6Z1T | pdb_00006z1t

MAP3K14 (NIK) in complex with 4S/3694

PDB DOI: https://doi.org/10.2210/pdb6Z1T/pdb

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

Deposited: 2020-05-14 Released: 2020-07-08
Deposition Author(s): Jacoby, E., van Vlijmen, H., Querolle, O., Stansfield, I., Meerpoel, L., Versele, M., Hynd, G., Attar, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.197 (Depositor), 0.197 (DCC)
R-Value Observed:
0.200 (Depositor)

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

FEP+ calculations predict a stereochemical SAR switch for first-in-class indoline NIK inhibitors for multiple myeloma

Jacoby, E., Vlijmen, H.V., Querolle, O., Stansfield, I., Meerpoel, L., Versele, M., Hynd, G., Attar, R.

(2020) Future Drug Discov 2

DOI: https://doi.org/10.4155/fdd-2020-0004

Macromolecule Content

Total Structure Weight: 78.32 kDa
Atom Count: 5,313
Modeled Residue Count: 665
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 14	A [auth AAA], B [auth BBB]	351	Homo sapiens	Mutation(s): 0 Gene Names: MAP3K14, NIK EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q99558 (Homo sapiens) Explore Q99558 Go to UniProtKB: Q99558
PHAROS: Q99558 GTEx: ENSG00000006062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99558
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Q55 Query on Q55 Download:Ideal Coordinates CCD File SDF format, chain D [auth BBB] SDF format, chain C [auth AAA] MOL2 format, chain D [auth BBB] MOL2 format, chain C [auth AAA] mmCIF format, chain D [auth BBB] mmCIF format, chain C [auth AAA]	C [auth AAA], D [auth BBB]	4S/3694 C₂₁ H₂₀ N₆ O₂ PTVSCHCHSJTBBB-NRFANRHFSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.197 (Depositor), 0.197 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.5	α = 90
b = 84.5	β = 90
c = 118.72	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2021-01-20
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description