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- PDB-9wdf: Crystal structure of PAK4-KPT-7523 complex -

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Basic information

Entry
Database: PDB / ID: 9wdf
TitleCrystal structure of PAK4-KPT-7523 complex
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsSTRUCTURAL PROTEIN / Serine/threonine-protein kinase PAK 4 / TRANSFERASE
Function / homology
Function and homology information


cadherin binding involved in cell-cell adhesion / negative regulation of triglyceride catabolic process / positive regulation of focal adhesion disassembly / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle ...cadherin binding involved in cell-cell adhesion / negative regulation of triglyceride catabolic process / positive regulation of focal adhesion disassembly / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / cellular response to starvation / adherens junction / regulation of cell growth / cell junction / positive regulation of angiogenesis / cell migration / protein kinase activity / protein-macromolecule adaptor activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein stabilization / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLee, S.J. / Park, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Structural basis for a p21-activated kinase 4 and nicotinamide phosphoribosyltransferase dual inhibitor.
Authors: Park, J. / Hong, H.R. / Han, S.H. / Song, J. / Son, S.Y. / Choi, S. / Park, S.M. / Lee, W.K. / Jiko, C. / Kim, J.H. / Jee, J.G. / Bang, J.K. / Park, I.Y. / Lee, S.J.
History
DepositionAug 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase PAK 4
B: Serine/threonine-protein kinase PAK 4
C: Serine/threonine-protein kinase PAK 4
D: Serine/threonine-protein kinase PAK 4
E: Serine/threonine-protein kinase PAK 4
F: Serine/threonine-protein kinase PAK 4
G: Serine/threonine-protein kinase PAK 4
H: Serine/threonine-protein kinase PAK 4
I: Serine/threonine-protein kinase PAK 4
J: Serine/threonine-protein kinase PAK 4
K: Serine/threonine-protein kinase PAK 4
L: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,56936
Polymers396,13612
Non-polymers12,43224
Water4,828268
1
A: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5292
Polymers33,0111
Non-polymers5181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5654
Polymers33,0111
Non-polymers1,5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5292
Polymers33,0111
Non-polymers5181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0473
Polymers33,0111
Non-polymers1,0362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Serine/threonine-protein kinase PAK 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5654
Polymers33,0111
Non-polymers1,5543
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.513, 208.671, 132.489
Angle α, β, γ (deg.)90.00, 103.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine/threonine-protein kinase PAK 4 / p21-activated kinase 4 / PAK-4


Mass: 33011.371 Da / Num. of mol.: 12 / Fragment: Protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK4, KIAA1142 / Production host: Escherichia coli (E. coli)
References: UniProt: O96013, non-specific serine/threonine protein kinase
#2: Chemical...
ChemComp-A1MBG / (~{E})-3-(6-azanylpyridin-3-yl)-~{N}-[[(2~{S})-7-chloranyl-5-(4-piperazin-1-ylcarbonylphenyl)-2,3-dihydro-1-benzofuran-2-yl]methyl]prop-2-enamide


Mass: 518.007 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C28H28ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% PEG 3350, 0.5M Urea, 10% MES (pH 6.5), 2% Phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→44.763 Å / Num. obs: 452527 / % possible obs: 96.56 % / Redundancy: 1.93 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 1.35
Reflection shellResolution: 2.19→2.22 Å / Rmerge(I) obs: 0.607 / Num. unique obs: 234536

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
PDB_EXTRACTdata extraction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.76 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 3843 0.85 %
Rwork0.2212 --
obs0.2215 452527 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27404 0 888 268 28560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128950
X-RAY DIFFRACTIONf_angle_d1.32639273
X-RAY DIFFRACTIONf_dihedral_angle_d23.26811117
X-RAY DIFFRACTIONf_chiral_restr0.074329
X-RAY DIFFRACTIONf_plane_restr0.0185021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.36691340.369415412X-RAY DIFFRACTION90
2.23-2.260.44731460.359516908X-RAY DIFFRACTION98
2.26-2.290.40691460.342916988X-RAY DIFFRACTION98
2.29-2.320.34451460.332916932X-RAY DIFFRACTION98
2.32-2.350.34691440.32216839X-RAY DIFFRACTION98
2.35-2.390.33861450.3216993X-RAY DIFFRACTION98
2.39-2.430.30181430.310516803X-RAY DIFFRACTION98
2.43-2.470.33191490.312616721X-RAY DIFFRACTION97
2.47-2.520.37161400.309616882X-RAY DIFFRACTION98
2.52-2.570.31261450.300216743X-RAY DIFFRACTION98
2.57-2.620.24761460.279817067X-RAY DIFFRACTION99
2.62-2.680.2981460.268417061X-RAY DIFFRACTION99
2.68-2.740.27171480.263916968X-RAY DIFFRACTION99
2.74-2.810.32471490.261817038X-RAY DIFFRACTION99
2.81-2.880.26811430.266517046X-RAY DIFFRACTION99
2.88-2.970.31991450.276516829X-RAY DIFFRACTION98
2.97-3.060.33181440.276516875X-RAY DIFFRACTION98
3.06-3.170.30121430.258216702X-RAY DIFFRACTION97
3.17-3.30.29451450.251116491X-RAY DIFFRACTION96
3.3-3.450.25731380.252616341X-RAY DIFFRACTION95
3.45-3.630.24881370.232916060X-RAY DIFFRACTION93
3.63-3.860.24191350.212416295X-RAY DIFFRACTION95
3.86-4.160.23941390.194816184X-RAY DIFFRACTION94
4.16-4.570.2261330.177416154X-RAY DIFFRACTION94
4.57-5.230.23981400.180816146X-RAY DIFFRACTION94
5.23-6.590.17681390.204515983X-RAY DIFFRACTION93
6.59-44.760.21381350.154716223X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -12.009 Å / Origin y: -37.2862 Å / Origin z: 26.6716 Å
111213212223313233
T0.51 Å20.0136 Å2-0.005 Å2-0.5277 Å2-0.0223 Å2--0.5288 Å2
L0.0476 °20.0444 °20.0022 °2-0.0262 °20.0068 °2--0.0587 °2
S-0.0197 Å °0.0339 Å °0.0189 Å °-0.0117 Å °0.0002 Å °0.0013 Å °-0.023 Å °0.0087 Å °0.0133 Å °
Refinement TLS groupSelection details: all

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