6R8J | pdb_00006r8j

Crystal structure of di-phosphorylated human CLK1 in complex with 4-(1-methyl-1H-indol-3-yl)pyrimidin-2-amine

PDB DOI: https://doi.org/10.2210/pdb6R8J/pdb

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

Deposited: 2019-04-02 Released: 2020-05-13
Deposition Author(s): Livnah, O., Domovich, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.263 (Depositor), 0.270 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Non-phosphorylated human CLK1 in complex with an indole inhibitor to 1.65 Ang

Livnah, O., Domovich, Y.

To be published.

Macromolecule Content

Total Structure Weight: 39.9 kDa
Atom Count: 2,910
Modeled Residue Count: 330
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity protein kinase CLK1	A	337	Homo sapiens	Mutation(s): 0 Gene Names: CLK1, CLK EC: 2.7.12.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49759 (Homo sapiens) Explore P49759 Go to UniProtKB: P49759
PHAROS: P49759 GTEx: ENSG00000013441
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49759
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JUW Query on JUW Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	4-(1-methylindol-3-yl)pyrimidin-2-amine C₁₃ H₁₂ N₄ IEYXYKBZJHPKGV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.263 (Depositor), 0.270 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.543	α = 90
b = 68.543	β = 90
c = 285.08	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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.