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- PDB-4idt: Crystal Structure of NIK with 11-bromo-5,6,7,8-tetrahydropyrimido... -

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Basic information

Entry
Database: PDB / ID: 4idt
TitleCrystal Structure of NIK with 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine (T28)
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTransferase/Transferase Inhibitor / NIK / Nuclear factor (NF)-kB / p100 processing / 2-aminopyrimidine / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center ...TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / 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 ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / 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-T28 / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, J. / Sudom, A. / Wang, Z.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Inhibiting NF-KB-inducing kinase (NIK): Discovery, structure-based design, synthesis, structure activity relationship, and co-crystal structures
Authors: Li, K. / McGee, L.R. / Fisher, B. / Sudom, A. / Liu, J. / Rubenstein, S.M. / Anwer, M.K. / Cushing, T.D. / Shin, Y. / Ayres, M. / Lee, F. / Eksterowicz, J. / Faulder, P. / Waszkowycz, B. / ...Authors: Li, K. / McGee, L.R. / Fisher, B. / Sudom, A. / Liu, J. / Rubenstein, S.M. / Anwer, M.K. / Cushing, T.D. / Shin, Y. / Ayres, M. / Lee, F. / Eksterowicz, J. / Faulder, P. / Waszkowycz, B. / Plotnikova, O. / Farrelly, E. / Xiao, S.H. / Chen, G. / Wang, Z.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 14
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0064
Polymers78,3472
Non-polymers6582
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-6 kcal/mol
Surface area27720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.530, 84.530, 117.947
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / HsNIK / Serine/threonine-protein kinase NIK


Mass: 39173.715 Da / Num. of mol.: 2 / Fragment: UNP residues 330-680
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NIK
References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-T28 / 11-bromo-5,6,7,8-tetrahydropyrimido[4',5':3,4]cyclohepta[1,2-b]indol-2-amine


Mass: 329.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13BrN4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.69 Å3/Da / Density % sol: 54.26 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→84.535 Å / Num. obs: 32431 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.533.70.3971.81758746960.397100
2.53-2.683.70.2872.61676544800.287100
2.68-2.873.70.23.71566341890.2100
2.87-3.13.70.1415.21466139290.141100
3.1-3.393.70.0927.71337235950.092100
3.39-3.793.70.06510.51210432620.065100
3.79-4.383.70.05611.41055928850.056100
4.38-5.373.60.05111.6875824370.05199.9
5.37-7.593.40.03916651418940.03999.7
7.59-84.5353.80.03513.8400910640.03599.9

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Processing

Software
NameVersionClassificationNB
SCALA3.1.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→59.772 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.8476 / SU ML: 0.29 / σ(F): 1 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1639 5.06 %
Rwork0.1911 --
obs0.1929 32431 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 143.67 Å2 / Biso mean: 36.2532 Å2 / Biso min: 8.94 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5191 0 40 317 5548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075375
X-RAY DIFFRACTIONf_angle_d1.1187283
X-RAY DIFFRACTIONf_chiral_restr0.052772
X-RAY DIFFRACTIONf_plane_restr0.005952
X-RAY DIFFRACTIONf_dihedral_angle_d16.8822013
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43590.32421450.2712572271798
2.4359-2.47390.27591340.25612613274798
2.4739-2.51450.2971370.24482573271099
2.5145-2.55780.27941710.23342582275399
2.5578-2.60430.29221230.24712583270698
2.6043-2.65440.28631190.23352659277898
2.6544-2.70860.29551580.22522557271598
2.7086-2.76750.24741110.21812580269199
2.7675-2.83190.22921400.2152631277199
2.8319-2.90270.26121720.20852606277899
2.9027-2.98120.25721320.21062559269199
2.9812-3.06890.24181340.20652595272999
3.0689-3.1680.28071360.20322626276299
3.168-3.28120.27891230.19232612273599
3.2812-3.41250.2071480.18782589273799
3.4125-3.56780.22491600.18252629278999
3.5678-3.75590.23221270.17712572269999
3.7559-3.99120.16531390.16422642278199
3.9912-4.29930.18491390.15042590272999
4.2993-4.73180.18761300.15082595272599
4.7318-5.41610.19481480.17472589273798
5.4161-6.82210.23031320.19742562269498
6.8221-59.7720.18591260.17472641276799

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