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

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Basic information

Entry
Database: PDB / ID: 9edy
TitleCrystal structure of Yck2 from Candida albicans in complex with inhibitor 2b: 6-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-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


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: 2.3 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)36,0395
Polymers35,6251
Non-polymers4144
Water1,35175
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)91.488, 91.488, 119.170
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 / Yck2


Mass: 35625.461 Da / Num. of mol.: 1 / Fragment: residues 35-345
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-A1BIN / 6-fluoro-2-(4-fluorophenyl)-3-(pyridin-4-yl)pyrazolo[1,5-a]pyridine


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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris pH 8, 0.025 M 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: Apr 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18077 Å / Relative weight: 1
ReflectionResolution: 2.3→47.64 Å / Num. obs: 16511 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 58.56 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.09 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.341 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1230 / CC1/2: 0.321 / Rpim(I) all: 1.138 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.62 Å / SU ML: 0.3475 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 34.7678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 976 5.92 %RANDOM
Rwork0.2024 15505 --
obs0.2046 16481 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 26 75 2561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212545
X-RAY DIFFRACTIONf_angle_d0.47623441
X-RAY DIFFRACTIONf_chiral_restr0.0379356
X-RAY DIFFRACTIONf_plane_restr0.0039451
X-RAY DIFFRACTIONf_dihedral_angle_d14.3578973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.37011150.34142195X-RAY DIFFRACTION98.47
2.42-2.570.32361210.29882236X-RAY DIFFRACTION99.54
2.57-2.770.30611470.27212222X-RAY DIFFRACTION99.71
2.77-3.050.30371320.252217X-RAY DIFFRACTION99.7
3.05-3.490.27231570.2182223X-RAY DIFFRACTION99.96
3.49-4.40.20731530.1612209X-RAY DIFFRACTION100
4.4-47.620.19521510.16622203X-RAY DIFFRACTION99.87
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)
18.96361987614-0.3476065493042.802822488175.292178984730.4868275660047.86619846087-0.2350832936850.741920417647-0.271085141173-1.57021250110.4221718198430.0738155425349-0.154949619547-0.507263381795-0.2572677500190.7712443992130.0017314264824-0.08499430899530.4325285948850.07759879536460.63963067516926.2260571676-7.73660798616-16.721853526
23.592949192120.3713040775010.09817417159294.24355410839-0.2957244190171.93754987248-0.0871969163559-0.08941736156930.9142202622480.06746509957860.04001989826980.103868896781-0.328964934313-0.3327291076310.05402013646050.2794514921510.0433366833906-0.009693916048880.398625768114-0.04066575183680.5509885944717.5787321818-21.1143547966-7.10190065468
34.00640595595-0.8409424949520.7001281589693.79169903934-0.08697867191633.501476513710.05029838955060.074029277251-0.234056709875-0.14282144767-0.06899650385770.2195747151370.136740086634-0.3318678411310.00675339383110.25550240483-0.0937376200920.02642325246090.386304736235-0.004032445778330.32503127977414.3116564613-36.9295096648-9.49077620905
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 35 through 83 )35 - 831 - 49
22chain 'A' and (resid 84 through 213 )84 - 21350 - 179
33chain 'A' and (resid 214 through 339 )214 - 339180 - 305

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