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- PDB-6z1q: MAP3K14 (NIK) in complex with DesF-3R/4076 -

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Basic information

Entry
Database: PDB / ID: 6z1q
TitleMAP3K14 (NIK) in complex with DesF-3R/4076
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTRANSFERASE / Free energy perturbation / Lead Optimization / Multiple Myeloma / NIK / JNJ64290694
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 / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic 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. ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic 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
DesF-3R/4076 / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.42 Å
AuthorsJacoby, E. / van Vlijmen, H. / Querolle, O. / Stansfield, I. / Meerpoel, L. / Versele, M. / Hynd, G. / Attar, R.
CitationJournal: Future Drug Discov / Year: 2020
Title: FEP+ calculations predict a stereochemical SAR switch for first-in-class indoline NIK inhibitors for multiple myeloma
Authors: Jacoby, E. / Vlijmen, H.V. / Querolle, O. / Stansfield, I. / Meerpoel, L. / Versele, M. / Hynd, G. / Attar, R.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Mitogen-activated protein kinase kinase kinase 14
BBB: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5224
Polymers77,5412
Non-polymers9812
Water1,38777
1
AAA: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2612
Polymers38,7701
Non-polymers4911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2612
Polymers38,7701
Non-polymers4911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.77, 84.77, 118.52
Angle α, β, γ (deg.)90, 90, 90
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: 38770.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NIK / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-Q58 / DesF-3R/4076 / 4-[[4-[(3~{R})-3-(hydroxymethyl)-3-methyl-1,2-dihydropyrrolo[2,3-b]pyridin-5-yl]pyrimidin-2-yl]amino]-3-methoxy-~{N}-(oxan-4-yl)benzamide


Mass: 490.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H30N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.6 / Details: 12-20% Ethanol, 0.1M Hepes pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.42→68.95 Å / Num. obs: 31830 / % possible obs: 99.6 % / Redundancy: 4.4 % / Rrim(I) all: 0.059 / Net I/σ(I): 19.3
Reflection shellResolution: 2.42→2.48 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2366 / Rrim(I) all: 0.663

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4IDT

4idt


Resolution: 2.42→68.95 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.24588 --
Rwork0.1902 --
obs0.19301 30188 99.51 %
Refinement stepCycle: LAST / Resolution: 2.42→68.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5118 0 72 77 5267

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