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 :  OPTIMIZATION OF A NOVEL BINDING MOTIF TO TO (E)-3-(3,5-DIFLUORO-4-((1R,3R)-2-(2-FLUORO-2-METHYLPROPYL)-3-METHYL-2, 3,4,9-TETRAHYDRO-1H-PYRIDO(3,4-B)INDOL-1-YL)PHENYL)ACRYLIC ACID (AZD9496), A POTENT AND ORALLY BIOAVAILABLE SELECTIVE ESTROGEN RECEPTOR DOWNREGULATOR AND ANTAGONIST
 
Authors :  R. A. Norman, R. H. Bradbury, C. De Almeida, D. M. Andrews, P. Ballard, D R. J. Callis, G. S. Currie, J. O. Curwen, C. D. Davies, C. De Savi, C. S. D L. J. L. Feron, S. C. Glossop, B. R. Hayter, G. Karoutchi, S. G. Lamont, P T. Moss, S. E. Pearson, A. A. Rabow, M. Tonge, G. E. Walker, H. M. Weir, Z.
Date :  28 Jul 15  (Deposition) - 14 Oct 15  (Release) - 12 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signaling Protein, Breast Cancer, Estrogen Receptor Downregulator, Fulvestrant, Azd9496, Nuclear Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. De Savi, R. H. Bradbury, A. A. Rabow, R. A. Norman, C. De Almeida, D. M. Andrews, P. Ballard, D. Buttar, R. Callis, G. S. Currie, C. Davies C. Donald, L. Feron, B. R. Hayter, S. Hussain, G. Karoutchi, S. Lamont, P. A. Macfaul, T. A. Moss, S. Pearson, M. Tonge, G. Walker, H. Weir, Z. Wilson
Optimization Of A Novel Binding Motif To (E)-3-(3, 5- Difluoro-4-((1R, 3R)-2-(2-Fluoro-2-Methylpropyl)-3-Methyl-2, 3, 4, 9-Tetrahydro-1H-Pyrido[3, 4-B]Indol-1-Yl)Phenyl)Acrylic Acid (Azd9496), A Potent And Orally Bioavailable Selective Estrogen Receptor Downregulator And Antagonist.
J. Med. Chem. V. 58 8128 2015
PubMed-ID: 26407012  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00984
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTROGEN RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Fragment: LIGAND-BINDING DOMAIN, UNP RESIDUES 307-554
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ER, ER-ALPHA, ESTRADIOL RECEPTOR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1, ESTROGEN RECEPTOR ALPHA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1XBR2Ligand/Ion3-(1-(4-CHLOROPHENYL)-3,4-DIHYDRO-1H-PYRIDO(3,4-B)INDOL-2(9H)-YL)PROPANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:346 , THR A:347 , ALA A:350 , GLU A:353 , LEU A:387 , PHE A:404 , ILE A:424 , GLY A:521 , HIS A:524 , LEU A:525 , VAL A:533BINDING SITE FOR RESIDUE XBR A1553
2AC2SOFTWARELEU B:346 , THR B:347 , LEU B:349 , LEU B:387 , ARG B:394 , MET B:421 , ILE B:424 , GLY B:521 , HIS B:524 , LEU B:525 , VAL B:533BINDING SITE FOR RESIDUE XBR B1547

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5AAU)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeehhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aau A 303 GSHMALSLTADQMVSALLDAEPPILYSEYSMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMVVPSYDLLLEMLDAHRLHAP 552
                                   312       322       341       351       361       371       381       391       401       411       421       431       441       451       461|      479       489       499       509       519       533       543         
                                                      331|                                                                                                                     461|                                                       528|                   
                                                       341                                                                                                                      470                                                        533                   


Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeehhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5aau B 310 LTADQMVSALLDAEPPILYSEYPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMVVPSYDLLLEMLDA 546
                                   319       329 ||    343       353       363       373       383       393       403       413       423       433       443       453       463|      480       490       500       510       520       534       544  
                                               331|                                                                                                                            463|                                                      528|             
                                                336                                                                                                                             471                                                       533
   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 5AAU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (98, 98)

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
    XBR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5aau)
 

(-) 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
  5aau
    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
  ESR1_HUMAN | P03372
    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
  ESR1_HUMAN | P03372
    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
        ESR1_HUMAN | P03372: 1a52 1akf 1ere 1err 1g50 1gwq 1gwr 1hcp 1hcq 1l2i 1pcg 1qkt 1qku 1r5k 1sj0 1uom 1x7e 1x7r 1xp1 1xp6 1xp9 1xpc 1xqc 1yim 1yin 1zky 2ayr 2b1v 2b1z 2b23 2bj4 2fai 2g44 2g5o 2i0j 2iog 2iok 2jf9 2jfa 2llo 2llq 2ocf 2ouz 2p15 2pog 2q6j 2q70 2qa6 2qa8 2qab 2qe4 2qgt 2qgw 2qh6 2qr9 2qse 2qxm 2qxs 2qzo 2r6w 2r6y 2yat 2yja 3cbm 3cbo 3cbp 3dt3 3erd 3ert 3hlv 3hm1 3l03 3os8 3os9 3osa 3q95 3q97 3uu7 3uua 3uuc 3uud 4aa6 4dma 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4jc3 4jdd 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgc 4mgd 4o6f 4pp6 4ppp 4pps 4pxm 4q13 4q50 4tuz 4tv1 4xi3 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 5aav 5acc 5ak2 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5egv 5ehj 5ei1 5eit 5fqp 5fqr 5fqs 5fqt 5fqv 5hyr 5jmm 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5n10 5t0x 5t92 5t97 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5tn9 5tnb 5u2b 5u2d

(-) Related Entries Specified in the PDB File

5aav OPTIMIZATION OF A NOVEL BINDING MOTIF TO TO (E)-3-( 3,5-DIFLUORO-4-((1R,3R)-2-(2-FLUORO-2-METHYLPROPYL )-3-METHYL-2,3,4,9-TETRAHYDRO-1H-PYRIDO(3,4-B) INDOL-1-YL)PHENYL)ACRYLIC ACID (AZD9496), A POTENT AND ORALLY BIOAVAILABLE SELECTIVE ESTROGEN RECEPTOR DOWNREGULATOR AND ANTAGONIST