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- PDB-9yic: Crystal structure of human IL-17A in complex with Compound 1 -

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Basic information

Entry
Database: PDB / ID: 9yic
TitleCrystal structure of human IL-17A in complex with Compound 1
ComponentsInterleukin-17A
KeywordsCYTOKINE / dimer / cysteine-knot
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / interleukin-17A-mediated signaling pathway / cell death / 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 / interleukin-17A-mediated signaling pathway / cell death / 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 / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory response / protein heterodimerization activity / innate immune response / external side of plasma membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsArmstrong, A.A. / Milligan, C.M. / Luo, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: A Novel Small Molecule Allosteric Inhibitor of IL-17A From a DNA-Encoded Library
Authors: Milla, M. / Blevitt, J. / Goldberg, S. / Armstrong, A. / de Laurier, K. / Herman, K. / Liu, A. / Luna, R. / Milligan, C. / Patrick, A. / Steele, R. / Bembenek, S. / Centrella, P. / Clark, M. ...Authors: Milla, M. / Blevitt, J. / Goldberg, S. / Armstrong, A. / de Laurier, K. / Herman, K. / Liu, A. / Luna, R. / Milligan, C. / Patrick, A. / Steele, R. / Bembenek, S. / Centrella, P. / Clark, M. / Cuozzo, J. / Disch, J. / Domingo, D. / Hunt, A. / Hupp, C. / Jackson, P. / Keefe, A. / Luo, J. / Mirzadegan, T. / Nelen, M. / Resnicow, D. / Sigel, E. / Soutter, H. / Troast, D. / Xue, X. / Yi, F. / Zhang, Y. / Edwards, J. / Lumb, K.
History
DepositionOct 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)57,8856
Polymers56,8404
Non-polymers1,0452
Water1267
1
A: Interleukin-17A
B: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9433
Polymers28,4202
Non-polymers5231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-28 kcal/mol
Surface area11140 Å2
MethodPISA
2
C: Interleukin-17A
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9433
Polymers28,4202
Non-polymers5231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-28 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.930, 122.690, 52.840
Angle α, β, γ (deg.)90.00, 93.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14209.944 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-A1CXF / (3S)-N-[(3-{[(1S)-2-anilino-1-cyclohexyl-2-oxoethyl]carbamoyl}phenyl)methyl]-2,2-dimethylthiomorpholine-3-carboxamide


Mass: 522.702 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H38N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.78 Å3/Da / Density % sol: 74.26 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion
Details: 13.7% PEG 6000, 0.1M sodium malonate pH 4.0, 1.3% methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→49.5 Å / Num. obs: 18428 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.082 / Net I/σ(I): 15.88
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.15-3.230.87213390.6881.0281
3.23-3.320.69113380.7530.8171
3.32-3.420.59112740.7790.6991
3.42-3.520.39512760.8930.4691
3.52-3.640.28111740.9230.3381
3.64-3.770.21911920.9570.261
3.77-3.910.15211380.9710.1821
3.91-4.070.12211080.9810.1451
4.07-4.250.07810290.9940.0921
4.25-4.450.06310040.9960.0751
4.45-4.70.0489550.9970.0571
4.7-4.980.0469080.9970.0551
4.98-5.320.0448430.9980.0531
5.32-5.750.0437930.9980.0511
5.75-6.30.0417200.9970.0481
6.3-7.040.0366730.9980.0421
7.04-8.130.0285760.9990.0331
8.13-9.960.0184880.9990.0221
9.96-14.090.0163890.9990.0191
14.09-49.50.01221110.0141

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev_1428refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→35.533 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 917 4.98 %
Rwork0.215 --
obs0.2163 18402 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→35.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 74 7 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023408
X-RAY DIFFRACTIONf_angle_d0.6034652
X-RAY DIFFRACTIONf_dihedral_angle_d12.0381244
X-RAY DIFFRACTIONf_chiral_restr0.023507
X-RAY DIFFRACTIONf_plane_restr0.003605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.3160.42211500.35052468X-RAY DIFFRACTION99
3.316-3.52360.33381380.29682480X-RAY DIFFRACTION99
3.5236-3.79530.28261140.24162498X-RAY DIFFRACTION100
3.7953-4.17670.24771590.19972465X-RAY DIFFRACTION100
4.1767-4.77990.17741110.16442533X-RAY DIFFRACTION99
4.7799-6.01740.23481380.19852500X-RAY DIFFRACTION100
6.0174-35.5330.21411070.2242541X-RAY DIFFRACTION99

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