6GR9 | pdb_00006gr9

Human AURKC INCENP complex bound to VX-680

PDB DOI: https://doi.org/10.2210/pdb6GR9/pdb

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

Deposited: 2018-06-10 Released: 2019-05-15
Deposition Author(s): Abdul Azeez, K.R., Sorrell, F.J., von Delft, F., Bountra, C., Knapp, S., Edwards, A.M., Arrowsmith, C., Elkins, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.224 (Depositor), 0.230 (DCC)
R-Value Work:
0.182 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (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

AURKC INCENP complex bound to BRD-7880

Abdul Azeez, K.R., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 41.03 kDa
Atom Count: 2,812
Modeled Residue Count: 317
Deposited Residue Count: 344
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase C	A	274	Homo sapiens	Mutation(s): 0 Gene Names: AURKC, AIE2, AIK3, AIRK3, ARK3, STK13 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQB9 (Homo sapiens) Explore Q9UQB9 Go to UniProtKB: Q9UQB9
PHAROS: Q9UQB9 GTEx: ENSG00000105146
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UQB9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inner centromere protein	B	70	Homo sapiens	Mutation(s): 0 Gene Names: INCENP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQS7 (Homo sapiens) Explore Q9NQS7 Go to UniProtKB: Q9NQS7
PHAROS: Q9NQS7 GTEx: ENSG00000149503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NQS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VX6 Query on VX6 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]	CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE C₂₃ H₂₈ N₈ O S GCIKSSRWRFVXBI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
VX6	BindingDB: 6GR9	Ki: 4.6 (nM) from 1 assay(s)
		Kd: min: 6, max: 6.3 (nM) from 2 assay(s)
		IC50: min: 18.3, max: 70 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.224 (Depositor), 0.230 (DCC)
R-Value Work: 0.182 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.617	α = 90
b = 82.617	β = 90
c = 121	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary