5DEY

Crystal structure of PAK1 in complex with an inhibitor compound G-5555

PDB DOI: https://doi.org/10.2210/pdb5DEY/pdb

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

Deposited: 2015-08-26 Released: 2016-01-27
Deposition Author(s): Oh, A., Tam, C., Wang, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.228
R-Value Work: 0.183
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Design of Selective PAK1 Inhibitor G-5555: Improving Properties by Employing an Unorthodox Low-pK a Polar Moiety.

Ndubaku, C.O., Crawford, J.J., Drobnick, J., Aliagas, I., Campbell, D., Dong, P., Dornan, L.M., Duron, S., Epler, J., Gazzard, L., Heise, C.E., Hoeflich, K.P., Jakubiak, D., La, H., Lee, W., Lin, B., Lyssikatos, J.P., Maksimoska, J., Marmorstein, R., Murray, L.J., O'Brien, T., Oh, A., Ramaswamy, S., Wang, W., Zhao, X., Zhong, Y., Blackwood, E., Rudolph, J.

(2015) ACS Med Chem Lett 6: 1241-1246

PubMed: 26713112 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5b00398
Primary Citation of Related Structures:
5DEY, 5DFP

PubMed Abstract:

Macromolecule Content

Total Structure Weight: 67.56 kDa
Atom Count: 4,762
Modelled Residue Count: 576
Deposited Residue Count: 594
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 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13153
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
59T Query on 59T Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one C₂₅ H₂₅ Cl N₆ O₃ ZBCMHWUFWQFPLV-VVOJOOEHSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
59T	Binding MOAD: 5DEY	Ki: 3.7 (nM) from 1 assay(s)
	BindingDB: 5DEY	Ki: min: 3.7, max: 11 (nM) from 2 assay(s)
	BindingDB: 5DEY	IC50: min: 11, max: 69 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.228
R-Value Work: 0.183
R-Value Observed: 0.186
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.661	α = 90
b = 81.863	β = 106.4
c = 65.916	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-01-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-27
Type: Initial release
Version 1.1: 2016-06-01
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.