8QM8

Potential drug binding sites for translation initiation factor eIF4E

PDB DOI: https://doi.org/10.2210/pdb8QM8/pdb

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-09-21 Released: 2025-01-15
Deposition Author(s): Cleasby, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.202 (Depositor), 0.205 (DCC)
R-Value Work:
0.165 (Depositor), 0.172 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Integrating fragment-based screening with targeted protein degradation and genetic rescue to explore eIF4E function

Sharp, Y.S., Martella, M., Milton, C.I., Ward, G., Woodhead, A.J., Richardson, C.J., Carr, M.G., Chiarparin, E., Cons, B.D., Coyle, J., D'Agostino, S., East, C.E., Hiscock, S.D., Martinez-Fleites, C., Mortenson, P.N., Palmer, N., Pathuri, P., Powers, M.V., Saalau, S.M., St.Denis, J.D., Swabey, K., Vinkovic, M., Williams, G., Clarke, P.A.

(2025) Nat Commun

DOI: https://doi.org/10.1038/s41467-024-54356-1

Macromolecule Content

Total Structure Weight: 51.75 kDa
Atom Count: 3,892
Modelled Residue Count: 408
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 4E	A, B	215	Homo sapiens	Mutation(s): 0 Gene Names: EIF4E
UniProt & NIH Common Fund Data Resources
Find proteins for P06730 (Homo sapiens) Explore P06730 Go to UniProtKB: P06730
PHAROS: P06730 GTEx: ENSG00000151247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06730
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W4K (Subject of Investigation/LOI) Query on W4K Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	(2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol C₂₀ H₂₆ F N O₃ FZXGUZYCKURVPY-VLIAUNLRSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	C [auth A] D [auth A] E [auth A] G [auth A] L [auth B] C [auth A], D [auth A], E [auth A], G [auth A], L [auth B], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	I [auth B], J [auth B], K [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]