7JYO | pdb_00007jyo

JAK2 JH2 in complex with JAK064

PDB DOI: https://doi.org/10.2210/pdb7JYO/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2020-08-31 Released: 2021-07-14
Deposition Author(s): Puleo, D.E., Krimmer, S.G., Newton, A.S., Schlessinger, J., Jorgensen, W.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.246 (Depositor), 0.246 (DCC)
R-Value Work:
0.185 (Depositor), 0.187 (DCC)
R-Value Observed:
0.188 (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

Indoloxytriazines as binding molecules for the JAK2 JH2 pseudokinase domain and its V617F variant

Newton, A.S., Liosi, M.E., Henry, S.P., Deiana, L., Faver, J.C., Krimmer, S.G., Puleo, D.E., Schlessinger, J., Jorgensen, W.L.

(2021) Tetrahedron Lett 77: 153248

DOI: https://doi.org/10.1016/j.tetlet.2021.153248

Macromolecule Content

Total Structure Weight: 33.56 kDa
Atom Count: 2,138
Modeled Residue Count: 270
Deposited Residue Count: 289
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein kinase JAK2	A	289	Homo sapiens	Mutation(s): 3 Gene Names: JAK2 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for O60674 (Homo sapiens) Explore O60674 Go to UniProtKB: O60674
PHAROS: O60674 GTEx: ENSG00000096968
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O60674
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VPS (Subject of Investigation/LOI) Query on VPS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-({4-amino-6-[(4-cyanophenyl)amino]-1,3,5-triazin-2-yl}oxy)benzoic acid C₁₇ H₁₂ N₆ O₃ WKFGNLUJVJDVRJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
VPS	BindingDB: 7JYO	Kd: 3.96e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.246 (Depositor), 0.246 (DCC)
R-Value Work: 0.185 (Depositor), 0.187 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.568	α = 90
b = 57.375	β = 111.004
c = 61.071	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GMO32136

Revision History (Full details and data files)

Version 1.0: 2021-07-14
Type: Initial release
Version 1.1: 2021-08-04
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description