4TXC | pdb_00004txc

Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor

PDB DOI:&nbsphttps://doi.org/10.2210/pdb4TXC/pdb

Classification:&nbspTRANSFERASE
Organism(s):&nbspHomo sapiens
Expression System:&nbspEscherichia coli BL21(DE3)
Mutation(s):&nbspNo&nbsp

Deposited:&nbsp2014-07-03&nbspReleased:&nbsp2014-07-23&nbsp
Deposition Author(s):&nbspSorrell, F.J., Krojer, T., Wilbek, T.S., Skovgaard, T., Berthelsen, J., Dixon-Clarke, S., Chalk, R., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Stromgaard, K., Knapp, S.

Experimental Data Snapshot

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.95 Å
R-Value Free:&nbsp
0.216 (Depositor), 0.220 (DCC)&nbsp
R-Value Work:&nbsp
0.180 (Depositor), 0.180 (DCC)&nbsp
R-Value Observed:&nbsp
0.181&nbsp(Depositor)&nbsp

Starting Models: experimental
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wwPDB Validation&nbsp 3D Report&nbspFull Report

Ligand Structure Quality Assessment&nbsp

This is version 1.4 of the entry. See complete&nbsphistory.&nbsp

Literature

Identification and characterization of a small-molecule inhibitor of death-associated protein kinase 1.

Wilbek, T.S.,&nbspSkovgaard, T.,&nbspSorrell, F.J.,&nbspKnapp, S.,&nbspBerthelsen, J.,&nbspStrmgaard, K.

(2015) Chembiochem&nbsp16: 59-63

PubMed:&nbsp25382253&nbspSearch on PubMedSearch on PubMed Central
DOI:&nbsphttps://doi.org/10.1002/cbic.201402512
Primary Citation of Related Structures: &nbsp
4TXC

Organizational Affiliation

Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen (Denmark).

Macromolecule Content

Total Structure Weight: 35.57 kDa&nbsp
Atom Count: 2,543&nbsp
Modelled Residue Count: 276&nbsp
Deposited Residue Count: 304&nbsp
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death-associated protein kinase 1	A	304	Homo sapiens	Mutation(s): 0&nbsp Gene Names:&nbspDAPK1,&nbspDAPK EC:&nbsp2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP53355&nbsp(Homo sapiens) Explore&nbspP53355&nbsp Go to UniProtKB: &nbspP53355
PHAROS: &nbspP53355 GTEx: &nbspENSG00000196730&nbsp
Entity Groups &nbsp
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands&nbsp2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
38G Query on 38G Download Ideal Coordinates CCD File&nbsp SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-(3-{3-[(R)-{[2-(dimethylamino)ethyl]amino}(hydroxy)methyl]phenyl}imidazo[1,2-b]pyridazin-6-yl)-2-methoxyphenol C₂₄ H₂₇ N₅ O₃ ASDVVHQAXNTHHM-XMMPIXPASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File&nbsp SDF format, chain F [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] 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 C [auth A] 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]

Experimental Data & Validation

Experimental Data

Method:&nbspX-RAY DIFFRACTION
Resolution:&nbsp1.95 Å
R-Value Free:&nbsp 0.216 (Depositor), 0.220 (DCC)&nbsp
R-Value Work:&nbsp 0.180 (Depositor), 0.180 (DCC)&nbsp
R-Value Observed:&nbsp0.181&nbsp(Depositor)&nbsp

Space Group:&nbspP 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.9	α = 90
b = 77.29	β = 90
c = 110.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment&nbsp

Entry History&nbsp

Deposition Data

Released Date:&nbsp2014-07-23&nbsp

Deposition Author(s):&nbsp

Revision History (Full details and data files)

Version 1.0: 2014-07-23
Type: Initial release
Version 1.1: 2014-11-19
Changes: Database references
Version 1.2: 2015-01-14
Changes: Database references
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Refinement description

Prepare Data

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Deposit Data

Help and Resources

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Crystal Structure of DAPK1 kinase domain in complex with a small molecule inhibitor

Identification and characterization of a small-molecule inhibitor of death-associated protein kinase 1.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups &nbsp

Sequence Annotations

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