9QKA | pdb_00009qka

NCS-1 bound to XChem ligand 4

PDB DOI: https://doi.org/10.2210/pdb9QKA/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2025-03-19 Released: 2026-09-16
Deposition Author(s): Munoz-Reyes, D., Sanchez-Barrena, M.J.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.278 (Depositor), 0.275 (DCC)
R-Value Work:
0.241 (Depositor), 0.241 (DCC)
R-Value Observed:
0.243 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9QKA

This is version 1.0 of the entry. See complete history.

Literature

A resource-efficient structure-based workflow for fragment progression enables parallel hit discovery and validation of functionally diverse modulators of NCS-1 protein-protein interactions

Munoz-Reyes, D., Fieseler, K.K., Winokan, M., Golding, M.N., Capkin, E., Ferla, M., Perez-Suarez, S., Tomlinson, C.W., Marples, P.G., Miro-Rodriguez, C., Aguado, L., Mansilla, A., Fearon, D., Thompson, W.A., von Delft, F., Sanchez-Barrena, M.J.

(2026) Chem Sci

DOI: https://doi.org/10.1039/D6SC02031C

Macromolecule Content

Total Structure Weight: 46.05 kDa
Atom Count: 3,222
Modeled Residue Count: 370
Deposited Residue Count: 380
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal calcium sensor 1	A [auth B], B [auth A]	190	Homo sapiens	Mutation(s): 0 Gene Names: NCS1, FLUP, FREQ
UniProt & NIH Common Fund Data Resources
Find proteins for P62166 (Homo sapiens) Explore P62166 Go to UniProtKB: P62166
PHAROS: P62166 GTEx: ENSG00000107130
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I7N( Subject of Investigation/LOI) Query on A1I7N Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain G [auth B] MOL2 format, chain P [auth A] MOL2 format, chain G [auth B] mmCIF format, chain P [auth A] mmCIF format, chain G [auth B]	G [auth B], P [auth A]	~{N}-[2,4-bis(fluoranyl)-3-methyl-phenyl]-2-methyl-5-piperidin-1-ylsulfonyl-furan-3-carboxamide C₁₈ H₂₀ F₂ N₂ O₄ S GPLFJUVOKHJOGM-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain P [auth A] Interactions & Density Focus chain G [auth B] Focus chain P [auth A]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain H [auth B] MOL2 format, chain R [auth A] MOL2 format, chain H [auth B] mmCIF format, chain R [auth A] mmCIF format, chain H [auth B]	H [auth B], R [auth A]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain R [auth A] Interactions & Density Focus chain H [auth B] Focus chain R [auth A]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain O [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A]	O [auth A], Q [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain Q [auth A] Interactions & Density Focus chain O [auth A] Focus chain Q [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain F [auth B] MOL2 format, chain N [auth A] MOL2 format, chain F [auth B] mmCIF format, chain N [auth A] mmCIF format, chain F [auth B]	F [auth B], N [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth B] Focus chain N [auth A] Interactions & Density Focus chain F [auth B] Focus chain N [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain E [auth B] SDF format, chain D [auth B] SDF format, chain C [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] MOL2 format, chain C [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B] mmCIF format, chain C [auth B]	C [auth B] D [auth B] E [auth B] J [auth A] K [auth A] C [auth B], D [auth B], E [auth B], J [auth A], K [auth A], L [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain E [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain I [auth B] MOL2 format, chain M [auth A] MOL2 format, chain I [auth B] mmCIF format, chain M [auth A] mmCIF format, chain I [auth B]	I [auth B], M [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain M [auth A] Interactions & Density Focus chain I [auth B] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.278 (Depositor), 0.275 (DCC)
R-Value Work: 0.241 (Depositor), 0.241 (DCC)
R-Value Observed: 0.243 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.209	α = 90
b = 55.939	β = 99.795
c = 80.401	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Munoz-Reyes, D.

Sanchez-Barrena, M.J.

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-137331OB-C31

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.