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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE NF-KAPPAB INDUCING KINASE (NIK) BOUND TO IMIDAZOBENZOXEPIN COMPOUND 3
 
Authors :  M. A. Smith, P. Mcewan, S. G. Hymowitz
Date :  08 Sep 16  (Deposition) - 11 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Serine/Threonine Kinase, Nf-Kappab, Map3K14, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Castanedo, N. Blaquiere, M. Beresini, B. Bravo, H. Brightbill, J. Chen, H. F. Cui, C. Eigenbrot, C. Everett, J. Feng, R. Godemann, E. Gogol, S. Hymowitz, A. Johnson, N. Kayagaki, P. B. Kohli, K. Knuppel J. Kraemer, S. Kruger, P. Loke, P. Mcewan, C. Montalbetti, D. A. Roberts, M. Smith, S. Steinbacher, S. Sujatha-Bhaskar, R. Takahashi, X. Wang, L. C. Wu, Y. Zhang, S. T. Staben
Structure-Based Design Of Tricyclic Nf-Kappa B Inducing Kinase (Nik) Inhibitors That Have High Selectivity Over Phosphoinositide-3-Kinase (Pi3K).
J. Med. Chem. V. 60 627 2017
PubMed-ID: 28005357  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01363

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 14
    Chains: A, B
    EC Number: 2.7.11.25
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Gene: MAP3K14, NIK
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: NF-KAPPA-BETA-INDUCING KINASE,SERINE/THREONINE-PROTEIN KINASE NIK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
176Z2Ligand/Ion10-(3-METHYL-3-OXIDANYL-BUT-1-YNYL)-5,6-DIHYDROIMIDAZO[1,2-D][1,4]BENZOXAZEPINE-2-CARBOXAMIDE
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
176Z1Ligand/Ion10-(3-METHYL-3-OXIDANYL-BUT-1-YNYL)-5,6-DIHYDROIMIDAZO[1,2-D][1,4]BENZOXAZEPINE-2-CARBOXAMIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
176Z1Ligand/Ion10-(3-METHYL-3-OXIDANYL-BUT-1-YNYL)-5,6-DIHYDROIMIDAZO[1,2-D][1,4]BENZOXAZEPINE-2-CARBOXAMIDE
2SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:637 , LYS A:638 , GLU A:639binding site for residue SO4 A 701
2AC2SOFTWAREARG A:410 , GLY A:411 , SER A:478 , GLN A:481 , 76Z A:705 , HOH A:830 , HOH B:861binding site for residue SO4 A 702
3AC3SOFTWAREARG A:650 , ARG A:651binding site for residue SO4 A 703
4AC4SOFTWARELYS A:519 , HIS A:596 , GLY B:350 , GLN B:351 , HOH B:816binding site for residue SO4 A 704
5AC5SOFTWAREGLY A:411 , VAL A:416 , ALA A:429 , GLU A:442 , VAL A:455 , ILE A:469 , MET A:471 , GLU A:472 , LEU A:473 , LEU A:474 , LEU A:524 , ASP A:536 , PHE A:537 , SO4 A:702binding site for residue 76Z A 705
6AC6SOFTWAREGLY A:350 , GLN A:351 , LYS B:519 , HIS B:596binding site for residue SO4 B 701
7AC7SOFTWAREARG B:637 , LYS B:638 , GLU B:639 , HIS B:642 , HOH B:860binding site for residue SO4 B 702
8AC8SOFTWAREARG B:410 , GLY B:411 , GLN B:481 , 76Z B:704binding site for residue SO4 B 703
9AC9SOFTWAREARG B:410 , GLY B:411 , VAL B:416 , ALA B:429 , GLU B:442 , ILE B:469 , MET B:471 , GLU B:472 , LEU B:473 , LEU B:474 , LEU B:524 , ASP B:536 , PHE B:537 , SO4 B:703binding site for residue 76Z B 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T8O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:405 -Pro A:406
2Gln B:405 -Pro B:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T8O)

(-) Exons   (0, 0)

(no "Exon" information available for 5T8O)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhh..eee.hhhhhhhhhhhhh..eeee.................eee............eeeeee.....eeeeeeee.hhhhhhhhhh...........eeeeeee..eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee...ee.........hhhhhhhhhhh..ee..hhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t8o A 334 PVEEYLVHALQGSVSSGQAHSLASLAKTWSDNEGVLLTEKLKPVDYEYREEVHWMTHQPRVGRGSFGEVHRMKDKQTGFQCAVKKVRLEVFRVEELVACAGLSSPRIVPLYGAVREGPWVNIFMELLEGGSLGQLIKQMGCLPEDRALYYLGQALEGLEYLHTRRILHGDVKADNVLLSSDGSRAALCDFGHALCLQGKSLLTGDYIPGTETHMAPEVVMGKPCDAKVDIWSSCCMMLHMLNGCHPWTQYFRGPLCLKIASEPPPIREIPPSCAPLTAQAIQEGLRKEPVHRASAMELRRKVGKALQEVGGLKSPWKGEYKEPR 675
                                   343       353       363|      387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537      |551       561       571       581       591       601       611       621       631       641       651       661       671    
                                                       363|                                                                                                                                                                   544|                                                                                                                              
                                                        378                                                                                                                                                                    549                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eee.hhhhhhhhhhh...eeeee.................eee............eeeeee.....eeeeeeee.hhhhhhhhhh...........eeeeeee..eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee.......ee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t8o B 334 PVEEYLVHALQGSVSSGQAHSLASLAKTWSDNEGVLLTEKLKPVDYEYREEVHWMTHQPRVGRGSFGEVHRMKDKQTGFQCAVKKVRLEVFRVEELVACAGLSSPRIVPLYGAVREGPWVNIFMELLEGGSLGQLIKQMGCLPEDRALYYLGQALEGLEYLHTRRILHGDVKADNVLLSSDGSRAALCDFGHALCLQPDGLGKSLLTGDYIPGTETHMAPEVVMGKPCDAKVDIWSSCCMMLHMLNGCHPWTQYFRGPLCLKIASEPPPIREIPPSCAPLTAQAIQEGLRKEPVHRASAMELRRKVGKALQEVGGLKSPWKGEYKEPR 675
                                   343       353       363|      387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667        
                                                       363|                                                                                                                                                                                                                                                                                                         
                                                        378
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5T8O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T8O)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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        M3K14_MOUSE | Q9WUL6: 4g3c 4g3e 4g3f 4g3g 5t8p 5t8q

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