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 :  BRAF IN COMPLEX WITH N-(3-(TERT-BUTYL)PHENYL)-4-METHYL-3-(6-MORPHOLINOPYRIMIDIN-4-YL)BENZAMIDE
 
Authors :  M. Mamo, B. A. Appleton
Date :  27 Mar 17  (Deposition) - 28 Jun 17  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Braf Serine/Threonine-Protein Kinase B-Raf, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. A. Nishiguchi, A. Rico, H. Tanner, R. J. Aversa, B. R. Taft, S. Subramanian, L. Setti, M. T. Burger, L. Wan, V. Tamez, A. Smith, Y. Lou, P. A. Barsanti, B. A. Appleton, M. Mamo, L. Tandeske, I. Dix, J. E. Tellew, S. Huang, L. A. Mathews Griner, V. G. Cooke, A. Van Abbema, H. Merritt, S. Ma, K. Gampa, F. Feng, J. Yuan, Y. Wang, J. R. Haling, S. Vaziri, M. Hekmat-Nejad, J. M. Jansen, V. Polyakov, R. Zang, V. Sethuraman, P. Amiri, M. Singh, E. Lees, W. Shao, D. D. Stuart, M. P. Dillon, S. Ramurthy
Design And Discovery Of N-(2-Methyl-5'-Morpholino-6'-((Tetrahydro-2H-Pyran-4-Yl)Oxy -[3, 3'-Bipyridin]-5-Yl)-3-(Trifluoromethyl)Benzamide (Raf709): A Potent, Selective, And Efficacious Raf Inhibito Targeting Ras Mutant Cancers.
J. Med. Chem. V. 60 4869 2017
PubMed-ID: 28557458  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01862

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Taxid: 10469
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 445-723
    Gene: BRAF, BRAF1, RAFB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE B-RAF,P94,V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
192D2Ligand/IonN-(3-TERT-BUTYLPHENYL)-4-METHYL-3-[6-(MORPHOLIN-4-YL)PYRIMIDIN-4-YL]BENZAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
192D1Ligand/IonN-(3-TERT-BUTYLPHENYL)-4-METHYL-3-[6-(MORPHOLIN-4-YL)PYRIMIDIN-4-YL]BENZAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
192D1Ligand/IonN-(3-TERT-BUTYLPHENYL)-4-METHYL-3-[6-(MORPHOLIN-4-YL)PYRIMIDIN-4-YL]BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:471 , ALA A:481 , LYS A:483 , GLU A:501 , VAL A:504 , LEU A:505 , LEU A:514 , THR A:529 , GLN A:530 , TRP A:531 , CYS A:532 , HIS A:574 , GLY A:593 , ASP A:594 , PHE A:595 , HOH A:969binding site for residue 92D A 801
2AC2SOFTWAREVAL B:471 , ALA B:481 , LYS B:483 , GLU B:501 , LEU B:514 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , GLY B:593 , ASP B:594 , PHE B:595 , HOH B:994binding site for residue 92D B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:522 -Pro A:523
2Lys B:522 -Pro B:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VAL)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeee..eeeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5val A 446 SSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGSILWMAPEVIRMKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS 720
                                   455       465       475       485       495       505       515       525       535       545       555       565       575       585       595||     624  ||   636       646       656       666       676       686       696       706       716    
                                                                                                                                                                                596|        627|                                                                                          
                                                                                                                                                                                 616         630                                                                                          


Chain B from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5val B 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLGSILWMAPEVIRMNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSL 721
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597|      624  ||   637       647       657       667       677       687       697       707       717    
                                                                                                                                                                               597|         627|                                                                                          
                                                                                                                                                                                615          631
   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 5VAL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

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
    92D  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:522 - Pro A:523   [ RasMol ]  
    Lys B:522 - Pro B:523   [ RasMol ]  
 
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
  5val
    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
  BRAF_HUMAN | P15056
    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)
  2.7.11.1
    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
  BRAF_HUMAN | P15056
    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
        BRAF_HUMAN | P15056: 1uwh 1uwj 2fb8 2l05 3c4c 3d4q 3idp 3ii5 3ny5 3og7 3ppj 3ppk 3prf 3pri 3psb 3psd 3q4c 3q96 3skc 3tv4 3tv6 4cqe 4dbn 4e26 4e4x 4ehe 4ehg 4fc0 4fk3 4g9c 4g9r 4h58 4jvg 4ksp 4ksq 4mbj 4mne 4mnf 4pp7 4r5y 4rzv 4rzw 4wo5 4xv1 4xv2 4xv3 4xv9 4yht 5c9c 5csw 5csx 5ct7 5fd2 5hi2 5hid 5hie 5ita 5j17 5j18 5j2r 5jrq 5jsm 5jt2 5vam

(-) Related Entries Specified in the PDB File

5vam