5NXC

LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736

PDB DOI: https://doi.org/10.2210/pdb5NXC/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2017-05-10 Released: 2017-05-24
Deposition Author(s): Mathea, S., Salah, E., Pike, A.C.W., Bushell, S., Carpenter, E.P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.298 (Depositor), 0.310 (DCC)
R-Value Work:
0.239 (Depositor), 0.250 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

LIM Domain Kinase (LIMK1) In Complex With PF-00477736

Mathea, S., Salah, E., Pike, A.C.W., Bushell, S., Carpenter, E.P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.N., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.41 kDa
Atom Count: 2,208
Modelled Residue Count: 274
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIM domain kinase 1	A [auth L]	310	Homo sapiens	Mutation(s): 0 Gene Names: LIMK1, LIMK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53667 (Homo sapiens) Explore P53667 Go to UniProtKB: P53667
PHAROS: P53667 GTEx: ENSG00000106683
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53667
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9DB Query on 9DB Download Ideal Coordinates CCD File SDF format, chain B [auth L] MOL2 format, chain B [auth L] mmCIF format, chain B [auth L]	B [auth L]	(2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide C₂₂ H₂₅ N₇ O₂ NDEXUOWTGYUVGA-LJQANCHMSA-N		Interactions Focus chain B [auth L] Interactions & Density Focus chain B [auth L]

Binding Affinity Annotations
ID	Source	Binding Affinity
9DB	BindingDB: 5NXC	IC50: min: 174, max: 1.00e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.298 (Depositor), 0.310 (DCC)
R-Value Work: 0.239 (Depositor), 0.250 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.387	α = 90
b = 95.836	β = 90
c = 84.392	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Carpenter, E.P.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.