9DUE | pdb_00009due

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-07-081a

PDB DOI: https://doi.org/10.2210/pdb9DUE/pdb

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

Deposited: 2024-10-02 Released: 2024-10-09
Deposition Author(s): Minasov, G., Winsor, J., Roy, S.M., Watterson, D.M., Shuvalova, L.
Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.184 (Depositor), 0.209 (DCC)
R-Value Work:
0.154 (Depositor)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal Structure of Human DAPK1 Catalytic Subunit Complexed with Compound SRM-07-081a

Minasov, G., Winsor, J., Roy, S.M., Watterson, D.M., Shuvalova, L.

To be published.

Macromolecule Content

Total Structure Weight: 34.63 kDa
Atom Count: 2,586
Modeled Residue Count: 276
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	294	Homo sapiens	Mutation(s): 0 Gene Names: DAPK1, DAPK EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P53355 (Homo sapiens) Explore P53355 Go to UniProtKB: P53355
PHAROS: P53355 GTEx: ENSG00000196730
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BB6 (Subject of Investigation/LOI) Query on A1BB6 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-chloro-6-(4-methylpiperazin-1-yl)-4-(pyridin-4-yl)pyridazine C₁₄ H₁₆ Cl N₅ GEGHOUWQCHWMKH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
BO3 Query on BO3 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]	BORIC ACID B H₃ O₃ KGBXLFKZBHKPEV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.184 (Depositor), 0.209 (DCC)
R-Value Work: 0.154 (Depositor)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.01	α = 90
b = 62.684	β = 90
c = 88.462	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

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: 2024-10-09
Type: Initial release
Version 2.0: 2026-01-21
Type: Coordinate replacement
Reason: Chirality error
Changes: Atomic model, Data collection, Structure summary