4B12

Plasmodium vivax N-myristoyltransferase with a bound benzofuran inhibitor (compound 23)

PDB DOI: https://doi.org/10.2210/pdb4B12/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: 1.79 Å
R-Value Free: 0.239
R-Value Work: 0.185
R-Value Observed: 0.188

Starting Model: experimental
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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 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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/jm301160h
Primary Citation of 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: 140.2 kDa
Atom Count: 11,137
Modelled Residue Count: 1,138
Deposited Residue Count: 1,155
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% 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 T [auth C] SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain T [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain T [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B], T [auth C]	2-oxopentadecyl-CoA C₃₆ H₆₄ N₇ O₁₇ P₃ S JKWHUJMJVNMKEF-UOCZADIYSA-J		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain T [auth C]
C23 Query on C23 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain S [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain S [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain S [auth C]	D [auth A], K [auth B], S [auth C]	1-[3-methyl-4-(piperidin-4-yloxy)-1-benzofuran-2-yl]-3-phenylpropan-1-one C₂₃ H₂₅ N O₃ ZUAGYVKWPGUWFU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain S [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	F [auth A] G [auth A] H [auth A] M [auth B] N [auth B] F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], U [auth C], V [auth C]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain U [auth C] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	I [auth A], Q [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B] Focus chain W [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain X [auth C] SDF format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B]	J [auth A], R [auth B], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Focus chain X [auth C] Interactions & Density Focus chain J [auth A] Focus chain R [auth B] Focus chain X [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
C23	PDBBind: 4B12	IC50: 1.02e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.239
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.47	α = 90
b = 121.92	β = 90
c = 178.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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: 2012-10-31
Changes: Atomic model
Version 1.2: 2012-11-07
Changes: Database references
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description