7CP3 | pdb_00007cp3

Crystal Structure of PAK4 in complex with inhibitor 47

PDB DOI: https://doi.org/10.2210/pdb7CP3/pdb

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

Deposited: 2020-08-05 Released: 2021-08-11
Deposition Author(s): Zhao, F., Li, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.267 (Depositor), 0.260 (DCC)
R-Value Work:
0.244 (Depositor), 0.250 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of 6-ethynyl-1H-indole-3-carboxamide Derivatives as Highly Potent and Selective p21-Activated Kinase 4 (PAK4) Inhibitors

Song, P., Zhao, F., Cheng, M.

To be published.

Macromolecule Content

Total Structure Weight: 33.47 kDa
Atom Count: 2,329
Modelled Residue Count: 290
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	292	Homo sapiens	Mutation(s): 0 Gene Names: PAK4, KIAA1142 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013 Go to UniProtKB: O96013
PHAROS: O96013 GTEx: ENSG00000130669
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O96013
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GC6 (Subject of Investigation/LOI) Query on GC6 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]	[(3R)-3-azanylpiperidin-1-yl]-[1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indol-3-yl]methanone C₂₆ H₃₀ N₆ O₂ DADSGHOHYQROCR-LJQANCHMSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.267 (Depositor), 0.260 (DCC)
R-Value Work: 0.244 (Depositor), 0.250 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.253	α = 90
b = 64.253	β = 90
c = 185.074	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary

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.