9EPU | pdb_00009epu

Crystal structure of the human CDKL5 kinase domain with compound CAF-382

PDB DOI: https://doi.org/10.2210/pdb9EPU/pdb

Classification: GENE REGULATION
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-03-20 Released: 2025-04-02
Deposition Author(s): Richardson, W., Chen, X., Newman, J.A., Bakshi, S., Lakshminarayana, B., Brooke, L., Bullock, A.N.
Funding Organization(s): Innovative Medicines Initiative

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.270 (Depositor), 0.268 (DCC)
R-Value Work:
0.226 (Depositor), 0.225 (DCC)
R-Value Observed:
0.228 (Depositor)

Starting Model: experimental
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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

Crystal structure of the human CDKL5 kinase domain with compound CAF-382

Capener, J.L., Kim, J.K., Richardson, W., Silvaroli, J.A., Martinez, G.V., Thorson, V.C., Li, J., Hoyt, K.R., Satoskar, A.A., Mallipattu, S.K., Davidson, A.J., Zepeda-Orozco, D., Bajwa, A., Bullock, A.N., Axtman, A.D., Pabla, N.S.

To be published.

Macromolecule Content

Total Structure Weight: 35.99 kDa
Atom Count: 2,275
Modeled Residue Count: 276
Deposited Residue Count: 304
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-dependent kinase-like 5	A	304	Homo sapiens	Mutation(s): 0 Gene Names: CDKL5, STK9 EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for O76039 (Homo sapiens) Explore O76039 Go to UniProtKB: O76039
PHAROS: O76039 GTEx: ENSG00000008086
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O76039
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1H6P (Subject of Investigation/LOI) Query on A1H6P 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]	~{N}-[5-[(5-propan-2-yl-1,3-oxazol-2-yl)methylsulfanyl]-1,3-thiazol-2-yl]piperidine-4-carboxamide C₁₆ H₂₂ N₄ O₂ S₂ MCLDWKVRXDHDEI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]