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- PDB-5bms: Crystal structure of P21-activated kinase 4 in complex with an in... -

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Basic information

Entry
Database: PDB / ID: 5bms
TitleCrystal structure of P21-activated kinase 4 in complex with an inhibitor compound 29
ComponentsSerine/threonine-protein kinase PAK 4
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase / Inhibitor / Complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle ...dendritic spine development / cadherin binding involved in cell-cell adhesion / Activation of RAC1 / RHOV GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / regulation of MAPK cascade / RHOH GTPase cycle / CDC42 GTPase cycle / RHOU GTPase cycle / cellular response to organic cyclic compound / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / negative regulation of endothelial cell apoptotic process / cytoskeleton organization / RAC1 GTPase cycle / regulation of cell growth / adherens junction / positive regulation of angiogenesis / cell migration / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cell cycle / phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / apoptotic process / Golgi apparatus / signal transduction / ATP binding / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...p21 activated kinase binding domain / CRIB domain superfamily / P21-Rho-binding domain / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4T6 / Serine/threonine-protein kinase PAK 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.903 Å
AuthorsRouge, L. / Wang, W.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structure-Guided Design of Group I Selective p21-Activated Kinase Inhibitors.
Authors: Crawford, J.J. / Lee, W. / Aliagas, I. / Mathieu, S. / Hoeflich, K.P. / Zhou, W. / Wang, W. / Rouge, L. / Murray, L. / La, H. / Liu, N. / Fan, P.W. / Cheong, J. / Heise, C.E. / Ramaswamy, S. ...Authors: Crawford, J.J. / Lee, W. / Aliagas, I. / Mathieu, S. / Hoeflich, K.P. / Zhou, W. / Wang, W. / Rouge, L. / Murray, L. / La, H. / Liu, N. / Fan, P.W. / Cheong, J. / Heise, C.E. / Ramaswamy, S. / Mintzer, R. / Liu, Y. / Chao, Q. / Rudolph, J.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4492
Polymers33,0681
Non-polymers3811
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.412, 64.412, 185.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 33068.422 Da / Num. of mol.: 1 / Fragment: Protein kinase domain residues 300-591
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-4T6 / N~2~-[(7-chloro-1H-benzimidazol-6-yl)methyl]-N~4~-(5-cyclopropyl-1H-pyrazol-3-yl)pyrimidine-2,4-diamine


Mass: 380.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17ClN8

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Tri-Potassium citrate and 20% PEG3350

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 9264 / % possible obs: 99.9 % / Redundancy: 11.3 % / Net I/σ(I): 25.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.903→37.588 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 431 4.68 %
Rwork0.1735 --
obs0.1761 9207 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.903→37.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 27 0 2327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042379
X-RAY DIFFRACTIONf_angle_d0.8553226
X-RAY DIFFRACTIONf_dihedral_angle_d14.399907
X-RAY DIFFRACTIONf_chiral_restr0.03360
X-RAY DIFFRACTIONf_plane_restr0.004415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9035-3.32340.28551410.21432820X-RAY DIFFRACTION99
3.3234-4.18620.25831230.18972906X-RAY DIFFRACTION100
4.1862-37.59110.20781670.15543050X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.51180.1118-0.35930.9563-0.14741.0737-0.25110.13190.3031-0.1460.08780.02230.0433-0.02260.00020.40430.05520.02740.5151-0.01820.5055-25.460416.3711-22.8605
21.88580.1441-1.53633.2661-1.5662.33610.2896-0.4259-0.19760.153-0.4850.015-0.11790.2154-0.0290.4550.02260.00540.46320.0840.4114-26.09116.0086-0.3093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 299:398
2X-RAY DIFFRACTION2chain A and resid 399:589 or chain A and resid 601

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