9XVS | pdb_00009xvs

Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor

PDB DOI: https://doi.org/10.2210/pdb9XVS/pdb

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

Deposited: 2025-11-27 Released: 2025-12-10
Deposition Author(s): Li, S., Zhou, L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.205 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Phosphoglycerate mutase 1 complexed with a novel scaffold inhibitor

Li, S., Zhou, L.

To be published.

Macromolecule Content

Total Structure Weight: 61.33 kDa
Atom Count: 4,036
Modeled Residue Count: 479
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase 1	A [auth B], 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1E1K (Subject of Investigation/LOI) Query on A1E1K Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain J [auth C] MOL2 format, chain C [auth B] MOL2 format, chain J [auth C] mmCIF format, chain C [auth B] mmCIF format, chain J [auth C]	C [auth B], J [auth C]	6-chloranyl-10-oxidanylidene-1,9-diazatricyclo[6.4.1.0^{4,13}]trideca-2,4(13),5,7-tetraene-2-carboxylic acid C₁₂ H₉ Cl N₂ O₃ HGYKKLWOPKBBFG-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain J [auth C] Interactions & Density Focus chain C [auth B] Focus chain J [auth C]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth C] MOL2 format, chain K [auth C] mmCIF format, chain K [auth C]	K [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Interactions & Density Focus chain K [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], L [auth C], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]