4B11 | pdb_00004b11

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 13)

PDB DOI: https://doi.org/10.2210/pdb4B11/pdb

Classification: TRANSFERASE
Organism(s): Plasmodium vivax
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-07-06 Released: 2012-10-17
Deposition Author(s): Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.219 (Depositor), 0.218 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Anti-Malarial Drug Discovery.

Yu, Z., Brannigan, J.A., Moss, D.K., Brzozowski, A.M., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

(2012) J Med Chem 55: 8879

PubMed: 23035716 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm301160h
Primary Citation Related Structures:
4B10, 4B11, 4B12, 4B13, 4B14

PubMed Abstract:
Design of inhibitors for N-myristoyltransferase (NMT), an enzyme responsible for protein trafficking in Plasmodium falciparum , the most lethal species of parasites that cause malaria, is described. Chemistry-driven optimization of compound 1 from a focused NMT inhibitor library led to the identification of two early lead compounds 4 and 25, which showed good enzyme and cellular potency and excellent selectivity over human NMT. These molecules provide a valuable starting point for further development.

Organizational Affiliation

Department of Chemistry, Imperial College London, London SW7 2AZ, UK.

Macromolecule Content

Total Structure Weight: 140 kDa
Atom Count: 11,552
Modeled Residue Count: 1,144
Deposited Residue Count: 1,155
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A, B, C	385	Plasmodium vivax	Mutation(s): 0 EC: 2.3.1.97
UniProt
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I)) Explore A5K1A2 Go to UniProtKB: A5K1A2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5K1A2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHW Query on NHW Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	E [auth A], K [auth B], P [auth C]	2-oxopentadecyl-CoA C₃₆ H₆₄ N₇ O₁₇ P₃ S JKWHUJMJVNMKEF-UOCZADIYSA-J		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C]
7I1 Query on 7I1 Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B], O [auth C]	3-methyl-N-(naphthalen-1-ylmethyl)-4-piperidin-4-yloxy-1-benzofuran-2-carboxamide C₂₆ H₂₆ N₂ O₃ JDZKIYVLMLQBQF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain O [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain F [auth A]	F [auth A], L [auth B], Q [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain Q [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain R [auth C] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain R [auth C]	H [auth A], M [auth B], R [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain T [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], S [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.219 (Depositor), 0.218 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.34	α = 90
b = 119.03	β = 90
c = 175.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-10-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-17
Type: Initial release
Version 1.1: 2012-11-07
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

4B11 | pdb_00004b11

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 13)

Literature

Design and Synthesis of Inhibitors of Plasmodium Falciparum N-Myristoyltransferase, a Promising Target for Anti-Malarial Drug Discovery.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand