9REF | pdb_00009ref

Crystal Structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F203

PDB DOI: https://doi.org/10.2210/pdb9REF/pdb

Classification: TRANSFERASE
Organism(s): Cricetulus griseus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-06-03 Released: 2025-12-31
Deposition Author(s): Sandner, A., Mueller, J.M., Wolter, M., Glinca, S., Klebe, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.177 (Depositor), 0.177 (DCC)
R-Value Work:
0.143 (Depositor), 0.143 (DCC)
R-Value Observed:
0.144 (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

Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target Exploring Options beyond the Flatland

Santura, A., Muller, J., Wolter, M., Tutzschky, I.C., Ruf, M., Metz, A., Sandner, A., Merkl, S., Klebe, G., Glinca, S., Czodrowski, P.

(2025) J Chem Inf Model

DOI: https://doi.org/10.1021/acs.jcim.5c01952

Macromolecule Content

Total Structure Weight: 42.27 kDa
Atom Count: 3,251
Modeled Residue Count: 339
Deposited Residue Count: 353
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0 Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321 Go to UniProtKB: P25321
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25321
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D8J (Subject of Investigation/LOI) Query on D8J Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-amino-1,4-anhydro-2,5-dideoxy-5-[(4-fluorobenzene-1-carbonyl)amino]-D-arabinitol C₁₂ H₁₅ F N₂ O₃ FDPRGBDPIJLPIW-MXWKQRLJSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]