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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN KINASE DOMAIN OF B-RAF WITH A DFG-OUT INHIBITOR
 
Authors :  J. K. Yano, K. Aertgeerts
Date :  23 May 12  (Deposition) - 08 Jan 14  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Serine/Theronine Protein Kinase, Kinase Drug Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hirose, M. Okaniwa, T. Miyazaki, T. Imada, T. Ohashi, Y. Tanaka, T. Arita, M. Yabuki, T. Kawamoto, S. Tsutsumi, A. Sumita, T. Takagi, B. C. Sang, J. Yano, K. Aertgeerts, S. Yoshida, T. Ishikawa
Design And Synthesis Of Novel Dfg-Out Raf/Vascular Endothelial Growth Factor Receptor 2 (Vegfr2) Inhibitors: 3 Evaluation Of 5-Amino-Linked Thiazolo[5, 4-D]Pyrimidine And Thiazolo[5, 4-B]Pyridine Derivatives.
Bioorg. Med. Chem. V. 20 5600 2012
PubMed-ID: 22883026  |  Reference-DOI: 10.1016/J.BMC.2012.07.032

(-) 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 Plasmid: PFASTBAC
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: KINASE DOMAIN (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/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
10T22Ligand/Ion2-CHLORO-3-[(2-CYANOPROPAN-2-YL)OXY]-N-{5-[{2-[(CYCLOPROPYLCARBONYL)AMINO][1,3]THIAZOLO[5,4-B]PYRIDIN-5-YL}(METHYL)AMINO]-2-FLUOROPHENYL}BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:480 , LYS A:482 , GLU A:500 , VAL A:503 , LEU A:504 , LEU A:513 , ILE A:526 , THR A:528 , GLN A:529 , TRP A:530 , CYS A:531 , GLY A:533 , ILE A:591 , GLY A:592 , ASP A:593 , PHE A:594 , HOH A:1034BINDING SITE FOR RESIDUE 0T2 A 901
2AC2SOFTWAREVAL B:470 , ALA B:480 , LYS B:482 , GLU B:500 , VAL B:503 , LEU B:504 , 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 , GLY B:592 , ASP B:593 , PHE B:594 , ALA B:597BINDING SITE FOR RESIDUE 0T2 B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FC0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:521 -Pro A:522

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FC0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FC0)

(-) Exons   (0, 0)

(no "Exon" information available for 4FC0)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains d4fc0a_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeee..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee.....eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee...eeee.....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fc0 A 447 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGGSILWMAPEVIRMNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLP 721
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       614       624 ||    637       647       657       667       677       687       697       707       717    
                                                                                                                                                                              595|         626|                                                                                           
                                                                                                                                                                               614          630                                                                                           


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fc0b_ 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.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fc0 B 447 DDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS 719
                                   456       466       476       486       496       506       516       526       536       546       556       566       576       586       596      |616       626       636       646       656       666       676       686       696       706       716   
                                                                                                                                                                                      603|                                                                                                         
                                                                                                                                                                                       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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FC0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FC0)

(-) Gene Ontology  (64, 64)

Asymmetric/Biological Unit(hide GO term definitions)

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  4fc0
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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 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

3q96 4dbn