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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN B-RAF BOUND TO A DFG-OUT INHIBITOR 5B
 
Authors :  J. K. Yano, O. Masanori
Date :  17 May 13  (Deposition) - 24 Jul 13  (Release) - 04 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
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, V-RAF MURINE SARCOMA VIRAL ONCOGENE HOMOLOG B1, P94
    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
11SW2Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]CARBAMOYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
11SW2Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]CARBAMOYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11SW1Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]CARBAMOYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11SW1Ligand/IonN-{7-CYANO-6-[4-FLUORO-3-({[3-(TRIFLUOROMETHYL)PHENYL]CARBAMOYL}AMINO)PHENOXY]-1,3-BENZOTHIAZOL-2-YL}CYCLOPROPANECARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA 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 , ILE A:591 , GLY A:592 , ASP A:593 , PHE A:594BINDING SITE FOR RESIDUE 1SW A 901
2AC2SOFTWAREALA B:480 , LYS B:482 , GLU B:500 , LEU B:504 , ILE B:512 , LEU B:513 , ILE B:526 , THR B:528 , GLN B:529 , TRP B:530 , CYS B:531 , GLY B:533 , LEU B:566 , HIS B:573 , PHE B:582 , ILE B:591 , GLY B:592 , ASP B:593 , PHE B:594BINDING SITE FOR RESIDUE 1SW B 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:521 -Pro A:522
2Lys B:521 -Pro B:522

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KSQ)

(-) 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeeee..eeeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeeehhheeee......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ksq A 447 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 721
                                   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                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeee....eeeeee...eeeeee......hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ksq B 448 DWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS 719
                                   457       467       477       487       497       507       517       527       537       547       557       567       577       587       614       624       634       644       654       664       674       684       694       704       714     
                                                                                                                                                                              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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (64, 64)

Asymmetric Unit(hide GO term definitions)

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  4ksq
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  BRAF_HUMAN | P15056
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  2.7.11.1
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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 4ehg 4fc0 4fk3 4g9c 4g9r 4h58 4jvg 4ksp 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
4ksp B-RAF BOUND TO A DFG-OUT INHIBITOR TAK-632