9HCL | pdb_00009hcl

Crystal structure of human TRF1 TRFH domain in complex with compound 12

PDB DOI: https://doi.org/10.2210/pdb9HCL/pdb

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

Deposited: 2024-11-11 Released: 2025-11-19
Deposition Author(s): Casale, G., Le Bihan, Y.-V., van Montfort, R.L.M., Guettler, S.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.220 (Depositor), 0.216 (DCC)
R-Value Work:
0.204 (Depositor), 0.198 (DCC)
R-Value Observed:
0.205 (Depositor)

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

Discovery of first-in-class inhibitors of the TRF1-TIN2 protein-protein interaction by fragment screening

Casale, G., Guettler, S.

To be published.

Macromolecule Content

Total Structure Weight: 26.58 kDa
Atom Count: 1,844
Modeled Residue Count: 199
Deposited Residue Count: 224
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Telomeric repeat-binding factor 1	A	224	Homo sapiens	Mutation(s): 0 Gene Names: TERF1, PIN2, TRBF1, TRF, TRF1
UniProt & NIH Common Fund Data Resources
Find proteins for P54274 (Homo sapiens) Explore P54274 Go to UniProtKB: P54274
PHAROS: P54274 GTEx: ENSG00000147601
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P54274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TWC (Subject of Investigation/LOI) Query on TWC Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain J [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain J [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain J [auth A]	B [auth A], C [auth A], J [auth A]	2-ethyl-5-(trifluoromethyl)-2,4-dihydro-3H-pyrazol-3-one C₆ H₇ F₃ N₂ O NESMTDYSHSBSJX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain J [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain J [auth A]
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]
DMS Query on DMS 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] 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] 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]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-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] 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]