4FW6 | pdb_00004fw6

Crystal Structure of the LpxC in complex with N-[(2S,3R)-3-HYDROXY-1-(HYDROXYAMINO)-1-OXOBUTAN-2-YL]-4-(PHENYLETHYNYL)BENZAMIDE inhibitor

PDB DOI: https://doi.org/10.2210/pdb4FW6/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-06-29 Released: 2013-05-15
Deposition Author(s): Kang, Y.N., Stuckey, J.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.197 (Depositor), 0.195 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the LpxC

Kang, Y.N., Stuckey, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 137.2 kDa
Atom Count: 10,394
Modeled Residue Count: 1,204
Deposited Residue Count: 1,208
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase	A, B, C, D	302	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: envA, lpxC, PA4406 EC: 3.5.1 (PDB Primary Data), 3.5.1.108 (UniProt)
UniProt
Find proteins for P47205 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P47205 Go to UniProtKB: P47205
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47205
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L59 Query on L59 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain EA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D]	EA [auth D], F [auth A], O [auth B], X [auth C]	N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]-4-(phenylethynyl)benzamide C₁₉ H₁₈ N₂ O₄ SFYISUPIFOZKLQ-DYVFJYSZSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain X [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], T [auth B], U [auth B], V [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain H [auth A] SDF format, chain GA [auth D] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] FA [auth D] G [auth A] GA [auth D] H [auth A] AA [auth C], FA [auth D], G [auth A], GA [auth D], H [auth A], P [auth B], Q [auth B], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain N [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D]	DA [auth D], E [auth A], N [auth B], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain E [auth A] Focus chain N [auth B] Focus chain W [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth D] SDF format, chain I [auth A] SDF format, chain HA [auth D] SDF format, chain CA [auth C] SDF format, chain BA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C]	BA [auth C] CA [auth C] HA [auth D] I [auth A] IA [auth D] BA [auth C], CA [auth C], HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], R [auth B], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BA [auth C] Focus chain CA [auth C] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain JA [auth D] MOL2 format, chain JA [auth D] mmCIF format, chain JA [auth D]	JA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain JA [auth D] Interactions & Density Focus chain JA [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
L59	BindingDB: 4FW6	Kd: 20.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free: 0.197 (Depositor), 0.195 (DCC)
R-Value Work: 0.163 (Depositor), 0.160 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.477	α = 90
b = 89.63	β = 90.08
c = 169.997	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MD2	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-15

Deposition Author(s):

Kang, Y.N.

Stuckey, J.A.

Revision History (Full details and data files)

Version 1.0: 2013-05-15
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations