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- PDB-9edw: Crystal structure of Yck2 from Candida albicans in complex with i... -

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Basic information

Entry
Database: PDB / ID: 9edw
TitleCrystal structure of Yck2 from Candida albicans in complex with inhibitor 1f: 7-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)imidazo[1,2-a]pyridine
ComponentsNon-specific serine/threonine protein kinase
KeywordsTRANSFERASE/INHIBITOR / YCK2 / KINASE / KINASE INHIBITOR / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL BIOLOY OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / TRANSFERASE / TRANSFERASE-INHIBITOR complex / Center for Structural Biology of Infectious Diseases / CSBID
Function / homology
Function and homology information


regulation of cell wall organization or biogenesis / regulation of filamentous growth / hyphal growth / regulation of single-species biofilm formation / biological process involved in interaction with host / cellular response to stress / endocytosis / extracellular vesicle / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity ...regulation of cell wall organization or biogenesis / regulation of filamentous growth / hyphal growth / regulation of single-species biofilm formation / biological process involved in interaction with host / cellular response to stress / endocytosis / extracellular vesicle / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / signal transduction / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsStogios, P.J. / Whitesell, L. / Cowen, L.E. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure-guided optimization of small molecules targeting Yck2 as a strategy to combat Candida albicans.
Authors: Puumala, E. / Nandakumar, M. / Yiu, B. / Stogios, P.J. / Strickland, B.G. / Zarnowski, R. / Wang, X. / Williams, N.S. / Savchenko, A. / Andes, D.R. / Robbins, N. / Whitesell, L. / Willson, T.M. / Cowen, L.E.
History
DepositionNov 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7403
Polymers35,3971
Non-polymers3432
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.175, 92.175, 118.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Non-specific serine/threonine protein kinase


Mass: 35397.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: YCK2, CAALFM_C305650WA, orf19.7001 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: A0A1D8PKB4, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BIP / 7-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)imidazo[1,2-a]pyridine


Mass: 307.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H11F2N3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: 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 modificationN

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8, 25 mM Magnesium chloride, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.18077 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18077 Å / Relative weight: 1
ReflectionResolution: 2.33→66.14 Å / Num. obs: 15999 / % possible obs: 99.9 % / Redundancy: 8.9 % / Biso Wilson estimate: 45.67 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.05 / Net I/σ(I): 8
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 7.4 % / Rmerge(I) obs: 2.113 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1164 / CC1/2: 0.265 / Rpim(I) all: 1.277 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→66.14 Å / SU ML: 0.4703 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 48.8243
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 822 5.15 %RANDOM
Rwork0.269 15132 --
obs0.2703 15954 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.91 Å2
Refinement stepCycle: LAST / Resolution: 2.33→66.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 24 7 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262554
X-RAY DIFFRACTIONf_angle_d0.55333452
X-RAY DIFFRACTIONf_chiral_restr0.0413358
X-RAY DIFFRACTIONf_plane_restr0.0043451
X-RAY DIFFRACTIONf_dihedral_angle_d15.1127978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.480.44881510.43222497X-RAY DIFFRACTION99.44
2.48-2.670.40771370.39392516X-RAY DIFFRACTION99.36
2.67-2.940.38061020.35542543X-RAY DIFFRACTION99.59
2.94-3.360.33231270.35332544X-RAY DIFFRACTION99.78
3.36-4.230.29981420.25692520X-RAY DIFFRACTION99.92
4.24-66.140.24961630.21662512X-RAY DIFFRACTION99.89
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)
16.30739217088-3.044531904883.597488847284.040279647291.04945705176.101413590960.498035712066-0.56369653287-0.2763555704590.2795941323480.2226148030510.2475171332811.07326369340.349355569076-0.5863205314290.482609399806-0.00625538909544-0.06168854347230.878897786393-0.1277267797141.19711418296-19.93157861418.595680973116.5309904006
25.27072551181.31542881587-0.7017533517715.88479047251-0.2606452335891.31361650504-0.02168848924190.002175478364650.00185781116466-0.419689632895-0.0091347416468-0.9455493145390.2849935531270.3519525978320.05761186978930.4776411615060.102901016081-0.01300076154450.427005298484-0.009916058861210.569275410678-27.20332929164.694505274527.29416882239
36.592018215890.671751397956-0.4311652293035.14535493768-0.113495393313.29166532978-0.497526914139-0.360267154005-0.346658663915-0.2426339450080.2344238030540.2998757906340.4782527277740.3442352123640.06651597796420.5936754883190.149615172527-0.03578724514270.2891250001330.005543747214840.346240857949-39.4676635938-5.5866552670910.1411397301
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 83 )37 - 831 - 47
22chain 'A' and (resid 84 through 213 )84 - 21348 - 177
33chain 'A' and (resid 214 through 342 )214 - 342178 - 306

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