7X09 | pdb_00007x09

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with inhibitors L95 and Halofuginone

PDB DOI: https://doi.org/10.2210/pdb7X09/pdb

Classification: LIGASE/LIGASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-21 Released: 2023-08-30
Deposition Author(s): Manickam, Y., Babbar, P., Pillai, P., Sharma, A.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.225 (Depositor), 0.223 (DCC)
R-Value Work:
0.195 (Depositor), 0.197 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Homo sapiens Prolyl-tRNA synthetase (HsPRS) with double inhibitors (HF and L95)

Manickam, Y., Babbar, P., Sharma, A.

To be published.

Macromolecule Content

Total Structure Weight: 117.34 kDa
Atom Count: 8,196
Modeled Residue Count: 955
Deposited Residue Count: 1,010
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional glutamate/proline--tRNA ligase	A, B	505	Homo sapiens	Mutation(s): 0 Gene Names: EPRS1, EPRS, GLNS, PARS, QARS, QPRS, PIG32 EC: 6.1.1.17 (PDB Primary Data), 6.1.1.15 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens) Explore P07814 Go to UniProtKB: P07814
PHAROS: P07814 GTEx: ENSG00000136628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07814
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFG Query on HFG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C₁₆ H₁₇ Br Cl N₃ O₃ LVASCWIMLIKXLA-CABCVRRESA-N		Interactions Focus chain C [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain J [auth B]
JE6 (Subject of Investigation/LOI) Query on JE6 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide C₂₂ H₂₂ N₄ O₂ FLWLQSFDWRRFDA-JOCHJYFZSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain K [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B]	E [auth A], G [auth A], L [auth B], N [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain R [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth B]	H [auth A], O [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain O [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B] Focus chain R [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	P [auth B], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain P [auth B] Focus chain Q [auth B]