9AVN | pdb_00009avn

Crystal Structure of CARD9 coiled-coil K156-K214 bound to Compound 1

PDB DOI: https://doi.org/10.2210/pdb9AVN/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-03-04 Released: 2025-03-12
Deposition Author(s): Raymond, D.D., Lemke, C.T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free:
0.299 (Depositor), 0.315 (DCC)
R-Value Work:
0.274 (Depositor), 0.289 (DCC)
R-Value Observed:
0.276 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Human genetics guides the discovery of novel CARD9 inhibitors with anti-inflammatory activity in vitro as well as in vivo

Raymond, D.D.

To be published.

Macromolecule Content

Total Structure Weight: 58.28 kDa
Atom Count: 3,713
Modeled Residue Count: 440
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase recruitment domain-containing protein 9	A, B, C, D, E A, B, C, D, E, F, G, H	60	Homo sapiens	Mutation(s): 0 Gene Names: CARD9
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H257 (Homo sapiens) Explore Q9H257 Go to UniProtKB: Q9H257
PHAROS: Q9H257 GTEx: ENSG00000187796
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H257
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AG7 (Subject of Investigation/LOI) Query on A1AG7 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth D]	I [auth A], J [auth D]	(2P)-2-(1-benzyl-3-phenyl-1H-pyrazol-4-yl)-5-chloro-1-[(1R)-1-cyclohexyl-2-(methylamino)-2-oxoethyl]-1H-1,3-benzimidazole-6-carboxylic acid C₃₃ H₃₂ Cl N₅ O₃ FZXOIQUTLQABCO-SSEXGKCCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.73 Å
R-Value Free: 0.299 (Depositor), 0.315 (DCC)
R-Value Work: 0.274 (Depositor), 0.289 (DCC)
R-Value Observed: 0.276 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.39	α = 90
b = 56.05	β = 97.75
c = 84.3	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XSCALE	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2025-03-12
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.