8TQD

NF-Kappa-B1 Bound with a Covalent Inhibitor

PDB DOI: https://doi.org/10.2210/pdb8TQD/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-08-07 Released: 2024-04-24
Deposition Author(s): Hilbert, B.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.227
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

DrugMap: A quantitative pan-cancer analysis of cysteine ligandability

Bar-Peled, L., Hara, M., White, R.D., Kryukov, G., Maynard, M., Martin, B., Guzman-Perez, A.

To be published.

Macromolecule Content

Total Structure Weight: 23.12 kDa
Atom Count: 1,713
Modelled Residue Count: 200
Deposited Residue Count: 207
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor NF-kappa-B p105 subunit	A	207	Homo sapiens	Mutation(s): 0 Gene Names: NFKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens) Explore P19838 Go to UniProtKB: P19838
PHAROS: P19838 GTEx: ENSG00000109320
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19838
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JMR (Subject of Investigation/LOI) Query on JMR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-(2-bromo-4-chlorophenyl)-N-{(3S)-1-[(E)-iminomethyl]pyrrolidin-3-yl}methanesulfonamide C₁₂ H₁₅ Br Cl N₃ O₂ S JCYNDVNUPRPXTG-LWHXSLQUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.227
R-Value Work: 0.182
R-Value Observed: 0.184
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.21	α = 90
b = 57.21	β = 90
c = 71.85	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-04-24
Type: Initial release

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 R01GM133198.