44HW | pdb_000044hw

Crystal structure of human glutaminyl cyclase in complex with Inhibitor

PDB DOI: https://doi.org/10.2210/pdb44HW/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2026-07-30 Released: 2026-11-11
Deposition Author(s): Li, G.-B., Chen, Z.-Y., Li, R.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.206 (Depositor), 0.206 (DCC)
R-Value Observed:
0.207 (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 methylimidazolylethyl-pyrimidinamine derivatives as new glutaminyl cyclase inhibitors

Li, R., Chen, Z.Y., Yang, L.L., Meng, F.B., Zhuang, Y.Q., Liu, W., Li, X., Ning, X.L., Wang, H.L., Yang, L.L., Li, G.B.

(2026) Eur J Med Chem : 119477

DOI: https://doi.org/10.1016/j.ejmech.2026.119477

Macromolecule Content

Total Structure Weight: 38.34 kDa
Atom Count: 2,996
Modeled Residue Count: 322
Deposited Residue Count: 329
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaminyl-peptide cyclotransferase	A	329	Homo sapiens	Mutation(s): 0 Gene Names: QPCT EC: 2.3.2.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q16769 (Homo sapiens) Explore Q16769 Go to UniProtKB: Q16769
PHAROS: Q16769 GTEx: ENSG00000115828
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1FDM (Subject of Investigation/LOI) Query on A1FDM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{N}-cyclopropyl-4-[2-[2-(5-methylimidazol-1-yl)ethylamino]-5-(trifluoromethyl)pyrimidin-4-yl]benzamide C₂₁ H₂₁ F₃ N₆ O HOTMCRPUSWVJMQ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]