4IDV Transferase Transferase Inhibitor date Dec 13, 2012
title Crystal Structure Of Nik With Compound 4-{3-[2-Amino-5-(2- Methoxyethoxy)Pyrimidin-4-Yl]-1h-Indol-5-Yl}-2-Methylbut-3- (13v)
authors J.Liu, A.Sudom, Z.Wang
compound source
Molecule: Mitogen-Activated Protein Kinase Kinase Kinase 14
Chain: A, B, C, D
Fragment: Unp Residues 330-680
Synonym: Nf-Kappa-Beta-Inducing Kinase, Hsnik, Serinethreo Protein Kinase Nik;
Ec: 2.7.11.25
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Map3k14, Nik
symmetry Space Group: P 21 21 21
R_factor 0.203 R_Free 0.269
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.378 146.014 254.701 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand 13V enzyme Transferase E.C.2.7.11.25 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceInhibiting NF-kappaB-inducing kinase (NIK): discovery, structure-based design, synthesis, structure-activity relationship, and co-crystal structures., Li K, McGee LR, Fisher B, Sudom A, Liu J, Rubenstein SM, Anwer MK, Cushing TD, Shin Y, Ayres M, Lee F, Eksterowicz J, Faulder P, Waszkowycz B, Plotnikova O, Farrelly E, Xiao SH, Chen G, Wang Z, Bioorg Med Chem Lett. 2013 Mar 1;23(5):1238-44. doi: 10.1016/j.bmcl.2013.01.012. , Epub 2013 Jan 11. PMID:23374866
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (219 Kb) [Save to disk]
  • Biological Unit Coordinates (4idv.pdb1.gz) 56 Kb
  • Biological Unit Coordinates (4idv.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (4idv.pdb3.gz) 56 Kb
  • Biological Unit Coordinates (4idv.pdb4.gz) 56 Kb
  • LPC: Ligand-Protein Contacts for 4IDV
  • CSU: Contacts of Structural Units for 4IDV
  • Structure Factors (1563 Kb)
  • Retrieve 4IDV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4IDV from S2C, [Save to disk]
  • Re-refined 4idv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4IDV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4IDV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4IDV, from MSDmotif at EBI
  • Fold representative 4idv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4idv_C] [4idv_D] [4idv_A] [4idv_B] [4idv]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4IDV: [STYKc ] by SMART
  • Other resources with information on 4IDV
  • Community annotation for 4IDV at PDBWiki (http://pdbwiki.org)

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