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- PDB-9d4v: Structure of PAK1 in complex with compound 7 -

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Basic information

Entry
Database: PDB / ID: 9d4v
TitleStructure of PAK1 in complex with compound 7
ComponentsSerine/threonine-protein kinase PAK 1
KeywordsTRANSFERASE / Serine/threonine-protein kinase / inhibitor
Function / homology
Function and homology information


negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / gamma-tubulin binding / RHO GTPases Activate ROCKs / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling ...negative regulation of cell proliferation involved in contact inhibition / protein localization to cytoplasmic stress granule / negative regulation of cell growth involved in cardiac muscle cell development / positive regulation of microtubule nucleation / hepatocyte growth factor receptor signaling pathway / gamma-tubulin binding / RHO GTPases Activate ROCKs / positive regulation of vascular associated smooth muscle cell migration / Activation of RAC1 / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of fibroblast migration / regulation of axonogenesis / RHOV GTPase cycle / positive regulation of intracellular estrogen receptor signaling pathway / branching morphogenesis of an epithelial tube / RHOJ GTPase cycle / establishment of cell polarity / stimulatory C-type lectin receptor signaling pathway / RHOQ GTPase cycle / Fc-gamma receptor signaling pathway involved in phagocytosis / exocytosis / RHO GTPases activate PAKs / RHOU GTPase cycle / regulation of MAPK cascade / CDC42 GTPase cycle / Generation of second messenger molecules / intercalated disc / RHOH GTPase cycle / Sema3A PAK dependent Axon repulsion / positive regulation of protein targeting to membrane / Smooth Muscle Contraction / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of insulin receptor signaling pathway / ephrin receptor signaling pathway / positive regulation of axon extension / collagen binding / positive regulation of vascular associated smooth muscle cell proliferation / RHO GTPases activate PKNs / neuron projection morphogenesis / positive regulation of stress fiber assembly / ruffle / positive regulation of microtubule polymerization / RAC1 GTPase cycle / EPHB-mediated forward signaling / CD209 (DC-SIGN) signaling / cerebellum development / cellular response to starvation / Signal transduction by L1 / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / actin filament / FCERI mediated MAPK activation / wound healing / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / Z disc / cellular response to insulin stimulus / G beta:gamma signalling through CDC42 / cell-cell junction / cell migration / lamellipodium / chromosome / actin cytoskeleton organization / nuclear membrane / response to hypoxia / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / chromatin remodeling / axon / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / dendrite / centrosome / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...p21 activated kinase binding domain / : / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / 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
Similarity search - Domain/homology
: / Serine/threonine-protein kinase PAK 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsDementiev, A. / Boone, C.D. / Suto, R.K. / Olland, A.M.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Identification of a p21-activated kinase 1 (PAK1) inhibitor with 10-fold selectivity against PAK2.
Authors: Johns, D.M. / Olejniczak, J. / Babbar, A. / Boone, C.D. / Cakici, O. / Cheng, M. / Cheng, Q.Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Kozlowski, R. / Lee, S.W. ...Authors: Johns, D.M. / Olejniczak, J. / Babbar, A. / Boone, C.D. / Cakici, O. / Cheng, M. / Cheng, Q.Q. / Dementiev, A. / Eick, M. / Ferdyan, N. / Fontano, E. / Forman, A. / Kozlowski, R. / Lee, S.W. / Mehta, S. / Mowery, K. / Murray, B. / Nguyen, V. / Olland, A. / Phan, K.B. / Rivera, L. / Sabat, M. / Sprengeler, P. / Srinivasan, K. / Sun, Z. / Suto, R.K. / Wilkinson, T. / Wang, C. / Yu, N. / Xu, M. / Goel, V. / Hirst, G. / Reich, S.
History
DepositionAug 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 16, 2025Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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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 1
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2614
Polymers66,5732
Non-polymers6892
Water1,36976
1
A: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6312
Polymers33,2861
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase PAK 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6312
Polymers33,2861
Non-polymers3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.727, 80.824, 65.857
Angle α, β, γ (deg.)90.000, 107.274, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine/threonine-protein kinase PAK 1 / Alpha-PAK / p21-activated kinase 1 / PAK-1 / p65-PAK


Mass: 33286.270 Da / Num. of mol.: 2 / Mutation: D389N,T423E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAK1
Details (production host): 6xHis-GST-TEV-PAK1(D389N/T423E)(249-545)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): One Shot BL21 Star (DE3)
References: UniProt: Q13153, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1A2P / N~2~-{[(1s,4s)-4-aminocyclohexyl]methyl}-N~4~-(5-cyclopropyl-1,3-thiazol-2-yl)pyrimidine-2,4-diamine


Mass: 344.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Na-malonate, pH 7.0, 0.15 M DL-malic acid, 4% propane-diol, and 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.84→59.9 Å / Num. obs: 54294 / % possible obs: 99.4 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.029 / Rrim(I) all: 0.063 / Net I/σ(I): 10.1
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.687 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2664 / CC1/2: 0.578 / Rpim(I) all: 0.875 / Rrim(I) all: 1.907 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→49.633 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.287 / WRfactor Rwork: 0.214 / SU B: 7.312 / SU ML: 0.193 / Average fsc free: 0.9029 / Average fsc work: 0.9242 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 3847 7.128 %RANDOM
Rwork0.1968 50121 --
all0.202 ---
obs-53968 98.988 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 65.625 Å2
Baniso -1Baniso -2Baniso -3
1--0.112 Å20 Å20.048 Å2
2--0.123 Å2-0 Å2
3----0.034 Å2
Refinement stepCycle: LAST / Resolution: 1.84→49.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 48 76 4522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0124547
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164340
X-RAY DIFFRACTIONr_angle_refined_deg2.541.6656172
X-RAY DIFFRACTIONr_angle_other_deg0.7921.5669992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8195580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.776521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90710797
X-RAY DIFFRACTIONr_dihedral_angle_6_deg1610184
X-RAY DIFFRACTIONr_chiral_restr0.1240.2718
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025274
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined0.2310.2996
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.24189
X-RAY DIFFRACTIONr_nbtor_refined0.1990.22267
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.22557
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.25
X-RAY DIFFRACTIONr_nbd_other0.180.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.26
X-RAY DIFFRACTIONr_mcbond_it9.5176.6732309
X-RAY DIFFRACTIONr_mcbond_other9.5176.6752309
X-RAY DIFFRACTIONr_mcangle_it11.6511.9292883
X-RAY DIFFRACTIONr_mcangle_other11.66711.9312884
X-RAY DIFFRACTIONr_scbond_it11.0347.1512238
X-RAY DIFFRACTIONr_scbond_other10.967.1332212
X-RAY DIFFRACTIONr_scangle_it13.95112.8833279
X-RAY DIFFRACTIONr_scangle_other13.91912.8433246
X-RAY DIFFRACTIONr_lrange_it15.34961.6145038
X-RAY DIFFRACTIONr_lrange_other15.34361.2425009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.84-1.8880.4752760.4535480.45240080.7860.81795.40920.372
1.888-1.9390.4622460.42636010.42839050.7070.74898.51470.34
1.939-1.9950.4112460.435470.438060.8620.8799.65840.318
1.995-2.0570.3922620.37934340.3837030.8520.86899.8110.311
2.057-2.1240.3282330.32533350.32635780.9030.9199.72050.253
2.124-2.1980.3582420.29132100.29534540.9110.93599.94210.23
2.198-2.2810.3092750.25830430.26233260.9320.95299.75950.205
2.281-2.3740.3242250.24330170.24932450.9360.96199.90750.197
2.374-2.4790.3372110.22928560.23630800.9330.96999.57790.194
2.479-2.60.2782090.22127440.22529630.9490.97399.66250.197
2.6-2.740.3152130.22126020.22828260.9430.97499.61080.204
2.74-2.9060.3081940.22424330.2326460.9390.9799.28190.219
2.906-3.1060.3051730.21523140.22125100.9450.97299.08370.22
3.106-3.3540.3431640.21321560.22223500.9210.97298.72340.224
3.354-3.6720.2651750.20219550.20721620.960.97998.51990.218
3.672-4.1030.2341320.16617740.1719450.9660.98597.99490.191
4.103-4.7320.2081150.13515700.13917270.9750.98997.5680.17
4.732-5.7820.2111090.16413360.16814690.9740.98798.36620.206
5.782-8.1230.224890.15710370.16211450.9730.98698.34060.204
8.123-49.6330.246580.1526090.1596690.9670.98699.7010.213

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