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

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Basic information

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


filamentous growth / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding
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: 2.42 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)35,7473
Polymers35,3971
Non-polymers3502
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.990, 91.990, 117.960
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: FOB64_000203 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR
References: UniProt: A0A8H6C375, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1BIQ / 2-(4-fluorophenyl)-3-(pyridin-4-yl)imidazo[1,2-a]pyridine-7-carbonitrile


Mass: 314.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H11FN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 2.71 Å3/Da / Density % sol: 54.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
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: 08ID-1 / Wavelength: 1.18077 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18077 Å / Relative weight: 1
ReflectionResolution: 2.42→29.18 Å / Num. obs: 14204 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 81.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.032 / Net I/σ(I): 15.1
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 10.2 % / Rmerge(I) obs: 2.903 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1065 / CC1/2: 0.368 / Rpim(I) all: 1.437 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→29.18 Å / SU ML: 0.3968 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 37.0902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 625 4.4 %RANDOM
Rwork0.2372 13577 --
obs0.2393 14202 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 118.9 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 25 0 2494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312555
X-RAY DIFFRACTIONf_angle_d0.58673453
X-RAY DIFFRACTIONf_chiral_restr0.041358
X-RAY DIFFRACTIONf_plane_restr0.0047451
X-RAY DIFFRACTIONf_dihedral_angle_d16.071956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.660.49012000.42893350X-RAY DIFFRACTION99.92
2.66-3.050.32051550.29863413X-RAY DIFFRACTION100
3.05-3.840.28281450.28193397X-RAY DIFFRACTION100
3.84-29.180.271250.20253417X-RAY DIFFRACTION99.97
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)
14.374146493041.763451807820.6402846043564.73354253764-2.326727931623.87953333166-0.1772676113060.01992219509650.845382917742-0.9170642269120.118327890520.691101938335-0.0555652252136-0.6353683961980.09692810325421.145668892830.192500328129-0.07635463861280.8788762146480.0186336684281.3283745433223.4138084743-8.59345490307-14.3045397122
26.65236164089-0.123325228291-0.7156481690558.248996426960.4971050117860.06585998740760.1518381894090.1556244662890.5626827381740.0443184109002-0.1449736346090.220653997714-0.267705795545-0.374526296340.01804803451890.6784714025110.064818696390.02865902260750.8545184688270.02292478391770.54625157527518.221910784-22.2076330926-6.82146110628
35.1978097992-0.1275406662810.5275081273047.826541756880.3181689498574.642272360470.0748488683580.45766418203-0.547023914202-0.166680867125-0.3805994531040.2477570947580.1514109041-0.6312855620620.3033934939610.578904113574-0.08868046205620.002996689352411.003515028920.02678129419340.64492826523714.7301200051-36.6032855149-10.1872893216
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 93 )37 - 931 - 57
22chain 'A' and (resid 94 through 209 )94 - 20958 - 173
33chain 'A' and (resid 210 through 342 )210 - 342174 - 306

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