5AFX | pdb_00005afx

T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1238

PDB DOI: https://doi.org/10.2210/pdb5AFX/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma brucei
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2015-01-27 Released: 2015-10-28
Deposition Author(s): Yang, G., Oldfield, E., No, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.334 (Depositor)
R-Value Work:
0.259 (Depositor), 0.269 (DCC)
R-Value Observed:
0.263 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation.

Yang, G., Zhu, W., Kim, K., Byun, S.Y., Choi, G., Wang, K., Cha, J.S., Cho, H., Oldfield, E., No, J.H.

(2015) Antimicrob Agents Chemother 59: 7530

PubMed: 26392508 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1128/AAC.01873-15
Primary Citation Related Structures:
5AEL, 5AFX, 5AHU

PubMed Abstract:
We report the results of a screen of a library of 925 potential prenyl synthase inhibitors against Trypanosoma brucei farnesyl diphosphate synthase (TbFPPS) and against T. brucei, the causative agent of human African trypanosomiasis. The most potent compounds were lipophilic analogs of the bone resorption drug zoledronate, some of which had submicromolar to low micromolar activity against bloodstream form T. brucei and selectivity indices of up to ∼ 300. We evaluated the effects of two such inhibitors on survival and parasitemia in a T. brucei mouse model of infection and found that survival increased by up to 16 days. We also investigated the binding of three lipophilic bisphosphonates to an expressed TbFPPS using crystallography and investigated the thermodynamics of binding using isothermal titration calorimetry.

Organizational Affiliation

Leishmania Research Laboratory, Institut Pasteur Korea, Seongnam-si, Gyeonggi-do, Republic of Korea Interdisciplinary Programs of Functional Genomics, Yonsei University, Seoul, Republic of Korea.

Macromolecule Content

Total Structure Weight: 84.97 kDa
Atom Count: 5,948
Modeled Residue Count: 714
Deposited Residue Count: 734
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FARNESYL PYROPHOSPHATE SYNTHASE	A, B	367	Trypanosoma brucei	Mutation(s): 0
UniProt
Find proteins for Q86C09 (Trypanosoma brucei) Explore Q86C09 Go to UniProtKB: Q86C09
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86C09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PVZ Query on PVZ Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	[1-hydroxy-2-(1-nonyl-1H-3lambda~5~-imidazol-3-yl)ethane-1,1-diyl]bis(phosphonic acid) C₁₄ H₂₉ N₂ O₇ P₂ ANVJZSKZYXLDSP-UHFFFAOYSA-O		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] G [auth B] H [auth B] C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.334 (Depositor)
R-Value Work: 0.259 (Depositor), 0.269 (DCC)
R-Value Observed: 0.263 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.471	α = 90
b = 119.026	β = 112.47
c = 63.47	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
CCP4	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Yang, G.

Oldfield, E.

No, J.H.

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2015-12-02
Changes: Database references
Version 1.2: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.3: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.4: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description