2XG5

E. coli P pilus chaperone-subunit complex PapD-PapH bound to pilus biogenesis inhibitor, pilicide 5d

PDB DOI: https://doi.org/10.2210/pdb2XG5/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-30 Released: 2010-07-14
Deposition Author(s): Remaut, H., Phan, G., Buelens, F., Chorell, E., Pinkner, J.S., Edvinsson, S., Almqvist, F., Hultgren, S.J., Waksman, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.215
R-Value Work: 0.189
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Design and Synthesis of C-2 Substituted Thiazolo and Dihydrothiazolo Ring-Fused 2-Pyridones: Pilicides with Increased Antivirulence Activity.

Chorell, E., Pinkner, J.S., Phan, G., Edvinsson, S., Buelens, F., Remaut, H., Waksman, G., Hultgren, S.J., Almqvist, F.

(2010) J Med Chem 53: 5690

PubMed: 20586493 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm100470t
Primary Citation of Related Structures:
2XG4, 2XG5

PubMed Abstract:
Pilicides block pili formation by binding to pilus chaperones and blocking their function in the chaperone/usher pathway in E. coli. Various C-2 substituents were introduced on the pilicide scaffold by design and synthetic method developments. Experimental evaluation showed that proper substitution of this position affected the biological activity of the compound. Aryl substituents resulted in pilicides with significantly increased potencies as measured in pili-dependent biofilm and hemagglutination assays. The structural basis of the PapD chaperone-pilicide interactions was determined by X-ray crystallography.

Organizational Affiliation

Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden.

Macromolecule Content

Total Structure Weight: 45.04 kDa
Atom Count: 3,106
Modelled Residue Count: 364
Deposited Residue Count: 391
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHAPERONE PROTEIN PAPD	A	218	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P15319 (Escherichia coli) Explore P15319 Go to UniProtKB: P15319
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15319
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PAP FIMBRIAL MINOR PILIN PROTEIN	B	173	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P07111 (Escherichia coli) Explore P07111 Go to UniProtKB: P07111
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07111
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EC5 Query on EC5 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(2R)-2-[5-CYCLOPROPYL-6-(HYDROXYSULFANYL)-4-(NAPHTHALEN-1-YLMETHYL)-2-OXOPYRIDIN-1(2H)-YL]-3-PHENYLPROPANOIC ACID C₂₈ H₂₅ N O₄ S RDAFPBNHIKAVPQ-DEOSSOPVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EC2 Query on EC2 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	(2R,3R)-8-CYCLOPROPYL-7-(NAPHTHALEN-1-YLMETHYL)-5-OXO-2-PHENYL-2,3-DIHYDRO-5H-[1,3]THIAZOLO[3,2-A]PYRIDINE-3-CARBOXYLIC ACID C₂₈ H₂₃ N O₃ S QSGWJHVTILGJTA-IZZNHLLZSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGO Query on PGO Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	S-1,2-PROPANEDIOL C₃ H₈ O₂ DNIAPMSPPWPWGF-VKHMYHEASA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B]	G [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
EC2	Binding MOAD: 2XG5	IC50: 2.20e+4 (nM) from 1 assay(s)
EC2	PDBBind: 2XG5	IC50: 2.20e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.215
R-Value Work: 0.189
R-Value Observed: 0.191
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.61	α = 90
b = 149.83	β = 90
c = 82.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-07-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-07-14
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description