4BBH

Plasmodium vivax N-myristoyltransferase with a bound benzothiophene inhibitor

PDB DOI: https://doi.org/10.2210/pdb4BBH/pdb

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

Deposited: 2012-09-23 Released: 2012-12-05
Deposition Author(s): Rackham, M.D., Brannigan, J.A., Moss, D.K., Yu, Z., Wilkinson, A.J., Holder, A.A., Tate, E.W., Leatherbarrow, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.264
R-Value Work: 0.214
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of Novel and Ligand-Efficient Inhibitors of Plasmodium Falciparum and Plasmodium Vivax N-Myristoyltransferase.

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

(2013) J Med Chem 56: 371

PubMed: 23170970 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm301474t
Primary Citation of Related Structures:
4BBH

PubMed Abstract:
N-Myristoyltransferase (NMT) is an attractive antiprotozoan drug target. A lead-hopping approach was utilized in the design and synthesis of novel benzo[b]thiophene-containing inhibitors of Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) NMT. These inhibitors are selective against Homo sapiens NMT1 (HsNMT), have excellent ligand efficiency (LE), and display antiparasitic activity in vitro. The binding mode of this series was determined by crystallography and shows a novel binding mode for the benzothiophene ring.

Organizational Affiliation

Department of Chemistry, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K.

Macromolecule Content

Total Structure Weight: 139.52 kDa
Atom Count: 10,684
Modelled Residue Count: 1,135
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A, B, C	384	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]	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]
YBN Query on YBN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C]	F [auth A], L [auth B], Q [auth C]	3-methoxybenzyl 3-(piperidin-4-yloxy)-1-benzothiophene-2-carboxylate C₂₂ H₂₃ N O₄ S GEVWCNOQZDSSIG-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]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 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 D [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C]	D [auth A], J [auth B], O [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-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]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C]	H [auth A], M [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain S [auth C] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B]	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]