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(-) Description

Title :  WDR5 BOUND TO INHIBITOR MM-589
 
Authors :  J. A. Stuckey
Date :  07 Apr 17  (Deposition) - 28 Jun 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Complex, Wd Repeat, Transcription, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Karatas, Y. Li, L. Liu, J. Ji, S. Lee, Y. Chen, J. Yang, L. Huang, D. Bernard, J. Xu, E. C. Townsend, F. Cao, X. Ran, X. Li, B. Wen, D. Sun, J. A. Stuckey, M. Lei, Y. Dou, S. Wang
Discovery Of A Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (Mm-589) Targeting The Wd Repeat Domain 5 Protein (Wdr5)-Mixed Lineage Leukemia (Mll) Protein-Protein Interaction.
J. Med. Chem. V. 60 4818 2017
PubMed-ID: 28603984  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01796

(-) Compounds

Molecule 1 - WD REPEAT-CONTAINING PROTEIN 5
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneWDR5, BIG3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBMP2-INDUCED 3-KB GENE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
19BA1Ligand/IonN-{(3R,6S,9S,12R)-6-ETHYL-12-METHYL-9-[3-(N'-METHYLCARBAMIMIDAMIDO)PROPYL]-2,5,8,11-TETRAOXO-3-PHENYL-1,4,7,10-TETRAAZACYCLOTETRADECAN-12-YL}-2-METHYLPROPANAMIDE
2EDO7Ligand/Ion1,2-ETHANEDIOL
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:49 , ILE A:90 , SER A:91 , ASP A:92 , ASP A:107 , PHE A:133 , CYS A:134 , SER A:175 , THR A:253 , GLY A:254 , LYS A:259 , TYR A:260 , CYS A:261 , PHE A:263 , THR A:290 , LYS A:291 , GLU A:292 , HOH A:519 , HOH A:530 , HOH A:542 , HOH A:564 , HOH A:567 , HOH A:609binding site for residue 9BA A 401
2AC2SOFTWAREHIS A:178 , LYS A:221 , EDO A:404 , HOH A:524 , HOH A:619 , HOH A:628binding site for residue SO4 A 402
3AC3SOFTWARELEU A:143 , LYS A:165 , THR A:200 , ALA A:201binding site for residue EDO A 403
4AC4SOFTWARETRP A:95 , SER A:97 , PHE A:137 , ASN A:138 , SO4 A:402binding site for residue EDO A 404
5AC5SOFTWARETYR A:228 , LYS A:250 , GLN A:289binding site for residue EDO A 405
6AC6SOFTWARELYS A:38 , LYS A:162 , LYS A:331 , ASP A:333 , HOH A:554binding site for residue EDO A 406
7AC7SOFTWAREILE A:113 , LYS A:123 , VAL A:158binding site for residue EDO A 407
8AC8SOFTWAREPHE A:39 , ALA A:74 , TYR A:75 , LEU A:329 , HOH A:656binding site for residue EDO A 408
9AC9SOFTWAREHOH A:535binding site for residue EDO A 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5VFC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VFC)

(-) Sequences/Alignments

Asymmetric/Biological 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee....eeeee.....eeeee.......eeeeee......eeeee...eeeeee....eeeeeee..........eeee.....eeee......eeeee.....eeeee......eeeeee.....eeeeee......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5vfc A  31 VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC 334
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330    

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  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 5VFC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        WDR5_HUMAN | P619642cnx 2co0 2g99 2g9a 2gnq 2h13 2h14 2h68 2h6k 2h6n 2h6q 2h9l 2h9m 2h9n 2h9p 2o9k 3eg6 3emh 3mxx 3n0d 3n0e 3p4f 3psl 3smr 3ur4 3uvk 3uvl 3uvm 3uvn 3uvo 4a7j 4cy1 4cy2 4erq 4ery 4erz 4es0 4esg 4ewr 4gm3 4gm8 4gm9 4gmb 4ia9 4o45 4ql1 4qqe 4y7r 5eal 5eam 5eap 5ear 5m23 5m25 5sxm

(-) Related Entries Specified in the PDB File

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