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(-) Description

Title :  CRYSTAL STRUCTURE OF EED IN COMPLEX WITH H3K27ME3 PEPTIDE AND 6-(BENZO[D][1,3]DIOXOL-4-YLMETHYL)-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE
 
Authors :  D. Bussiere, W. Shu
Date :  07 Dec 16  (Deposition) - 11 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Eed, Fragment-Based Generation, Oncology, Transcription-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Lingel, M. Sendzik, Y. Huang, M. D. Shultz, J. Cantwell, M. P. Dillon X. Fu, J. Fuller, T. Gabriel, J. Gu, X. Jiang, L. Li, F. Liang, M. Mckenna W. Qi, W. Rao, X. Sheng, W. Shu, J. Sutton, B. Taft, L. Wang, J. Zeng, H. Zhang, M. Zhang, K. Zhao, M. Lindvall, D. E. Bussiere
Structure-Guided Design Of Eed Binders Allosterically Inhibiting The Epigenetic Polycomb Repressive Complex 2 (Prc2) Methyltransferase.
J. Med. Chem. V. 60 415 2017
PubMed-ID: 27992714  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01473

(-) Compounds

Molecule 1 - POLYCOMB PROTEIN EED
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI K-12
    Expression System Taxid83333
    FragmentUNP RESIDUES 76-441
    GeneEED
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHEED,WD PROTEIN ASSOCIATING WITH INTEGRIN CYTOPLASMIC TAILS 1,WAIT-1
 
Molecule 2 - HISTONE-LYSINE N-METHYLTRANSFERASE EZH2
    ChainsC, D
    EC Number2.1.1.43
    EngineeredYES
    FragmentUNP RESIDUES 39-68
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENX-1,ENHANCER OF ZESTE HOMOLOG 2,LYSINE N-METHYLTRANSFERASE 6
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
17WD2Ligand/Ion(6S)-6-[(2H-1,3-BENZODIOXOL-4-YL)METHYL]-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE
2GOL1Ligand/IonGLYCEROL
3YT32Ligand/IonYTTRIUM (III) ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
17WD1Ligand/Ion(6S)-6-[(2H-1,3-BENZODIOXOL-4-YL)METHYL]-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE
2GOL1Ligand/IonGLYCEROL
3YT32Ligand/IonYTTRIUM (III) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17WD1Ligand/Ion(6S)-6-[(2H-1,3-BENZODIOXOL-4-YL)METHYL]-5,6,7,8-TETRAHYDROIMIDAZO[1,5-A]PYRIDIN-3-AMINE
2GOL-1Ligand/IonGLYCEROL
3YT3-1Ligand/IonYTTRIUM (III) ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:326 , SER A:359 , GLN A:360 , ASP A:362 , HOH A:725binding site for residue GOL A 501
2AC2SOFTWAREARG B:269 , HIS B:295binding site for residue YT3 A 502
3AC3SOFTWAREARG A:269 , LYS A:293 , HIS A:295binding site for residue YT3 A 503
4AC4SOFTWAREPHE A:97 , TYR A:148 , ASN A:194 , GLU A:238 , ASP A:310 , TYR A:365 , MET A:366 , ARG A:367 , ARG A:414 , HOH A:604 , HOH A:613binding site for residue 7WD A 504
5AC5SOFTWAREPHE B:97 , ASN B:194 , GLU B:238 , ASP B:310 , TYR B:365 , MET B:366 , ARG B:367 , ARG B:414 , HOH B:635 , HOH B:645 , HOH B:784binding site for residue 7WD B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U62)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U62)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U62)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U62)

(-) Exons   (0, 0)

(no "Exon" information available for 5U62)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeee.........eeeeeee..eeeeeee.....eeeeeeee.......eeeeeeee......eeeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee....eeeeee.........eeeeee.....eeeeee....eeeee..hhhhhhhhhhhhhh.....eee....eee.........eeeee..eeeee....eeeeeee.....hhhhh......eeeeeeee..........eee.....eeeee.....eeeee....eee........eeeeee.....eeeeee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u62 A  79 KYSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL 440
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278 ||    294       304       314       324       334       344       354       364       374       384       401       411       421       431         
                                                                                                                                                                                                                                   280|                                                                                                       393|                                       
                                                                                                                                                                                                                                    287                                                                                                        401                                       

Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee......eeeeee.........eeeeeee..eeeeeee.....eeeeeeee.......eeeeeeee......eeeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee....eeeeee.........eeeeee.....eeeeee....eeeee..hhhhhhhhhhhhhh...........eee....eee.........eeeee..eeeee....eeeeeee................eeeeeeee..........eee.....eeeee.....eeeee....eee........eeeeee.....eeeeee...eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5u62 B  80 YSFKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDRL 440
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389   ||  406       416       426       436    
                                                                                                                                                                                                                                                                                                                                                   393|                                       
                                                                                                                                                                                                                                                                                                                                                    401                                       

Chain C from PDB  Type:PROTEIN  Length:26
                                                          
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 5u62 C  43 SSNRQKILERTEILNQEWKQRRIQPV  68
                                    52        62      

Chain D from PDB  Type:PROTEIN  Length:28
                                                            
               SCOP domains ---------------------------- SCOP domains
               CATH domains ---------------------------- CATH domains
               Pfam domains ---------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------- SAPs(SNPs)
                    PROSITE ---------------------------- PROSITE
                 Transcript ---------------------------- Transcript
                 5u62 D  41 MFSSNRQKILERTEILNQEWKQRRIQPV  68
                                    50        60        

   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 5U62)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U62)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U62)

(-) Gene Ontology  (66, 79)

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  EZH2_HUMAN | Q15910
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 Related Entries

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

UniProtKB/Swiss-Prot
        EED_HUMAN | O755303iiw 3iiy 3ij0 3ij1 3ijc 3jpx 3jzg 3jzh 3jzn 3k26 3k27 4x3e 5gsa 5h13 5h14 5h15 5h17 5h19 5h24 5h25 5hyn 5ij7 5ij8 5k0m 5ls6 5ttw 5u5h 5u5k 5u5t 5u69 5u6d 5u8a 5u8f 5wuk
        EZH2_HUMAN | Q159102c6v 4mi0 4mi5 5gsa 5h14 5h15 5h17 5h19 5h24 5h25 5hyn 5ij7 5ij8 5ls6 5u5t 5wuk

(-) Related Entries Specified in the PDB File

5u5h 5u5k 5u5t