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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN B-RAF BOUND TO A DFG-OUT INHIBITOR TAK-632
 
Authors :  J. K. Yano, O. Masanori
Date :  17 May 13  (Deposition) - 24 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.93
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Human Serine/Theronine Protein Kinase, Kinase Drug Complex, , Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Okaniwa, M. Hirose, T. Arita, M. Yabuki, A. Nakamura, T. Takagi, T. Kawamoto, N. Uchiyama, A. Sumita, S. Tsutsumi, T. Tottori, Y. Inui, B. C. Sang, J. Yano, K. Aertgeerts, S. Yoshida, T. Ishikawa
Discovery Of A Selective Kinase Inhibitor (Tak-632) Targeting Pan-Raf Inhibition: Design, Synthesis, And Biological Evaluation Of C-7-Substituted 1, 3-Benzothiazole Derivatives.
J. Med. Chem. V. 56 6478 2013
PubMed-ID: 23906342  |  Reference-DOI: 10.1021/JM400778D

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 445-726
    Gene: BRAF, BRAF1, P94, RAFB1, V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1
    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): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
11SU2Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]ACETYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11SU2Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]ACETYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11SU1Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]ACETYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11SU1Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]ACETYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:470 , ALA A:480 , LYS A:482 , GLU A:500 , LEU A:504 , LEU A:513 , ILE A:526 , THR A:528 , GLN A:529 , TRP A:530 , CYS A:531 , GLY A:533 , HIS A:573 , PHE A:582 , GLY A:592 , ASP A:593 , PHE A:594BINDING SITE FOR RESIDUE 1SU A 901
2AC2SOFTWAREILE B:462 , VAL B:470 , ALA B:480 , LYS B:482 , GLU B:500 , LEU B:504 , ILE B:526 , THR B:528 , GLN B:529 , TRP B:530 , CYS B:531 , LEU B:566 , HIS B:573 , PHE B:582 , GLY B:592 , ASP B:593 , PHE B:594 , HOH B:1008BINDING SITE FOR RESIDUE 1SU B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KSP)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4kspa_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee..eeeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee.....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ksp A 447 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 721
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       614       624       634       644       654       664       674       684       694       704       714       
                                                                                                                                                                              595|                                                                                                           
                                                                                                                                                                               614                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains d4kspb_ B: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee..eeeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ksp B 447 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS 719
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       596|      623       633       643       653       663       673       683       693       703       713      
                                                                                                                                                                               596|                                                                                                         
                                                                                                                                                                                614
   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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
    1SU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ksp)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4ksp
    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 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 5val 5vam

(-) Related Entries Specified in the PDB File

3q96 B-RAF INHIBITOR
4dbn B-RAF INHIBITOR
4ksq B-RAF BOUND TO A DFG-OUT INHIBITOR 5B