8Z6C | pdb_00008z6c

Crystal structure of HDGFRP2 PWWP domain in complex with 4-(4-bromo-1H-pyrazol-3-yl) pyridine

PDB DOI: https://doi.org/10.2210/pdb8Z6C/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.236 (Depositor), 0.236 (DCC)
R-Value Work:
0.189 (Depositor), 0.189 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

Wei, X., Ruan, K.

To be published.

Macromolecule Content

Total Structure Weight: 33.12 kDa
Atom Count: 2,397
Modeled Residue Count: 276
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 2	A, B, C	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7Z4V5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1D73 (Subject of Investigation/LOI) Query on A1D73 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	D [auth A], G [auth B], J [auth C]	4-(4-bromanyl-1~{H}-pyrazol-3-yl)pyridine C₈ H₆ Br N₃ LKKNQJJSEMQTHQ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C]	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C]