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- PDB-5di1: MAP4K4 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 5di1
TitleMAP4K4 in complex with an inhibitor
ComponentsMitogen-activated protein kinase kinase kinase kinase 4
KeywordsTRANSFERASE/INHIBITOR / kinase / inhibitor / complex / medicinal chemistry / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity ...positive regulation of ARF protein signal transduction / creatine kinase activity / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / regulation of MAPK cascade / regulation of JNK cascade / neuron projection morphogenesis / positive regulation of GTPase activity / MAPK cascade / microtubule binding / Oxidative Stress Induced Senescence / non-specific serine/threonine protein kinase / positive regulation of cell migration / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / negative regulation of apoptotic process / ATP binding / cytoplasm
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / Citron homology (CNH) domain / CNH domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-5DF / Mitogen-activated protein kinase kinase kinase kinase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLiu, S.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Discovery of an in Vivo Tool to Establish Proof-of-Concept for MAP4K4-Based Antidiabetic Treatment.
Authors: Ammirati, M. / Bagley, S.W. / Bhattacharya, S.K. / Buckbinder, L. / Carlo, A.A. / Conrad, R. / Cortes, C. / Dow, R.L. / Dowling, M.S. / El-Kattan, A. / Ford, K. / Guimaraes, C.R. / Hepworth, ...Authors: Ammirati, M. / Bagley, S.W. / Bhattacharya, S.K. / Buckbinder, L. / Carlo, A.A. / Conrad, R. / Cortes, C. / Dow, R.L. / Dowling, M.S. / El-Kattan, A. / Ford, K. / Guimaraes, C.R. / Hepworth, D. / Jiao, W. / LaPerle, J. / Liu, S. / Londregan, A. / Loria, P.M. / Mathiowetz, A.M. / Munchhof, M. / Orr, S.T. / Petersen, D.N. / Price, D.A. / Skoura, A. / Smith, A.C. / Wang, J.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase kinase 4
B: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2383
Polymers70,8972
Non-polymers3401
Water63135
1
A: Mitogen-activated protein kinase kinase kinase kinase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7892
Polymers35,4491
Non-polymers3401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase kinase 4


Theoretical massNumber of molelcules
Total (without water)35,4491
Polymers35,4491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-13 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 91.740, 96.620
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 Mitogen-activated protein kinase kinase kinase kinase 4 / HPK/GCK-like kinase HGK / MAPK/ERK kinase kinase kinase 4 / MEKKK 4 / Nck-interacting kinase


Mass: 35448.703 Da / Num. of mol.: 2 / Fragment: UNP residues 1-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP4K4, HGK, KIAA0687, NIK
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: O95819, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-5DF / 4-{6-amino-5-[4-(methylsulfonyl)phenyl]pyridin-3-yl}phenol


Mass: 340.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16N2O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM HEPES pH7.0, 0.3 M NaCl, 30% PEG NNE 2000m 0.1 M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. obs: 15489 / % possible obs: 93.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 74.49 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 29.9
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.7 / % possible all: 45

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Processing

Software
NameVersionClassification
BUSTER2.9.5refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3M

1f3m


Resolution: 2.9→41.44 Å / Cor.coef. Fo:Fc: 0.9278 / Cor.coef. Fo:Fc free: 0.8787 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.404
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 756 4.9 %RANDOM
Rwork0.1979 ---
obs0.2004 15427 93.92 %-
Displacement parametersBiso mean: 65.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.3314 Å20 Å20 Å2
2--2.9082 Å20 Å2
3----6.2396 Å2
Refine analyzeLuzzati coordinate error obs: 0.434 Å
Refinement stepCycle: 1 / Resolution: 2.9→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4714 0 24 35 4773
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014869HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.266600HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1706SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes121HARMONIC2
X-RAY DIFFRACTIONt_gen_planes693HARMONIC5
X-RAY DIFFRACTIONt_it4869HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion21.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion623SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5502SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3556 92 4.71 %
Rwork0.263 1860 -
all0.2673 1952 -
obs--93.92 %
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)
10.73010.76420.58523.86261.92172.30080.0060.03370.14410.053-0.03160.2799-0.2654-0.02760.0256-0.1510.00440.1097-0.07320.01390.002973.459246.226811.1642
23.3809-0.6744-0.79551.3050.15052.72030.0391-0.20570.40730.28370.072-0.197-0.42010.4634-0.111-0.113-0.0956-0.0546-0.1063-0.0639-0.0359101.40732.845922.1955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|14 - A|173 A|186 - A|309 }
2X-RAY DIFFRACTION2{ B|10 - B|309 }

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