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- PDB-8cn2: Pa.FabF-C164Q in complex with N-isobutyl-1H-pyrazole-3-carboxamide -

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Basic information

Entry
Database: PDB / ID: 8cn2
TitlePa.FabF-C164Q in complex with N-isobutyl-1H-pyrazole-3-carboxamide
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / FabF / complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
Chem-V60 / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsGeorgiou, C. / Brenk, R.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway273588 Norway
Citation
Journal: Eur.J.Med.Chem. / Year: 2025
Title: Towards new antibiotics: P. aeruginosa FabF ligands discovered by crystallographic fragment screening followed by hit expansion.
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhins'ky, V. / Haug, B.E. / Mainkar, P.S. / Brenk, R.
#1: Journal: Chemrxiv / Year: 2023
Title: New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhinsky, V. / Haug, B.E. / Mainkar, P. / Brenk, R.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,69926
Polymers86,6452
Non-polymers2,05324
Water7,566420
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10100 Å2
ΔGint-13 kcal/mol
Surface area24950 Å2
Unit cell
Length a, b, c (Å)70.881, 64.779, 84.298
Angle α, β, γ (deg.)90.00, 102.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43322.715 Da / Num. of mol.: 2 / Mutation: C164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-V60 / ~{N}-(2-methylpropyl)-1~{H}-pyrazole-3-carboxamide


Mass: 167.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.18 Å3/Da / Density % sol: 43.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.20M ammonium formate and 31.2% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.878→82.57 Å / Num. obs: 60857 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.979 / Rmerge(I) obs: 0.297 / Net I/σ(I): 7.9
Reflection shellResolution: 1.878→1.911 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3032 / CC1/2: 0.628 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→69.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.45 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20141 2983 4.9 %RANDOM
Rwork0.16821 ---
obs0.16986 57705 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å2-0 Å20.67 Å2
2---0.87 Å2-0 Å2
3----0.46 Å2
Refinement stepCycle: 1 / Resolution: 1.88→69.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 112 420 6606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136372
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156091
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.6328613
X-RAY DIFFRACTIONr_angle_other_deg1.441.57513954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.075853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64820.456329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36915995
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0031559
X-RAY DIFFRACTIONr_chiral_restr0.0810.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027967
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021497
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7392.243332
X-RAY DIFFRACTIONr_mcbond_other1.7392.2393331
X-RAY DIFFRACTIONr_mcangle_it2.4393.3534172
X-RAY DIFFRACTIONr_mcangle_other2.4393.3544173
X-RAY DIFFRACTIONr_scbond_it2.9452.7413040
X-RAY DIFFRACTIONr_scbond_other2.9452.7423041
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4543.9384428
X-RAY DIFFRACTIONr_long_range_B_refined5.68628.597224
X-RAY DIFFRACTIONr_long_range_B_other5.6228.4327166
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.927 Å
RfactorNum. reflection% reflection
Rfree0.277 213 -
Rwork0.248 4245 -
obs--98.87 %

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