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(-) Description

Title :  B-RAF KINASE DOMAIN IN COMPLEX WITH AN AMINOPYRIDIMINE-BASED INHIBITOR
 
Authors :  W. C. Voegtli
Date :  02 Apr 12  (Deposition) - 24 Apr 13  (Release) - 24 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mathieu, S. N. Gradl, L. Ren, Z. Wen, I. Aliagas, J. Gunzner-Toste, W. Lee, R. Pulk, G. Zhao, B. Alicke, J. W. Boggs, A. J. Buckmelter, E. F. Choo, V. Dinkel, S. L. Gloor, S. E. Gould, J. D. Hansen, G. Hastings G. Hatzivassiliou, E. R. Laird, D. Moreno, Y. Ran, W. C. Voegtli, S. Wenglowsky, J. Grina, J. Rudolph
Potent And Selective Aminopyrimidine-Based B-Raf Inhibitors With Favorable Physicochemical And Pharmacokinetic Properties.
J. Med. Chem. V. 55 2869 2012
PubMed-ID: 22335519  |  Reference-DOI: 10.1021/JM300016V

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Fragment: KINASE DOMAIN
    Gene: BRAF, BRAF1, RAFB1
    Mutation: YES
    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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1RI92Ligand/IonN-{2,4-DIFLUORO-3-[({6-[(2-HYDROXYETHYL)AMINO]PYRIMIDIN-4-YL}CARBAMOYL)AMINO]PHENYL}PROPANE-1-SULFONAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:481 , VAL A:482 , LYS A:483 , LEU A:514 , ILE A:527 , GLN A:530 , TRP A:531 , CYS A:532 , GLY A:534 , PHE A:583 , ASP A:594 , PHE A:595 , GLY A:596 , ARG B:671BINDING SITE FOR RESIDUE RI9 A 801
2AC2SOFTWAREALA B:481 , VAL B:482 , LYS B:483 , LEU B:505 , LEU B:514 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , GLY B:534 , SER B:535 , PHE B:583 , ASP B:594 , PHE B:595 , GLY B:596BINDING SITE FOR RESIDUE RI9 B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Pro A:490 -Thr A:491
2Pro A:492 -Gln A:493
3Thr A:599 -Glu A:600
4Pro B:490 -Thr B:491
5Pro B:492 -Gln B:493

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EHG)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee..eeeeeee...eeeeee........hhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...........eeee...eeee..............hhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ehg A 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATEGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK 723
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       597  ||   621       631       641       651       661       671       681       691       701       711       721  
                                                                                                                                                                                  600|                                                                                                            
                                                                                                                                                                                   615                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeeee...eeeeee.........hhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee............hhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ehg B 448 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPK 723
                                   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       723
                                                                                                                                                                               597|                                                                                                             
                                                                                                                                                                                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  (0, 0)

(no "SCOP Domain" information available for 4EHG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Pro A:490 - Thr A:491   [ RasMol ]  
    Pro A:492 - Gln A:493   [ RasMol ]  
    Pro B:490 - Thr B:491   [ RasMol ]  
    Pro B:492 - Gln B:493   [ RasMol ]  
    Thr A:599 - Glu A:600   [ RasMol ]  
 

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 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 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 5val 5vam

(-) Related Entries Specified in the PDB File

4ehe