6WPP | pdb_00006wpp

HUMAN NIK IN COMPLEX WITH LIGAND COMPOUND X

• PDB DOI: https://doi.org/10.2210/pdb6WPP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2020-04-27 Released: 2020-08-26 
• Deposition Author(s): Shih, A.Y., Hack, M., Mirzadegan, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.256 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Impact of Protein Preparation on Resulting Accuracy of FEP Calculations.

Shih, A.Y., Hack, M., Mirzadegan, T.

(2020) J Chem Inf Model 60: 5287-5289

• PubMed: 32786514 
• DOI: https://doi.org/10.1021/acs.jcim.0c00445
• Primary Citation Related Structures: 
  6WPP


• PubMed Abstract: 
  

  Relative free energy perturbation (FEP) methods have become increasingly popular within the pharmaceutical industry; however, despite time constraints within drug discovery cycles, caution should be applied in the deployment of such methods as protein preparation and system setup can greatly impact the accuracy of free energy predictions.

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Organizational Affiliation: 
• Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California 92121, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.41 kDa 
• Atom Count: 4,989 
• Modeled Residue Count: 627 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 14	A, B	347	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PZ4 (Subject of Investigation/LOI)	C [auth A], D [auth B]	5-fluoro-N-methyl-2-(7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrimidin-4-amine C11 H9 F N6 VCAWVIOIVGOEIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.256 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.483	α = 90
b = 81.521	β = 111.43
c = 78.42	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Shih, A.Y., Hack, M., Mirzadegan, T.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Data collection
• Version 1.2: 2020-12-02
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Advisory, Data collection, Database references