8RIB | pdb_00008rib

N-terminal domain of Trypanosoma brucei PEX14 in complex with a pyrazolo-pyrazolo[4,3-c]pyridin-3-yl compound showing a novel binding pose

PDB DOI: https://doi.org/10.2210/pdb8RIB/pdb

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

Deposited: 2023-12-18 Released: 2025-01-29
Deposition Author(s): Napolitano, V., Janna Olmos, J., Popowicz, G.M., Dubin, G.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free:
0.162 (Depositor), 0.163 (DCC)
R-Value Work:
0.126 (Depositor), 0.126 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Quantum Chemistry in a Pocket

Menezes, F., Napolitano, V., Frohlich, T., Rioton, S., Janna Olmos, J.D., Dubin, G., Popowicz, G.M.

To be published.

Macromolecule Content

Total Structure Weight: 17.8 kDa
Atom Count: 1,384
Modeled Residue Count: 124
Deposited Residue Count: 138
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal membrane protein PEX14	A, B	69	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8IEW2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OJN (Subject of Investigation/LOI) Query on OJN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	1-(2-azanylethyl)-5-[(4-methoxynaphthalen-1-yl)methyl]-~{N}-[(4-methylsulfanylphenyl)methyl]-6,7-dihydro-4~{H}-pyrazolo[4,3-c]pyridine-3-carboxamide C₂₉ H₃₃ N₅ O₂ S STRRFWBWQPHLDR-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B]	J [auth A], O [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain O [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain K [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]