-polymers5341
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-21 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.601, 85.42, 120.161
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 14251.060 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16552
#2: Chemical ChemComp-A1ISH / (E)-N-[(1S)-1-[4,4-bis(fluoranyl)cyclohexyl]-2-oxidanylidene-2-[[5-[(2-oxidanylidene-3H-benzimidazol-1-yl)methyl]-1,3-thiazol-2-yl]amino]ethyl]-3-cyclopropyl-2-fluoranyl-prop-2-enamide


Mass: 533.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26F3N5O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.91 Å3/Da / Density % sol: 57.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1M citric acid pH 5.5 10% PEG 10000 12% iso-propanol 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000015 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000015 Å / Relative weight: 1
ReflectionResolution: 2.117→51.525 Å / Num. obs: 18490 / % possible obs: 95.6 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.016 / Rrim(I) all: 0.05 / Net I/σ(I): 17.5
Reflection shellResolution: 2.117→2.153 Å / Redundancy: 10.4 % / Rmerge(I) obs: 3.904 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 970 / CC1/2: 0.394 / Rpim(I) all: 1.252 / Rrim(I) all: 4.104 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.117→51.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 933 -RANDOM
Rwork0.2368 ---
obs0.237 18408 95.2 %-
Displacement parametersBiso mean: 83.28 Å2
Baniso -1Baniso -2Baniso -3
1-5.9833 Å20 Å20 Å2
2---6.2485 Å20 Å2
3---0.2652 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.117→51.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1600 0 37 28 1665
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081686HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.962305HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d567SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes282HARMONIC5
X-RAY DIFFRACTIONt_it1686HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion215SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1071SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion12.47
LS refinement shellResolution: 2.12→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3529 22 -
Rwork0.3831 --
obs0.3814 401 88.15 %
Refinement TLS params.

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)
16.8942-1.4129-5.29240.81621.32495.40310.3975-0.1801-0.2943-0.1801-0.1387-0.278-0.2943-0.278-0.2588-0.0393-0.01460.0309-0.01230.0915-0.0557-20.6512-8.2032-11.3427
27.0148-0.2771-5.82080.39750.47165.3844-0.4496-0.02540.6693-0.0254-0.0152-0.21020.6693-0.21020.4647-0.0031-0.0370.056-0.00320.0308-0.0755-20.4506-20.5268-11.0598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A42 - 151
2X-RAY DIFFRACTION1{ A|* }A201
3X-RAY DIFFRACTION2{ B|* }B42 - 150

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