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(-) Description

Title :  BRAFV600E KINASE DOMAIN IN COMPLEX WITH CHEMICALLY LINKED VEMURAFENIB INHIBITOR VEM-3-VEM
 
Authors :  M. J. Grasso, R. Marmorstein
Date :  08 May 16  (Deposition) - 14 Sep 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Kinase, Dimer, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Grasso, M. A. Estrada, C. Ventocilla, M. Samanta, J. Maksimoska, J. Villanueva, J. D. Winkler, R. Marmorstein
Chemically Linked Vemurafenib Inhibitors Promote An Inactiv Braf(V600E) Conformation.
Acs Chem. Biol. V. 11 2876 2016
PubMed-ID: 27571413  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00529

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE B-RAF
    Chains: A, B, C, D
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: KINASE DOMAIN (UNP RESIDUES 448-723)
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
16NB2Ligand/IonN,N'-{ETHANE-1,2-DIYLBIS[OXYETHANE-2,1-DIYLOXY-4,1-PHENYLENE-1H-PYRROLO[2,3-B]PYRIDINE-5,3-DIYLCARBONYL(2,4-DIFLUORO-3,1-PHENYLENE)]}DI(PROPANE-1-SULFONAMIDE)
2BEN2Ligand/IonBENZAMIDINE
3CL3Ligand/IonCHLORIDE ION
4DMS6Ligand/IonDIMETHYL SULFOXIDE
5EOH3Ligand/IonETHANOL
6GOL1Ligand/IonGLYCEROL
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
16NB1Ligand/IonN,N'-{ETHANE-1,2-DIYLBIS[OXYETHANE-2,1-DIYLOXY-4,1-PHENYLENE-1H-PYRROLO[2,3-B]PYRIDINE-5,3-DIYLCARBONYL(2,4-DIFLUORO-3,1-PHENYLENE)]}DI(PROPANE-1-SULFONAMIDE)
2BEN2Ligand/IonBENZAMIDINE
3CL-1Ligand/IonCHLORIDE ION
4DMS4Ligand/IonDIMETHYL SULFOXIDE
5EOH3Ligand/IonETHANOL
6GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
16NB1Ligand/IonN,N'-{ETHANE-1,2-DIYLBIS[OXYETHANE-2,1-DIYLOXY-4,1-PHENYLENE-1H-PYRROLO[2,3-B]PYRIDINE-5,3-DIYLCARBONYL(2,4-DIFLUORO-3,1-PHENYLENE)]}DI(PROPANE-1-SULFONAMIDE)
2BEN-1Ligand/IonBENZAMIDINE
3CL-1Ligand/IonCHLORIDE ION
4DMS2Ligand/IonDIMETHYL SULFOXIDE
5EOH-1Ligand/IonETHANOL
6GOL-1Ligand/IonGLYCEROL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:568 , PHE A:635binding site for residue DMS A 801
02AC2SOFTWAREGLY A:464 , SER A:465 , GLY A:466 , ASN A:580 , HOH A:927 , HOH A:929 , HOH A:969 , 6NB B:801binding site for residue DMS A 802
03AC3SOFTWARELEU A:678binding site for residue DMS A 803
04AC4SOFTWARETRP A:450 , ARG A:509 , PHE A:516 , MET A:517 , ASP D:449 , TRP D:450 , GLU D:451 , MET D:517 , CL D:802binding site for residue BEN A 804
05AC5SOFTWAREASP A:587 , GLY D:455binding site for residue EOH A 805
06AC6SOFTWAREGLN A:461 , ILE A:463 , VAL A:471 , ALA A:481 , LYS A:483 , LEU A:514 , THR A:529 , GLN A:530 , TRP A:531 , CYS A:532 , SER A:535 , HIS A:539 , PHE A:583 , GLY A:593 , ASP A:594 , PHE A:595 , GLY A:596 , DMS A:802 , HOH A:927 , GLN B:461 , ILE B:463 , VAL B:471 , ALA B:481 , LYS B:483 , LEU B:514 , THR B:529 , GLN B:530 , TRP B:531 , CYS B:532 , SER B:535 , HIS B:539 , PHE B:583 , GLY B:593 , ASP B:594 , PHE B:595 , GLY B:596 , DMS B:802 , HOH B:911 , HOH B:926binding site for residue 6NB B 801
07AC7SOFTWAREGLY B:464 , SER B:465 , VAL B:471 , 6NB B:801binding site for residue DMS B 802
08AC8SOFTWAREPHE B:447 , LYS B:499 , VAL B:502 , GLY B:503 , ARG B:506binding site for residue CL B 803
09AC9SOFTWARELEU B:485 , VAL B:487binding site for residue EOH B 805
10AD1SOFTWARELYS B:507 , TYR B:566 , LYS B:570binding site for residue GOL B 806
11AD2SOFTWAREASP B:449 , TRP B:450 , MET B:517 , CL B:808 , TRP C:450 , ARG C:509 , MET C:517 , HOH C:938binding site for residue BEN B 807
12AD3SOFTWARETRP B:450 , PHE B:516 , BEN B:807 , HOH C:938binding site for residue CL B 808
13AD4SOFTWAREGLN C:461 , ILE C:463 , VAL C:471 , ALA C:481 , LYS C:483 , LEU C:514 , THR C:529 , GLN C:530 , TRP C:531 , CYS C:532 , SER C:535 , HIS C:539 , PHE C:583 , GLY C:593 , ASP C:594 , PHE C:595 , GLY C:596 , DMS C:802 , HOH C:917 , GLN D:461 , ILE D:463 , VAL D:471 , ALA D:481 , LYS D:483 , LEU D:514 , THR D:529 , GLN D:530 , TRP D:531 , CYS D:532 , SER D:535 , PHE D:583 , GLY D:593 , ASP D:594 , PHE D:595 , GLY D:596 , HOH D:929binding site for residue 6NB C 801
14AD5SOFTWAREILE C:463 , HIS C:539 , 6NB C:801binding site for residue DMS C 802
15AD6SOFTWARESER D:465 , ASN D:580 , HOH D:929binding site for residue DMS D 801
16AD7SOFTWAREBEN A:804 , HOH A:960 , TRP D:450 , PHE D:516binding site for residue CL D 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JSM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:522 -Pro A:523
2Lys B:522 -Pro B:523
3Lys C:522 -Pro C:523
4Lys D:522 -Pro D:523

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JSM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JSM)

(-) Exons   (0, 0)

(no "Exon" information available for 5JSM)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.........hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsm A 445 SEFDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATEKSGSILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELAREL 721
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594      |616       626       636       646       656       666       676       686       696       706       716     
                                                                                                                                                                                      601|                                                                                                           
                                                                                                                                                                                       614                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......eeeeeeeee..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsm B 444 GSEFDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATEKSRSILWMAPEVIRMNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELAREL 721
                                   453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603|      625 ||    638       648       658       668       678       688       698       708       718   
                                                                                                                                                                                         603|        627|                                                                                          
                                                                                                                                                                                          616         631                                                                                          


Chain C from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeeee..eeeeeee...eeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.............hhhhhh.......hhhhhhhhhhhhhhhhhhh..........hhhhhhhh.....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsm C 445 SEFDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATESILWMAPEVIRMQDSNPYSFQSDVYAFGIVLYELMTGQLPYSNINNDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELARELS 722
                                   454       464       474       484       494       504       514       524       534       544       554       564       574       584       594     ||619       629       639       649       659 ||    670       680       690       700       710       720  
                                                                                                                                                                                     600|                                          661|                                                           
                                                                                                                                                                                      616                                           663                                                           


Chain D from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......eeeeeeeee..eeeeeee...eeeeeee...hhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhh....hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsm D 444 GSEFDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHASETKFEMKKLIDIARQTARGMDYLHAKSIIHRDLKSNNIFLHEDNTVKIGDFGLATEKSSGSILWMAPEVIRMNPYSFQSDVYAFGIVLYELMTGQLPYSNIDQIIEMVGRGSLSPDLSKVRSNCPKRMKRLMAECLKKKRDERPSFPRILAEIEELAREL 721
                                   453       463       473       483   ||  495       505       515       525       535       545       555       565       575       585       595      |616       626||     639       649       659|      672       682       692       702       712         
                                                                     487|                                                                                                             602|          627|                         659|                                                          
                                                                      490                                                                                                              614           631                          663
   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 5JSM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JSM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JSM)

(-) Gene Ontology  (64, 64)

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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 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 5jt2 5val 5vam

(-) Related Entries Specified in the PDB File

5jrq 5jt2