Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  TARGETING CONSERVED WATER MOLECULES: DESIGN OF 4-ARYL-5-CYANOPYRROLO[2,3-D]PYRIMIDINE HSP90 INHIBITORS USING FRAGMENT-BASED SCREENING AND STRUCTURE-BASED OPTIMIZATION
 
Authors :  N. G. Davies, H. Browne, B. Davis, N. Foloppe, S. Geoffrey, B. Gibbons, T M. J. Drysdale, H. Mansell, A. Massey, N. Matassova, J. D. Moore, J. Mur R. Pratt, S. Ray, S. D. Roughley, M. R. Jensen, J. Schoepfer, K. Scriven H. Simmonite, S. Stokes, A. Surgenor, P. Webb, L. Wright, P. Brough
Date :  25 May 12  (Deposition) - 24 Oct 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Heat Shock Protein, Hsp90, Atpase, Fragments, Structure-Based Design, Chaperone-Chaperone Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. Davies, H. Browne, B. Davis, M. J. Drysdale, N. Foloppe, S. Geoffrey, B. Gibbons, T. Hart, R. Hubbard, M. R. Jensen, H. Mansell, A. Massey, N. Matassova, J. D. Moore, J. Murray, R. Pratt, S. Ray, A. Robertson, S. D. Roughley, J. Schoepfer, K. Scriven, H. Simmonite, S. Stokes, A. Surgenor, P. Webb, M. Wood, L. Wright, P. Brough
Targeting Conserved Water Molecules: Design Of 4-Aryl-5-Cyanopyrrolo[2, 3-D]Pyrimidine Hsp90 Inhibitors Using Fragment-Based Screening And Structure-Based Optimization.
Bioorg. Med. Chem. V. 20 6770 2012
PubMed-ID: 23018093  |  Reference-DOI: 10.1016/J.BMC.2012.08.050

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN HSP 90-ALPHA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HSP90AA1, HSP90A, HSPC1, HSPCA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEAT SHOCK 86 KDA, HSP 86, HSP86, RENAL CARCINOMA ANTIGEN NY-REN-38

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
10TM1Ligand/Ion2-{[4-(2-CHLORO-4,5-DIMETHOXYPHENYL)-5-CYANO-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL]SULFANYL}-N,N-DIMETHYLACETAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10TM1Ligand/Ion2-{[4-(2-CHLORO-4,5-DIMETHOXYPHENYL)-5-CYANO-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL]SULFANYL}-N,N-DIMETHYLACETAMIDE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
10TM2Ligand/Ion2-{[4-(2-CHLORO-4,5-DIMETHOXYPHENYL)-5-CYANO-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL]SULFANYL}-N,N-DIMETHYLACETAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:48 , ASN A:51 , SER A:52 , ALA A:55 , LYS A:58 , ASP A:93 , GLY A:97 , MET A:98 , ASN A:106 , LEU A:107 , PHE A:138 , THR A:184 , HOH A:402 , HOH A:594 , HOH A:702 , HOH A:741BINDING SITE FOR RESIDUE 0TM A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FCR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FCR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FCR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FCR)

(-) Exons   (0, 0)

(no "Exon" information available for 4FCR)

(-) 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:207
                                                                                                                                                                                                                                               
               SCOP domains d4fcra_ A: HSP90                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeee.....hhhhhhhhh.....hhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeeee........eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fcr A  16 EVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIASGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVE 223
                                    25        35        45        55        65        75        85        95       105     ||116       126       136       146       156       166       176       186       196       206       216       
                                                                                                                         111|                                                                                                              
                                                                                                                          113
   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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FCR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FCR)

(-) Gene Ontology  (81, 81)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    0TM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4fcr)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  4fcr
    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
  HS90A_HUMAN | P07900
    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
  HS90A_HUMAN | P07900
    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
        HS90A_HUMAN | P07900: 1byq 1osf 1uy6 1uy7 1uy8 1uy9 1uyc 1uyd 1uye 1uyf 1uyg 1uyh 1uyi 1uyk 1uyl 1yc1 1yc3 1yc4 1yer 1yes 1yet 2bsm 2bt0 2bug 2byh 2byi 2bz5 2c2l 2ccs 2cct 2ccu 2fwy 2fwz 2h55 2jjc 2k5b 2qf6 2qfo 2qg0 2qg2 2uwd 2vci 2vcj 2wi1 2wi2 2wi3 2wi4 2wi5 2wi6 2wi7 2xab 2xdk 2xdl 2xds 2xdu 2xdx 2xhr 2xht 2xhx 2xjg 2xjj 2xjx 2xk2 2ye2 2ye3 2ye4 2ye5 2ye6 2ye7 2ye8 2ye9 2yea 2yeb 2yec 2yed 2yee 2yef 2yeg 2yeh 2yei 2yej 2yi0 2yi5 2yi6 2yi7 2yjw 2yjx 2yk2 2yk9 2ykb 2ykc 2yke 2yki 2ykj 3b24 3b25 3b26 3b27 3b28 3bm9 3bmy 3d0b 3eko 3ekr 3ft5 3ft8 3hek 3hhu 3hyy 3hyz 3hz1 3hz5 3inw 3inx 3k97 3k98 3k99 3mnr 3o0i 3ow6 3owb 3owd 3q6m 3q6n 3qdd 3qtf 3r4m 3r4n 3r4o 3r4p 3r91 3r92 3rkz 3rlp 3rlq 3rlr 3t0h 3t0z 3t10 3t1k 3t2s 3tuh 3vha 3vhc 3vhd 3wha 3wq9 4aif 4awo 4awp 4awq 4b7p 4bqg 4bqj 4cgq 4cgu 4cgv 4cgw 4cwf 4cwn 4cwo 4cwp 4cwq 4cwr 4cws 4cwt 4eeh 4eft 4efu 4egh 4egi 4egk 4fcp 4fcq 4hy6 4jql 4l8z 4l90 4l91 4l93 4l94 4lwe 4lwf 4lwg 4lwh 4lwi 4nh7 4nh8 4o04 4o05 4o07 4o09 4o0b 4r3m 4u93 4w7t 4xip 4xiq 4xir 4xit 4ykq 4ykr 4ykt 4yku 4ykw 4ykx 4yky 4ykz 5cf0 5fnc 5fnd 5fnf 5ggz 5m4e 5m4h

(-) Related Entries Specified in the PDB File

4fcp 4fcq