5UZK | pdb_00005uzk

Crystal Structure of PKA bound to an pyrrolo pyridine inhibitor

PDB DOI: https://doi.org/10.2210/pdb5UZK/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens, Oryctolagus cuniculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-26 Released: 2018-03-07
Deposition Author(s): Jacobs, M.D., Brown, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.253 (Depositor), 0.258 (DCC)
R-Value Work:
0.188 (Depositor), 0.192 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

ROCK inhibitors 3: Design, synthesis and structure-activity relationships of 7-azaindole-based Rho kinase (ROCK) inhibitors.

Bandarage, U.K., Cao, J., Come, J.H., Court, J.J., Gao, H., Jacobs, M.D., Marhefka, C., Nanthakumar, S., Green, J.

(2018) Bioorg Med Chem Lett 28: 2622-2626

PubMed: 30082069 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2018.06.040
Primary Citation Related Structures:
5UZJ, 5UZK

PubMed Abstract:
Rho kinase (ROCK) inhibitors are potential therapeutic agents for the treatment of a variety of disorders including hypertension, glaucoma and erectile dysfunction. Here we disclose a series of potent and selective ROCK inhibitors based on a substituted 7-azaindole scaffold. Substitution of the 3-position of 7-azaindole led to compounds such as 37, which possess excellent ROCK inhibitory potency and high selectivity against the closely related kinase PKA.

Organizational Affiliation

Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA 02210, USA. Electronic address: upul_bandarage@vrtx.com.

Macromolecule Content

Total Structure Weight: 43.26 kDa
Atom Count: 3,195
Modeled Residue Count: 355
Deposited Residue Count: 369
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	351	Homo sapiens	Mutation(s): 0 Gene Names: PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612 Go to UniProtKB: P17612
PHAROS: P17612 GTEx: ENSG00000072062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17612
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I]	18	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P61926 (Oryctolagus cuniculus) Explore P61926 Go to UniProtKB: P61926
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61926
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
504 Query on 504 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-{3-[3-(piperidin-4-yl)propoxy]phenyl}-N-[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)-1,3-thiazol-2-yl]acetamide C₂₆ H₂₉ N₅ O₂ S OKUPZBPYLVKVSU-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.253 (Depositor), 0.258 (DCC)
R-Value Work: 0.188 (Depositor), 0.192 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.17	α = 90
b = 78.18	β = 90
c = 80.26	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Jacobs, M.D.

Brown, K.

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-07-11
Changes: Data collection, Database references
Version 1.2: 2018-08-22
Changes: Data collection, Database references
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary