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(-) Description

Title :  B-RAF KINASE IN COMPLEX WITH BIRB796
 
Authors :  H. Lavoie, N. Thevakumaran, G. Gavory, J. Li, A. Padeganeh, S. Guiral, J. Duchaine, D. Y. L. Mao, M. Bouvier, F. Sicheri, M. Therrien
Date :  25 Mar 13  (Deposition) - 29 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Kinase, Phosphotransferase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Lavoie, N. Thevakumaran, G. Gavory, J. J. Li, A. Padeganeh, S. Guiral, J. Duchaine, D. Y. Mao, M. Bouvier, F. Sicheri, M. Therrien
Inhibitors That Stabilize A Closed Raf Kinase Domain Conformation Induce Dimerization.
Nat. Chem. Biol. V. 9 428 2013
PubMed-ID: 23685672  |  Reference-DOI: 10.1038/NCHEMBIO.1257

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    ChainsB, A, C, D
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentKINASE DOMAIN
    GeneBRAF, BRAF1, RAFB1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROTO-ONCOGENE B-RAF, P94, V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x) B  
Biological Unit 2 (1x)A   
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1B964Ligand/Ion1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1B961Ligand/Ion1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1B961Ligand/Ion1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1B961Ligand/Ion1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1B961Ligand/Ion1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:481 , LYS B:483 , GLU B:501 , VAL B:504 , ILE B:527 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , HIS B:574 , GLY B:593 , ASP B:594BINDING SITE FOR RESIDUE B96 B 801
2AC2SOFTWAREALA A:481 , LYS A:483 , GLU A:501 , ILE A:527 , THR A:529 , GLN A:530 , TRP A:531 , CYS A:532 , HIS A:574 , PHE A:583 , GLY A:593 , ASP A:594 , THR A:599BINDING SITE FOR RESIDUE B96 A 801
3AC3SOFTWAREALA C:481 , LYS C:483 , GLU C:501 , VAL C:504 , ILE C:527 , THR C:529 , GLN C:530 , TRP C:531 , CYS C:532 , GLY C:593 , ASP C:594 , PHE C:595BINDING SITE FOR RESIDUE B96 C 801
4AC4SOFTWAREALA D:481 , LYS D:483 , GLU D:501 , VAL D:504 , ILE D:527 , THR D:529 , GLN D:530 , TRP D:531 , CYS D:532 , HIS D:574 , GLY D:593 , ASP D:594BINDING SITE FOR RESIDUE B96 D 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:467 -Phe B:468

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JVG)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jvga_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee...eeeeeee.......hhhhhhhhhhhhhh.........eeeee....eeeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee...............hhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvg A 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597    || 620       630       640       650       660       670       680       690       700       710       720  
                                                                                                                                                                                    602|                                                                                                          
                                                                                                                                                                                     616                                                                                                          

Chain B from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains d4jvgb_ B: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee...eeeeee........hhhhhhhhhhhhhh.........eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeeehhheeee............hhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvg B 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597 ||    623       633       643       653       663       673       683       693       703       713         
                                                                                                                                                                                 599|                                                                                                          
                                                                                                                                                                                  616                                                                                                          

Chain C from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains d4jvgc_ C: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee...........hhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jvg C 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLASILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597||     624       634       644       654       664       674       684       694       704       714        
                                                                                                                                                                                598|                                                                                                          
                                                                                                                                                                                 616                                                                                                          

Chain D from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jvgd_ D: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee....eeeeee...eeeeeee.......hhhhhhhhhhhhhh.........eeeee....eeeeee...eeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee..........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jvg D 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATVKSSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597    || 620       630       640       650       660       670       680       690       700       710       720  
                                                                                                                                                                                    602|                                                                                                          
                                                                                                                                                                                     616                                                                                                          

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRAF_HUMAN | P150561uwh 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 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 5val 5vam

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4JVG)