5DEW | pdb_00005dew

Crystal structure of PAK1 in complex with an inhibitor compound 5

PDB DOI: https://doi.org/10.2210/pdb5DEW/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-08-26 Released: 2016-09-21
Deposition Author(s): Oh, A., Tam, C., Wang, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.215 (Depositor), 0.217 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.177 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Design of Selective PAK1 Inhibitor G-5555: Improving Proper-ties by Employing an Unorthodox Low-pKa Polar Moiety

Ndubaku, C.O.

To be published.

Macromolecule Content

Total Structure Weight: 67.58 kDa
Atom Count: 5,019
Modeled Residue Count: 576
Deposited Residue Count: 594
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 1	A, B	297	Homo sapiens	Mutation(s): 2 Gene Names: PAK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens) Explore Q13153 Go to UniProtKB: Q13153
PHAROS: Q13153 GTEx: ENSG00000149269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
59N Query on 59N Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	8-[(trans-4-aminocyclohexyl)methyl]-6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]-2-(ethylamino)pyrido[2,3-d]pyrimidin-7(8H)-one C₂₇ H₃₀ Cl N₇ O PJYRMGKJLXENCU-IRJFHVNHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.215 (Depositor), 0.217 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.556	α = 90
b = 81.053	β = 106.39
c = 66.499	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-09-21
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.