27WI | pdb_000027wi

UBE2D2 bound with compound XY54

• PDB DOI: https://doi.org/10.2210/pdb27WI/pdb

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


• Deposited: 2026-06-15 Released: 2026-10-28 
• Deposition Author(s): Huang, Y., Liu, S., Min, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Electrophile-First Screening Identifies Covalent Aminothiazole Scaffold Inhibitors for Ubiquitin-Conjugating Enzyme UBE2D2

Liu, S., Zheng, T., Wu, X., Wang, H., Ni, S., Dou, Y., Li, B., Wang, L., Huang, Y., Chen, X., Min, J.

(2026) J Med Chem 

• DOI: https://doi.org/10.1021/acs.jmedchem.6c01896

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.45 kDa 
• Atom Count: 1,463 
• Modeled Residue Count: 162 
• Deposited Residue Count: 165 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A	165	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1FCQ (Subject of Investigation/LOI)	B [auth A], C [auth A]	methyl 2-(2-chloranylethanoylamino)-5-methyl-1,3-thiazole-4-carboxylate C8 H9 Cl N2 O3 S QYVGMIRODGKLHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.275	α = 90
b = 43.971	β = 90
c = 78.568	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Huang, Y., Liu, S., Min, J.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32570711

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release