5MMA | pdb_00005mma

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and the INSTI XZ379 (compound 5'g)

• PDB DOI: https://doi.org/10.2210/pdb5MMA/pdb
• NAKB: 5MMA

• Classification: VIRAL PROTEIN
• Organism(s): Human spumaretrovirus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-12-09 Released: 2017-08-02 
• Deposition Author(s): Maskell, D.P., Pye, V.E., Cherepanov, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.207 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Optimization of HIV Integrase Strand Transfer Inhibitors.

Zhao, X.Z., Smith, S.J., Maskell, D.P., Metifiot, M., Pye, V.E., Fesen, K., Marchand, C., Pommier, Y., Cherepanov, P., Hughes, S.H., Burke, T.R.

(2017) J Med Chem 60: 7315-7332

• PubMed: 28737946 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00596
• Primary Citation Related Structures: 
  5MMA, 5MMB, 5NO1


• PubMed Abstract: 
  

  Integrase mutations can reduce the effectiveness of the first-generation FDA-approved integrase strand transfer inhibitors (INSTIs), raltegravir (RAL) and elvitegravir (EVG). The second-generation agent, dolutegravir (DTG), has enjoyed considerable clinical success; however, resistance-causing mutations that diminish the efficacy of DTG have appeared. Our current findings support and extend the substrate envelope concept that broadly effective INSTIs can be designed by filling the envelope defined by the DNA substrates. Previously, we explored 1-hydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxamides as an INSTI scaffold, making a limited set of derivatives, and concluded that broadly effective INSTIs can be developed using this scaffold. Herein, we report an extended investigation of 6-substituents as well the first examples of 7-substituted analogues of this scaffold. While 7-substituents are not well-tolerated, we have identified novel substituents at the 6-position that are highly effective, with the best compound (6p) retaining better efficacy against a broad panel of known INSTI resistant mutants than any analogues we have previously described.

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Organizational Affiliation: 
• Chromatin Structure and Mobile DNA, The Francis Crick Institute , London NW1 1AT, United Kingdom.
Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.
Imperial College London , St-Mary's Campus, Norfolk Place, London W2 1PG, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.52 kDa 
• Atom Count: 5,538 
• Modeled Residue Count: 585 
• Deposited Residue Count: 826 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
integrase	A, B	395	Human spumaretrovirus	Mutation(s): 2  Gene Names: pol EC: 2.7.7.49 (PDB Primary Data), 2.7.7.7 (PDB Primary Data), 3.1.26.4 (PDB Primary Data), 3.4.23 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P14350 (Human spumaretrovirus) Explore P14350  Go to UniProtKB:  P14350

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')	C	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*A)-3')	D	17	synthetic construct

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VHT	U [auth A]	methyl 2-[[3-[[2,4-bis(fluoranyl)phenyl]methylcarbamoyl]-1-oxidanyl-2-oxidanylidene-1,8-naphthyridin-4-yl]amino]ethanoate C19 H16 F2 N4 O5 DPDVGSIUVKMEDW-UHFFFAOYSA-N
MES	V [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
HEZ	AA [auth B], W [auth A]	HEXANE-1,6-DIOL C6 H14 O2 XXMIOPMDWAUFGU-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], K [auth A], Y [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	BA [auth C], CA [auth C], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A], G [auth A], X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.207 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.57	α = 90
b = 159.57	β = 90
c = 124.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Maskell, D.P., Pye, V.E., Cherepanov, P.

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Database references
• Version 1.2: 2020-09-30
  Changes: Derived calculations
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Refinement description