3U6K | pdb_00003u6k

Ef-tu (escherichia coli) in complex with nvp-ldk733

PDB DOI: https://doi.org/10.2210/pdb3U6K/pdb

Classification: translation factor/antibiotic
Organism(s): Escherichia coli K-12, Planobispora rosea
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-12 Released: 2012-02-08
Deposition Author(s): Palestrant, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.298 (Depositor), 0.296 (DCC)
R-Value Work:
0.224 (Depositor), 0.222 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Antibacterial optimization of 4-aminothiazolyl analogues of the natural product GE2270 A: identification of the cycloalkylcarboxylic acids.

LaMarche, M.J., Leeds, J.A., Amaral, K., Brewer, J.T., Bushell, S.M., Dewhurst, J.M., Dzink-Fox, J., Gangl, E., Goldovitz, J., Jain, A., Mullin, S., Neckermann, G., Osborne, C., Palestrant, D., Patane, M.A., Rann, E.M., Sachdeva, M., Shao, J., Tiamfook, S., Whitehead, L., Yu, D.

(2011) J Med Chem 54: 8099-8109

PubMed: 21999529 Search on PubMed
DOI: https://doi.org/10.1021/jm200938f
Primary Citation Related Structures:
3U6B, 3U6K

PubMed Abstract:
4-Aminothiazolyl analogues of the antibiotic natural product GE2270 A (1) were designed, synthesized, and optimized for their activity against Gram positive bacterial infections. Optimization efforts focused on improving the physicochemical properties (e.g., aqueous solubility and chemical stability) of the 4-aminothiazolyl natural product template while improving the in vitro and in vivo antibacterial activity. Structure-activity relationships were defined, and the solubility and efficacy profiles were improved over those of previous analogues and 1. These studies identified novel, potent, soluble, and efficacious elongation factor-Tu inhibitors, which bear cycloalkylcarboxylic acid side chains, and culminated in the selection of development candidates amide 48 and urethane 58.

Organizational Affiliation

Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States. matthew.lamarche@novartis.com

Macromolecule Content

Total Structure Weight: 90.47 kDa
Atom Count: 6,311
Modeled Residue Count: 796
Deposited Residue Count: 812
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongation factor Tu 1	A, B	394	Escherichia coli K-12	Mutation(s): 0 Gene Names: tufA, b3339, JW3301 EC: 3.6.5.3
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12)) Explore P0CE47 Go to UniProtKB: P0CE47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CE47
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thiocillin GE2270 analogue NVP-LDK733	C, D	12	Planobispora rosea	Mutation(s): 0
UniProt
Find proteins for Q7M0J8 (Planobispora rosea) Explore Q7M0J8 Go to UniProtKB: Q7M0J8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7M0J8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]

Modified Residues 6 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
9BB Query on 9BB	C, D	PEPTIDE-LIKE	C₁₀ H₁₆ N₂ O₄ S		--
BB6 Query on BB6	C, D	PEPTIDE LINKING	C₄ H₇ N O₂ S		CYS
BB7 Query on BB7	C, D	PEPTIDE LINKING	C₅ H₉ N O₃ S		CYS
BB8 Query on BB8	C, D	L-PEPTIDE LINKING	C₉ H₁₁ N O₃		PHE
BB9 Query on BB9	C, D	PEPTIDE LINKING	C₃ H₅ N O₂ S		CYS
MEN Query on MEN	C, D	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN
MH6 Query on MH6	C, D	PEPTIDE LINKING	C₃ H₅ N O₃		SER

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001073 Query on PRD_001073	C, D	Thiocillin GE2270 analogue NVP-LDK733	Thiopeptide / Antibiotic		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.298 (Depositor), 0.296 (DCC)
R-Value Work: 0.224 (Depositor), 0.222 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.372	α = 90
b = 82.216	β = 90
c = 129.9	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-08

Deposition Author(s):

Palestrant, D.J.

Revision History (Full details and data files)

Version 1.0: 2012-02-08
Type: Initial release
Version 1.1: 2012-04-18
Changes: Structure summary
Version 1.2: 2012-12-12
Changes: Other
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary