6GGH | pdb_00006ggh

Human jak1 kinase domain in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6GGH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2018-05-03 Released: 2019-05-22 
• Deposition Author(s): Read, J.A., Augustin, M., Lammens, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Inhibition of local lung inflammation by a potent and selective JAK1 inhibitor; activation of JAK1, but not JAK3, is critical to IL-4R mediated immune cell signalling

Nilsson, M.

To be published.

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: 68.36 kDa 
• Atom Count: 5,118 
• Modeled Residue Count: 568 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK1	A, B	292	Homo sapiens	Mutation(s): 0  EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P23458 (Homo sapiens) Explore P23458  Go to UniProtKB:  P23458
PHAROS:  P23458 GTEx:  ENSG00000162434

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EYQ (Subject of Investigation/LOI)	C [auth A], D [auth B]	~{N}-[5-methyl-4-[7-[[(2~{R})-2-(4-methylpiperazin-1-yl)propanoyl]amino]-1~{H}-indol-3-yl]pyrimidin-2-yl]cyclopropanecarboxamide C25 H31 N7 O2 IMKONRLYDLGQAV-MRXNPFEDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
EYQ	BindingDB:  6GGH	IC50: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.987	α = 90
b = 170.327	β = 94.06
c = 45.026	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Read, J.A., Augustin, M., Lammens, A.

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary