9LG2 | pdb_00009lg2

Phosphoglycerate mutase 1 complexed with a covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9LG2/pdb

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


• Deposited: 2025-01-09 Released: 2025-05-14 
• Deposition Author(s): Li, S., Wu, X., Zhou, L., Lu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.229 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Proteome-Wide Data Guides the Discovery of Lysine-Targeting Covalent Inhibitors Using DNA-Encoded Chemical Libraries.

Wu, X., Li, S., Liang, T., Yu, Q., Zhang, Y., Liu, J., Li, K., Liu, Z., Cui, M., Zhao, Y., Han, X., Jin, R., Tan, M., Chen, X.H., Zhao, Y., Zheng, M., Sun, Y., Zhou, L., Lu, X.

(2025) Angew Chem Int Ed Engl 64: e202505581-e202505581

• PubMed: 40223230 
• DOI: https://doi.org/10.1002/anie.202505581
• Primary Citation Related Structures: 
  9LG2, 9LHJ


• PubMed Abstract: 
  

  Broadening the application of covalent inhibitors requires the exploration of nucleophilic residues beyond cysteine. The covalent DNA-encoded chemical library (CoDEL) represents an advanced technology for covalent drug discovery. However, its application in lysine-targeting inhibitors remains uncharted territory. Here, we report the utilization of CoDEL selection guided by proteome-wide data to identify lysine-targeting covalent inhibitors. A comprehensive assessment of activity-based protein profiling (ABPP) data on lysine distribution and ligandability reveals potential targets for selective covalent inhibition, including phosphoglycerate mutase 1 (PGAM1), bromodomain (BRD) family proteins, and ubiquitin-conjugating enzyme E2 N (UBE2N). The 10.7-million-member CoDELs, featuring diverse lysine-reactive warheads, enable the discovery of a series of covalent inhibitors, covering photo-covalent, reversible covalent, and irreversible covalent reaction mechanisms. In-depth characterization of binding sites and modes of action provides structural and functional insights. Notably, irreversible covalent inhibitors unveil a novel mechanism for regulating UBE2N-mediated ubiquitination by modulating the conformation of the protein complex. Our work adopts the ABPP-CoDEL strategy, offering an efficient and versatile selection method for the development of covalent inhibitors targeting functional lysines.

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Organizational Affiliation: 
• State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.
School of Pharmacy, Fudan University, Shanghai, 201203, China.
Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310029, China.
Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310029, China.
Department of Thyroid Surgery, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023, China.
Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 60.47 kDa 
• Atom Count: 4,260 
• Modeled Residue Count: 491 
• Deposited Residue Count: 524 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	A [auth B]	262	Homo sapiens	Mutation(s): 0  Gene Names: PGAM1, PGAMA, CDABP0006 EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens) Explore P18669  Go to UniProtKB:  P18669
PHAROS:  P18669 GTEx:  ENSG00000171314

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	B [auth C]	262	Homo sapiens	Mutation(s): 0  Gene Names: PGAM1, PGAMA, CDABP0006 EC: 5.4.2.11 (PDB Primary Data), 5.4.2.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P18669 (Homo sapiens) Explore P18669  Go to UniProtKB:  P18669
PHAROS:  P18669 GTEx:  ENSG00000171314

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EJR	A [auth B]	L-PEPTIDE LINKING	C36 H38 Br N5 O8		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.229 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.226	α = 90
b = 74.586	β = 90
c = 172.327	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Li, S., Wu, X., Zhou, L., Lu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077019

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2025-06-25
  Changes: Database references