6HXF

Human STK10 bound to a maleimide inhibitor

PDB DOI: https://doi.org/10.2210/pdb6HXF/pdb

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

Deposited: 2018-10-17 Released: 2018-10-31
Deposition Author(s): Sorrell, F.J., Salah, E., Serafim, R.A.M., Savitsky, P.A., Krojer, T., Bailey, H.J., Pinkas, D., Burgess-Brown, N.A., von Delft, F., Knapp, S., Arrowsmith, C., Bountra, C., Edwards, A.M., Elkins, J.M.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.219
R-Value Work: 0.190
R-Value Observed: 0.192

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human STK10 bound to a maleimide inhibitor

Sorrell, F.J., Salah, E., Serafim, R.A.M., Elkins, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 140.28 kDa
Atom Count: 9,913
Modelled Residue Count: 1,151
Deposited Residue Count: 1,208
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 10	A [auth B], B [auth A], C, D	302	Homo sapiens	Mutation(s): 0 Gene Names: STK10, LOK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O94804 (Homo sapiens) Explore O94804 Go to UniProtKB: O94804
PHAROS: O94804 GTEx: ENSG00000072786
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O94804
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R70 Query on R70 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain J [auth A] SDF format, chain L [auth C] SDF format, chain N [auth D] MOL2 format, chain E [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] mmCIF format, chain E [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D]	E [auth B], J [auth A], L [auth C], N [auth D]	3-(2-methoxyphenyl)-4-[[4-(phenylcarbonyl)phenyl]amino]pyrrole-2,5-dione C₂₄ H₁₈ N₂ O₄ CXBAABOAUNPLDL-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth B] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D]	F [auth B] G [auth B] H [auth B] I [auth B] M [auth C] F [auth B], G [auth B], H [auth B], I [auth B], M [auth C], O [auth D], P [auth D], Q [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
R70	BindingDB: 6HXF	Ki: 600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.219
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.84	α = 90
b = 101.67	β = 90
c = 198	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-31

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2018-10-31
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

Prepare Data

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Deposit Data

Help and Resources

6HXF

Human STK10 bound to a maleimide inhibitor

Human STK10 bound to a maleimide inhibitor

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)