8Z6O | pdb_00008z6o

Crystal structure of HDGFRP2 PWWP domain in complex with Varenicline

• PDB DOI: https://doi.org/10.2210/pdb8Z6O/pdb

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


• Deposited: 2024-04-19 Released: 2025-04-23 
• Deposition Author(s): Wei, X., Ruan, K.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Fragment based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain

Wei, X., Ruan, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.6 kDa 
• Atom Count: 1,632 
• Modeled Residue Count: 180 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 2	A, B	93	Homo sapiens	Mutation(s): 0  Gene Names: HDGFL2, HDGF2, HDGFRP2, HRP2, UNQ785/PRO1604
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4V5 (Homo sapiens) Explore Q7Z4V5  Go to UniProtKB:  Q7Z4V5
GTEx:  ENSG00000167674

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QMR (Subject of Investigation/LOI)	D [auth B]	VARENICLINE C13 H13 N3 JQSHBVHOMNKWFT-DTORHVGOSA-N
DMS (Subject of Investigation/LOI)	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.054	α = 63.16
b = 39.012	β = 70.31
c = 41.72	γ = 73.59

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Wei, X., Ruan, K.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22377119

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release