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- PDB-9inv: Crystal structure of DAPK1 in complex with isoliquiritigenin -

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Basic information

Entry
Database: PDB / ID: 9inv
TitleCrystal structure of DAPK1 in complex with isoliquiritigenin
ComponentsDeath-associated protein kinase 1
KeywordsTRANSFERASE / DAPK1 / kinase / inhibitor / isoliquiritigenin
Function / homology
Function and homology information


cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : ...cellular response to hydroperoxide / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / defense response to tumor cell / Caspase activation via Dependence Receptors in the absence of ligand / calcium/calmodulin-dependent protein kinase activity / regulation of NMDA receptor activity / syntaxin-1 binding / : / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of autophagy / regulation of autophagy / apoptotic signaling pathway / cellular response to type II interferon / actin cytoskeleton / regulation of apoptotic process / protein autophosphorylation / negative regulation of translation / postsynaptic density / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / negative regulation of apoptotic process / GTP binding / apoptotic process / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat ...Death-associated protein kinase 1 / Roc domain profile. / Roc domain / Ankyrin repeats (many copies) / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2',4,4'-TRIHYDROXYCHALCONE / Death-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsYokoyama, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Discovery and optimization of isoliquiritigenin as a death-associated protein kinase 1 inhibitor.
Authors: Yokoyama, T. / Hisatomi, K. / Oshima, S. / Tanaka, I. / Okada, T. / Toyooka, N.
History
DepositionJul 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Death-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1493
Polymers33,7961
Non-polymers3522
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-6 kcal/mol
Surface area13990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.623, 62.279, 88.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Death-associated protein kinase 1 / DAP kinase 1


Mass: 33796.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAPK1, DAPK / Production host: Escherichia coli (E. coli)
References: UniProt: P53355, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-HCC / 2',4,4'-TRIHYDROXYCHALCONE


Mass: 256.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H12O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, ammonium sulfate, MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.61→46.62 Å / Num. obs: 34197 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rpim(I) all: 0.024 / Rrim(I) all: 0.064 / Net I/σ(I): 20.1
Reflection shellResolution: 1.61→1.64 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1652 / CC1/2: 0.74 / Rpim(I) all: 0.379 / Rrim(I) all: 1.006

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→37.32 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.205 1664 4.87 %
Rwork0.1726 --
obs0.1742 34135 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 24 215 2468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016
X-RAY DIFFRACTIONf_angle_d1.482
X-RAY DIFFRACTIONf_dihedral_angle_d15.415866
X-RAY DIFFRACTIONf_chiral_restr0.123342
X-RAY DIFFRACTIONf_plane_restr0.012399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.660.25031460.22042642X-RAY DIFFRACTION100
1.66-1.710.25741460.212639X-RAY DIFFRACTION100
1.71-1.770.27921250.20082683X-RAY DIFFRACTION100
1.77-1.840.24021490.1832671X-RAY DIFFRACTION100
1.84-1.930.23131390.17262666X-RAY DIFFRACTION100
1.93-2.030.21731530.16262667X-RAY DIFFRACTION100
2.03-2.160.18491360.15522701X-RAY DIFFRACTION100
2.16-2.320.18531280.15892705X-RAY DIFFRACTION100
2.32-2.560.211270.17272712X-RAY DIFFRACTION100
2.56-2.930.23471430.1822719X-RAY DIFFRACTION100
2.93-3.680.20671350.17042772X-RAY DIFFRACTION100
3.69-37.320.17431370.16962894X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.5604 Å / Origin y: 7.3166 Å / Origin z: -12.8705 Å
111213212223313233
T0.1838 Å20.0026 Å2-0.019 Å2-0.1907 Å20.0005 Å2--0.2012 Å2
L0.6781 °20.2147 °2-0.4816 °2-0.5558 °2-0.1964 °2--0.9755 °2
S0.0146 Å °0.0352 Å °-0.0422 Å °0.0046 Å °0.0346 Å °0.0724 Å °0.0566 Å °-0.07 Å °-0.0605 Å °
Refinement TLS groupSelection details: not resname HOH

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