4V0G | pdb_00004v0g

JAK3 in complex with a covalent EGFR inhibitor

PDB DOI: https://doi.org/10.2210/pdb4V0G/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-09-16 Released: 2016-01-13
Deposition Author(s): Debreczeni, J.E., Hennessy, E.J., Chuaquini, C., Ashton, S., Coclough, N., Cross, D.A.E., Eberlein, C., Gingipalli, L., Klinowska, T.C.M., Orme, J.P., Sha, L., Wu, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.295 (Depositor), 0.296 (DCC)
R-Value Work:
0.252 (Depositor), 0.246 (DCC)
R-Value Observed:
0.254 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Utilisation of Structure Based Design to Identify Novel, Irreversible Inhibitors of the Epidermal Growth Factor Receptor (Egfr) Harboring the Gatekeeper T790M Mutation

Hennessy, E.J., Chuaquini, C., Ashton, S., Coclough, N., Cross, D.A.E., Debreczeni, J.E., Eberlein, C., Gingipalli, L., Klinowska, T.C.M., Orme, J.P., Sha, L., Wu, X.

To be published.

Macromolecule Content

Total Structure Weight: 65.71 kDa
Atom Count: 4,460
Modeled Residue Count: 543
Deposited Residue Count: 566
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE JAK3	A	283	Homo sapiens	Mutation(s): 0 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens) Explore P52333 Go to UniProtKB: P52333
PHAROS: P52333 GTEx: ENSG00000105639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52333
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE JAK3	B	283	Homo sapiens	Mutation(s): 0 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P52333 (Homo sapiens) Explore P52333 Go to UniProtKB: P52333
PHAROS: P52333 GTEx: ENSG00000105639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52333
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G9B Query on G9B Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	N-[3-(2-{3-amino-6-[1-(1-methylpiperidin-4-yl)-1H-pyrazol-4-yl]pyrazin-2-yl}-1H-benzimidazol-1-yl)phenyl]propanamide C₂₉ H₃₁ N₉ O KKUKNIKTWVWHBF-UHFFFAOYSA-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	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.295 (Depositor), 0.296 (DCC)
R-Value Work: 0.252 (Depositor), 0.246 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.14	α = 90
b = 99.032	β = 90
c = 111.373	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Other, Structure summary