6RT2 | pdb_00006rt2

Crystal structure of Trypanosoma Brucei PEX14 N-terminal domain in complex with small molecules designed to investigate the water envelope

PDB DOI: https://doi.org/10.2210/pdb6RT2/pdb

Classification: SIGNALING PROTEIN
Organism(s): Trypanosoma brucei brucei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-22 Released: 2020-04-08
Deposition Author(s): Napolitano, V., Ratkova, E.L., Dawidowski, M., Dubin, G., Fino, R., Popowicz, G., Sattler, M., Tetko, I.V.
Funding Organization(s): Accelerated Early staGe drug dIScovery

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.189 (Depositor), 0.158 (DCC)
R-Value Work:
0.161 (Depositor), 0.165 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Water envelope has a critical impact on the design of protein-protein interaction inhibitors.

Ratkova, E.L., Dawidowski, M., Napolitano, V., Dubin, G., Fino, R., Ostertag, M.S., Sattler, M., Popowicz, G., Tetko, I.V.

(2020) Chem Commun (Camb) 56: 4360-4363

PubMed: 32195483 Search on PubMed
DOI: https://doi.org/10.1039/c9cc07714f
Primary Citation Related Structures:
6RT2

PubMed Abstract:
We show that a water envelope network plays a critical role in protein-protein interactions (PPI). The potency of a PPI inhibitor is modulated by orders of magnitude on manipulation of the solvent envelope alone. The structure-activity relationship of PEX14 inhibitors was analyzed as an example using in silico and X-ray data.

Organizational Affiliation

Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany. grzegorz.popowicz@helmholtz-muenchen.de i.tetko@helmholtz-muenchen.de and Medicinal Chemistry, Cardiovascular, Renal and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden. ekaterina.ratkova@astrazeneca.com.

Macromolecule Content

Total Structure Weight: 34.02 kDa
Atom Count: 3,010
Modeled Residue Count: 260
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxin 14	A, B, C, D	67	Trypanosoma brucei brucei	Mutation(s): 0 Gene Names: PEX14
UniProt
Find proteins for Q8IEW2 (Trypanosoma brucei brucei) Explore Q8IEW2 Go to UniProtKB: Q8IEW2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IEW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CV5 (Subject of Investigation/LOI) Query on CV5 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	E [auth A], H [auth B], M [auth C], O [auth D]	(3~{S})-3-[[1-(2-hydroxyethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridin-3-yl]carbonylamino]-3-phenyl-propanoic acid C₃₀ H₃₂ N₄ O₅ FEINFPMXJVPOSJ-VWLOTQADSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain M [auth C] Focus chain O [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth A] I [auth B] J [auth B] K [auth B] P [auth D] F [auth A], I [auth B], J [auth B], K [auth B], P [auth D], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth D] Focus chain Q [auth D]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	G [auth A], L [auth B], N [auth C], R [auth D]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.189 (Depositor), 0.158 (DCC)
R-Value Work: 0.161 (Depositor), 0.165 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.78	α = 90
b = 115.52	β = 101.39
c = 38.87	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Accelerated Early staGe drug dIScovery	Poland	675555

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2020-04-29
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description