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- PDB-9h4o: Crystal structure of IL-17A in complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 9h4o
TitleCrystal structure of IL-17A in complex with compound 11
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 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 21, 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
C: Interleukin-17A
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,78413
Polymers57,0044
Non-polymers1,7799
Water1,35175
1
A: Interleukin-17A
B: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5368
Polymers28,5022
Non-polymers1,0346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-96 kcal/mol
Surface area12860 Å2
MethodPISA
2
C: Interleukin-17A
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2485
Polymers28,5022
Non-polymers7463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-58 kcal/mol
Surface area10820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.187, 59.064, 71.185
Angle α, β, γ (deg.)90, 101.82, 90
Int Tables number4
Space group name H-MP1211

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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.: 4
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1ISG / (E)-N-[(1S)-1-[4,4-bis(fluoranyl)cyclohexyl]-2-oxidanylidene-2-[[5-[[(4S)-2-oxidanylidene-4-(trifluoromethyl)imidazolidin-1-yl]methyl]-1,3-thiazol-2-yl]amino]ethyl]-3-cyclopropyl-2-fluoranyl-prop-2-enamide


Mass: 553.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25F6N5O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M bis-tris pH 5.5 0.2 M lithium sulfate monohydrate 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000026 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000026 Å / Relative weight: 1
ReflectionResolution: 1.966→45.054 Å / Num. obs: 33332 / % possible obs: 93.7 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.026 / Rrim(I) all: 0.059 / Net I/σ(I): 12.3
Reflection shellResolution: 1.966→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 2.585 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1744 / CC1/2: 0.337 / Rpim(I) all: 1.335 / Rrim(I) all: 2.919 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→25.67 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.214 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.174 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1570 -RANDOM
Rwork0.2359 ---
obs0.2372 31323 92.7 %-
Displacement parametersBiso mean: 64.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.8494 Å20 Å25.7712 Å2
2---4.61 Å20 Å2
3---8.4594 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2→25.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 109 75 3454
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083469HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994752HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1152SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes578HARMONIC5
X-RAY DIFFRACTIONt_it3469HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2386SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion12.92
LS refinement shellResolution: 2→2.01 Å
RfactorNum. reflection% reflection
Rfree0.3693 41 -
Rwork0.4097 --
obs0.407 627 91.4 %
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)
10.6246-0.1210.99230.4426-1.18923.87720.0559-0.0882-0.0903-0.0882-0.05590.2056-0.09030.20560.00010.07860.01430.0158-0.07570.0015-0.014-19.07548.7923-33.3129
20.35720.19090.97740.44610.57325.48230.0824-0.11460.1935-0.11460.0128-0.31110.1935-0.3111-0.09520.07650.0072-0.0301-0.08990.0091-0.0107-26.3808-0.234-31.5466
31.0021-0.20252.37480.20920.228613.86030.0947-0.04-0.3624-0.040.30441.0979-0.36241.0979-0.3991-0.0958-0.08530.04420.2101-0.1617-0.18698.68766.1482-47.8881
40.1611-0.06931.13510.09020.101416.8340.08190.03211.01430.03210.2382-0.17941.0143-0.1794-0.32010.0666-0.0079-0.0158-0.02920.0061-0.1153-2.63230.0862-45.5236
518.73750.5305-4.242816.6309-0.97679.0927-0.311-0.42040.0757-0.4204-0.0257-0.30850.0757-0.30850.33670.20030.163-0.0911-0.12880.0054-0.1405-22.90324.1165-24.9657
612.6669-3.16760.701516.63095.28399.88050.36550.40420.55960.4042-0.47440.38690.55960.38690.1089-0.0208-0.0033-0.0070.0475-0.07-0.11092.40514.8015-53.375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|42-155 }A42 - 155
2X-RAY DIFFRACTION2{ B|40-155 }B40 - 155
3X-RAY DIFFRACTION3{ C|42-149 }C42 - 149
4X-RAY DIFFRACTION4{ D|42-152 }D42 - 152
5X-RAY DIFFRACTION5{ B|201 }B201
6X-RAY DIFFRACTION6{ C|201 }C201

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