Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  POLYCOMB PROTEIN EED IN COMPLEX WITH INHIBITOR: 2-[4-(4-{(3S,4R)-4-(DIMETHYLAMINO)-1-[(2-FLUORO-6-METHYLPHENYL)METHYL]PYRROLIDIN-3-YL}PHENYL)-1H-PYRAZOL-1-YL]ACETAMIDE
 
Authors :  C. G. Jakob, H. Zhu
Date :  07 Dec 16  (Deposition) - 15 Mar 17  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Wd40 Prc2, Protein Binding, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Curtin, M. A. Pliushchev, H. Q. Li, M. Torrent, J. D. Dietrich, C. G. Jakob, H. Zhu, H. Zhao, Y. Wang, Z. Ji, R. F. Clark, K. A. Sarris, S. Selvaraju, B. Shaw, M. A. Algire, Y. He, P. L. Richardson, R. F. Sweis C. Sun, G. G. Chiang, M. R. Michaelides
Sar Of Amino Pyrrolidines As Potent And Novel Protein-Protein Interaction Inhibitors Of The Prc2 Complex Through Eed Binding.
Bioorg. Med. Chem. Lett. V. 27 1576 2017
PubMed-ID: 28254486  |  Reference-DOI: 10.1016/J.BMCL.2017.02.030

(-) Compounds

Molecule 1 - POLYCOMB PROTEIN EED
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: EED
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEED,WD PROTEIN ASSOCIATING WITH INTEGRIN CYTOPLASMIC TAILS 1,WAIT-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
17XG1Ligand/Ion2-[4-(4-{(3S,4R)-4-(DIMETHYLAMINO)-1-[(2-FLUORO-6-METHYLPHENYL)METHYL]PYRROLIDIN-3-YL}PHENYL)-1H-PYRAZOL-1-YL]ACETAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:95 , PHE A:97 , TYR A:148 , ASN A:194 , GLU A:238 , LEU A:240 , ASP A:310 , TYR A:365 , ARG A:367 , ARG A:414 , ASP A:430 , HOH A:654binding site for residue 7XG A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5U6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5U6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5U6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5U6D)

(-) Exons   (0, 0)

(no "Exon" information available for 5U6D)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeeee.........eeeeeee..eeeeeee.....eeeeeeee.......eeeeeeee......eeeeeee...eeeeee....eeeeeee.....eeeeee......eeeeee....eeeee....eeeeee.........eeeeee.....eeeeee....eeeee..hhhhhhhhhhhhhhhhhhh......eee....eee.........eeeee..eeeee....eeeeeee.....hhhhh......eeeeeeee..........eee.....eeeee.....eeeee....hhhhheeeee........eeeeee.....eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u6d A  82 FKCVNSLKEDHNQPLFGVQFNWHSKEGDPLVFATVGSNRVTLYECHSQGEIRLLQSYVDADADENFYTCAWTYDSNTSHPLLAVAGSRGIIRIINPITMQCIKHYVGHGNAINELKFHPRDPNLLLSVSKDHALRLWNIQTDTLVAIFGGVEGHRDEVLSADYDLLGEKIMSCGMDHSLKLWRINSKRMMNAIKESYDYNPNKTNRPFISQKIHFPDFSTRDIHRNYVDCVRWLGDLILSKSCENAIVCWKPGKMEDDIDKIKPSESNVTILGRFDYSQCDIWYMRFSMDFWQKMLALGNQVGKLYVWDLEVEDPHKAKCTTLTHHKCGAAIRQTSFSRDSSILIAVCDDASIWRWDR 439
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431
   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 5U6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5U6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5U6D)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    7XG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5u6d)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5u6d
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EED_HUMAN | O75530
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EED_HUMAN | O75530
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EED_HUMAN | O75530: 3iiw 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 5u62 5u69 5u8a 5u8f 5wuk

(-) Related Entries Specified in the PDB File

5u69