9YLH | pdb_00009ylh

Human p38 ALPHA MAPK:MW01-8-105SRM N,N-Dimethyl-6-phenyl-5-(4-pyridinyl)-3-pyridazinamine inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb9YLH/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-10-08 Released: 2025-11-19
Deposition Author(s): Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free:
0.239 (Depositor), 0.237 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9YLH

Ligand Structure Quality Assessment

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

Literature

Human p38 ALPHA MAPK:MW01-8-105SRM N,N-Dimethyl-6-phenyl-5-(4-pyridinyl)-3-pyridazinamine inhibitor complex

Brunzelle, J.S., Shuvalova, L., Roy, S.M., Watterson, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 42.08 kDa
Atom Count: 2,868
Modeled Residue Count: 339
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0 Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539 Go to UniProtKB: Q16539
PHAROS: Q16539 GTEx: ENSG00000112062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CX9 Query on A1CX9 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	N,N-dimethyl-6-phenyl-5-(pyridin-4-yl)pyridazin-3-amine C₁₇ H₁₆ N₄ JZNLARIEJUCAJO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
GG5 Query on GG5 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]	4-[3-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]PYRIDINE C₁₄ H₁₀ F N₃ BILJSHVAAVZERY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.02 Å
R-Value Free: 0.239 (Depositor), 0.237 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.89	α = 90
b = 74.849	β = 90
c = 77.929	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
DIMPLE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-19

Deposition Author(s):

Brunzelle, J.S.

Watterson, D.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	AG066722

Revision History (Full details and data files)

Version 1.0: 2025-11-19
Type: Initial release

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