5OBR

Aurora A kinase in complex with 2-(3-chloro-5-fluorophenyl)quinoline-4-carboxylic acid and JNJ-7706621

PDB DOI: https://doi.org/10.2210/pdb5OBR/pdb

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

Deposited: 2017-06-29 Released: 2017-08-09
Deposition Author(s): Rossmann, M., Janecek, M., Hyvonen, M.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.292
R-Value Work: 0.223
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

Cole, D.J., Janecek, M., Stokes, J.E., Rossmann, M., Faver, J.C., McKenzie, G.J., Venkitaraman, A.R., Hyvonen, M., Spring, D.R., Huggins, D.J., Jorgensen, W.L.

(2017) Chem Commun (Camb) 53: 9372-9375

PubMed: 28787041 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1039/c7cc05379g
Primary Citation of Related Structures:
5OBJ, 5OBR

PubMed Abstract:
Free energy perturbation theory, in combination with enhanced sampling of protein-ligand binding modes, is evaluated in the context of fragment-based drug design, and used to design two new small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction.

Organizational Affiliation

Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA and School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK. [email protected].

Macromolecule Content

Total Structure Weight: 32.18 kDa
Atom Count: 2,127
Modelled Residue Count: 255
Deposited Residue Count: 272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A	A	272	Homo sapiens	Mutation(s): 0 Gene Names: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14965 (Homo sapiens) Explore O14965 Go to UniProtKB: O14965
PHAROS: O14965 GTEx: ENSG00000087586
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14965
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SKE Query on SKE 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]	4-({5-amino-1-[(2,6-difluorophenyl)carbonyl]-1H-1,2,4-triazol-3-yl}amino)benzenesulfonamide C₁₅ H₁₂ F₂ N₆ O₃ S KDKUVYLMPJIGKA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
9QT Query on 9QT 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]	2-(3-chloranyl-5-fluoranyl-phenyl)quinoline-4-carboxylic acid C₁₆ H₉ Cl F N O₂ NIKQCFUMVUWEJP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.292
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.7	α = 90
b = 83.7	β = 90
c = 169.7	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-08-09

Deposition Author(s):

Rossmann, M.

Janecek, M.

Hyvonen, M.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	090340/Z/09/Z

Revision History (Full details and data files)

Version 1.0: 2017-08-09
Type: Initial release
Version 1.1: 2017-08-23
Changes: Database references
Version 1.2: 2017-08-30
Changes: Database references
Version 1.3: 2018-01-24
Changes: Source and taxonomy
Version 2.0: 2024-05-08
Changes: Atomic model, Data collection, Database references