6OYT | pdb_00006oyt

ASK1 kinase domain in complex with GS-4997

PDB DOI: https://doi.org/10.2210/pdb6OYT/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-15 Released: 2019-11-27
Deposition Author(s): Marcotte, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.290 (Depositor), 0.288 (DCC)
R-Value Work:
0.232 (Depositor), 0.235 (DCC)
R-Value Observed:
0.235 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Rational Design and Optimization of a Novel Class of Macrocyclic Apoptosis Signal-Regulating Kinase 1 Inhibitors.

Himmelbauer, M.K., Xin, Z., Jones, J.H., Enyedy, I., King, K., Marcotte, D.J., Murugan, P., Santoro, J.C., Hesson, T., Spilker, K., Johnson, J.L., Luzzio, M.J., Gilfillan, R., de Turiso, F.G.

(2019) J Med Chem 62: 10740-10756

PubMed: 31710475 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.9b01206
Primary Citation Related Structures:
6OYT, 6OYW

PubMed Abstract:
Structural analysis of a known apoptosis signal-regulating kinase 1 (ASK1) inhibitor bound to its kinase domain led to the design and synthesis of the novel macrocyclic inhibitor 8 (cell IC ₅₀ = 1.2 μM). The profile of this compound was optimized for CNS penetration following two independent strategies: a rational design approach leading to 19 and a parallel synthesis approach leading to 26 . Both analogs are potent ASK1 inhibitors in biochemical and cellular assays ( 19 , cell IC ₅₀ = 95 nM; 26 , cell IC ₅₀ = 123 nM) and have moderate to low efflux ratio (ER) in an MDR1-MDCK assay ( 19 , ER = 5.2; 26 , ER = 1.5). In vivo PK studies revealed that inhibitor 19 had moderate CNS penetration ( K _puu = 0.17) and analog 26 had high CNS penetration ( K _puu = 1.0).

Macromolecule Content

Total Structure Weight: 129.12 kDa
Atom Count: 7,556
Modeled Residue Count: 949
Deposited Residue Count: 1,120
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 5	A, B, C, D	280	Homo sapiens	Mutation(s): 0 Gene Names: MAP3K5, ASK1, MAPKKK5, MEKK5 EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q99683 (Homo sapiens) Explore Q99683 Go to UniProtKB: Q99683
PHAROS: Q99683 GTEx: ENSG00000197442
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99683
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NJV Query on NJV Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth C] SDF format, chain N [auth D] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth D] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth D] mmCIF format, chain G [auth B]	E [auth A], G [auth B], K [auth C], N [auth D]	5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide C₂₄ H₂₄ F N₇ O YIDDLAAKOYYGJG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth D] SDF format, chain M [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth D] MOL2 format, chain M [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth D] mmCIF format, chain M [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	F [auth A] H [auth B] I [auth B] J [auth B] L [auth C] F [auth A], H [auth B], I [auth B], J [auth B], L [auth C], M [auth D], O [auth D], P [auth D], Q [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth D] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.290 (Depositor), 0.288 (DCC)
R-Value Work: 0.232 (Depositor), 0.235 (DCC)
R-Value Observed: 0.235 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.51	α = 90
b = 73.59	β = 97.77
c = 95.14	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-11-27

Deposition Author(s):

Marcotte, D.J.

Revision History (Full details and data files)

Version 1.0: 2019-11-27
Type: Initial release
Version 1.1: 2019-12-04
Changes: Database references
Version 1.2: 2019-12-25
Changes: Database references
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary