9L3S | pdb_00009l3s

Staphylococcus aureus lipase-Penfluridol complex (in space)

PDB DOI: https://doi.org/10.2210/pdb9L3S/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-12-19 Released: 2025-04-30
Deposition Author(s): Kitadokoro, J., Hirokawa, T., Kamo, M., Furubayasi, N., Inaka, K., Kamitani, S., Kitadokoro, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.227 (Depositor), 0.226 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural analysis shows the mode of inhibition for Staphylococcus aureus lipase by antipsychotic penfluridol.

Kitadokoro, J., Hirokawa, T., Kamo, M., Furubayashi, N., Okuno, Y., Hikima, T., Yamamoto, M., Inaka, K., Maenaka, K., Kamitani, S., Kitadokoro, K.

(2025) Sci Rep 15: 11876-11876

PubMed: 40229318 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41598-025-94981-4
Primary Citation Related Structures:
9L3C, 9L3S

PubMed Abstract:
It is now well-established that Staphylococcus aureus can produce a range of toxin proteins, resulting in a spectrum of pathological conditions when it infects individuals with pre-existing medical conditions or immunocompromised. Among these, MRSA is one of the most prominent antimicrobial-resistant organisms and a significant cause of mortality in many patients. It has been demonstrated that Staphylococcus aureus lipase (SAL) is a vital factor in the proliferation of this bacterium. A combination of in silico screening and X-ray crystallography was employed to analyze inhibitors of SAL, and the results were highly significant. In silico screening identified a number of compounds, and the enzyme activity assay demonstrated that the antipsychotic drug penfluridol exhibited potent inhibitory activity against SAL. We have conducted co-crystallization of penfluridol and SAL on the ground and in space. The resulting co-crystals were subjected to data measurement using the synchrotron radiation facility at SPring-8, and the complex structure was determined. The crystal structure of the penfluridol-SAL complex was determined at 2.2 Å resolution, thereby providing the structural basis for developing new anti-infective agents that inhibit the growth of Staphylococcus aureus. These findings are anticipated to facilitate the development of compounds with potent inhibitory activity.

Organizational Affiliation

Faculty of Molecular Chemistry and Engineering, Graduate School of Science and Technology, Kyoto Institute of Technology, Hashigami-cho, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.

Macromolecule Content

Total Structure Weight: 95.07 kDa
Atom Count: 6,269
Modeled Residue Count: 764
Deposited Residue Count: 816
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipase 2	A, B	408	Staphylococcus aureus	Mutation(s): 0 Gene Names: lip, BN1321_80040 EC: 3.1.1.3
UniProt
Find proteins for Q2G155 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G155 Go to UniProtKB: Q2G155
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2G155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1L60 Query on A1L60 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain H [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain H [auth A]	H [auth A], Y [auth B]	Penfluridol C₂₈ H₂₇ Cl F₅ N O MDLAAYDRRZXJIF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Y [auth B] Interactions & Density Focus chain H [auth A] Focus chain Y [auth B]
11A Query on 11A Download:Ideal Coordinates CCD File SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	W [auth B], X [auth B]	UNDECANOIC ACID C₁₁ H₂₂ O₂ ZDPHROOEEOARMN-UHFFFAOYSA-N		Interactions Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain W [auth B] Focus chain X [auth B]
OCA Query on OCA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth A] MOL2 format, chain C [auth A] MOL2 format, chain O [auth A] mmCIF format, chain C [auth A] mmCIF format, chain O [auth A]	C [auth A], O [auth A]	OCTANOIC ACID (CAPRYLIC ACID) C₈ H₁₆ O₂ WWZKQHOCKIZLMA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth A] Interactions & Density Focus chain C [auth A] Focus chain O [auth A]
6NA Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain EA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain EA [auth B]	EA [auth B], N [auth A]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Focus chain N [auth A] Interactions & Density Focus chain EA [auth B] Focus chain N [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth B] MOL2 format, chain F [auth A] MOL2 format, chain U [auth B] mmCIF format, chain F [auth A] mmCIF format, chain U [auth B]	F [auth A], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain U [auth B] Interactions & Density Focus chain F [auth A] Focus chain U [auth B]
BUA Query on BUA Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain T [auth B] SDF format, chain S [auth A] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain V [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain V [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B], HA [auth B], S [auth A], T [auth B], V [auth B]	butanoic acid C₄ H₈ O₂ FERIUCNNQQJTOY-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain S [auth A] Focus chain T [auth B] Focus chain V [auth B] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain S [auth A] Focus chain T [auth B] Focus chain V [auth B]
PPI Query on PPI Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A]	BA [auth B], D [auth A], E [auth A], G [auth A], K [auth A]	PROPANOIC ACID C₃ H₆ O₂ XBDQKXXYIPTUBI-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A] Interactions & Density Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain L [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain L [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain L [auth A]	CA [auth B], L [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain L [auth A] Interactions & Density Focus chain CA [auth B] Focus chain L [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain Z [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	AA [auth B], I [auth A], J [auth A], Z [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain Z [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain M [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain M [auth A]	DA [auth B], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain M [auth A] Interactions & Density Focus chain DA [auth B] Focus chain M [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	FA [auth B], P [auth A], Q [auth A], R [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain FA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain FA [auth B] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]