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), 0.198 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6GGH

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23458
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EYQ (Subject of Investigation/LOI) Query on EYQ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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

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), 0.198 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Revision History (Full details and data files)

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

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.