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), 0.220 (DCC)
R-Value Work:
0.195 (Depositor), 0.190 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
View more details

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

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 J [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain C [auth A]	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]