3ZC6

Crystal structure of JAK3 kinase domain in complex with an indazole substituted pyrrolopyrazine inhibitor

PDB DOI: https://doi.org/10.2210/pdb3ZC6/pdb

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

Deposited: 2012-11-16 Released: 2013-09-25
Deposition Author(s): Kuglstatter, A., Jestel, A., Nagel, S., Boettcher, J., Blaesse, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.254
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Strategic Use of Conformational Bias and Structure Based Design to Identify Potent Jak3 Inhibitors with Improved Selectivity Against the Jak Family and the Kinome.

Lynch, S.M., Devicente, J., Hermann, J.C., Jaime-Figueroa, S., Jin, S., Kuglstatter, A., Li, H., Lovey, A., Menke, J., Niu, L., Patel, V., Roy, D., Soth, M., Steiner, S., Tivitmahaisoon, P., Vu, M.D., Yee, C.

(2013) Bioorg Med Chem Lett 23: 2793

PubMed: 23540648 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.02.012
Primary Citation of Related Structures:
3ZC6

PubMed Abstract:
Using a structure based design approach we have identified a series of indazole substituted pyrrolopyrazines, which are potent inhibitors of JAK3. Intramolecular electronic repulsion was used as a strategy to induce a strong conformational bias within the ligand. Compounds bearing this conformation participated in a favorable hydrophobic interaction with a cysteine residue in the JAK3 binding pocket, which imparted high selectivity versus the kinome and improved selectivity within the JAK family.

Organizational Affiliation

Discovery Chemistry, Hoffmann-La Roche, pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley, NJ 07110, USA. stephen.lynch@roche.com

Macromolecule Content

Total Structure Weight: 134.42 kDa
Atom Count: 9,695
Modelled Residue Count: 1,103
Deposited Residue Count: 1,152
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN KINASE JAK3	A, B, C, D	288	Homo sapiens	Mutation(s): 2 EC: 2.7.10.2 (PDB Primary Data), 2.7.1.112 (PDB Primary Data)
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52333
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VFC Query on VFC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D]	E [auth A], J [auth B], M [auth C], O [auth D]	N-[(2R)-1-(3-cyanoazetidin-1-yl)-1-oxidanylidene-propan-2-yl]-2-(6-fluoranyl-1-methyl-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide C₂₂ H₁₉ F N₈ O₂ AGTYRXOJPORGGM-LLVKDONJSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	K [auth B], N [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain K [auth B] Focus chain N [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth D]	G [auth A], H [auth A], I [auth A], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth D]