Chlorine in PDB 5jsm: BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem

Enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem

All present enzymatic activity of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem:
2.7.11.1;

Protein crystallography data

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem, PDB code: 5jsm was solved by M.J.Grasso, R.Marmorstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 62.91 / 2.19
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 64.608, 68.258, 276.007, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 26

Other elements in 5jsm:

The structure of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem (pdb code 5jsm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem, PDB code: 5jsm:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5jsm

Go back to Chlorine Binding Sites List in 5jsm
Chlorine binding site 1 out of 3 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl803

b:53.2
occ:1.00
 NH2 B:ARG506 2.9 31.7 0.1
NH1 B:ARG506 2.9 28.6 0.9
O B:LYS499 3.1 43.2 1.0
N B:GLY503 3.3 38.9 1.0
NE B:ARG506 3.4 33.4 0.1
CA B:GLY503 3.4 30.8 1.0
CD1 B:PHE447 3.4 30.9 1.0
CZ B:ARG506 3.5 32.6 0.1
CG1 B:VAL502 3.6 35.8 1.0
CB B:PHE447 3.7 35.5 1.0
C B:VAL502 3.9 39.6 1.0
CD B:ARG506 3.9 32.5 0.9
CA B:PHE447 4.0 35.0 1.0
CG B:PHE447 4.0 34.9 1.0
CB B:VAL502 4.0 36.5 1.0
C B:LYS499 4.1 44.7 1.0
CZ B:ARG506 4.1 33.6 0.9
O B:HOH902 4.4 26.7 1.0
O B:VAL502 4.4 34.5 1.0
N B:PHE447 4.4 31.7 1.0
NE B:ARG506 4.5 35.3 0.9
CA B:LYS499 4.5 40.4 1.0
CE1 B:PHE447 4.5 35.2 1.0
CA B:VAL502 4.5 38.5 1.0
CD B:ARG506 4.6 32.9 0.1
CB B:LYS499 4.8 48.9 1.0
NH1 B:ARG506 4.8 32.5 0.1
C B:GLY503 4.9 33.8 1.0

Chlorine binding site 2 out of 3 in 5jsm

Go back to Chlorine Binding Sites List in 5jsm
Chlorine binding site 2 out of 3 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl808

b:54.4
occ:1.00
 N1 B:BEN807 2.8 34.8 1.0
O C:HOH938 2.9 33.3 1.0
HN1 B:BEN807 3.2 41.8 1.0
O B:PHE516 3.2 33.9 1.0
O B:HOH960 3.2 47.5 1.0
HN21 B:BEN807 3.3 43.8 1.0
CZ3 B:TRP450 3.6 29.2 1.0
CH2 B:TRP450 3.8 35.5 1.0
C B:BEN807 3.8 25.1 1.0
CA B:MET517 3.9 24.9 1.0
N2 B:BEN807 3.9 36.5 1.0
CD2 B:LEU515 3.9 38.2 1.0
CH2 C:TRP476 4.0 37.5 1.0
CG B:LEU515 4.1 36.1 1.0
CD1 B:LEU515 4.2 31.5 1.0
CZ2 C:TRP476 4.2 35.0 1.0
C B:PHE516 4.2 29.8 1.0
CG B:MET517 4.4 33.7 1.0
O B:MET517 4.5 26.8 1.0
NH1 B:ARG509 4.5 27.5 1.0
O B:HOH952 4.5 41.5 1.0
C B:MET517 4.5 28.7 1.0
N B:MET517 4.6 28.9 1.0
CB B:MET517 4.6 31.9 1.0
O C:HOH906 4.8 41.4 1.0
HN22 B:BEN807 4.8 43.8 1.0
CE3 B:TRP450 4.8 35.0 1.0

Chlorine binding site 3 out of 3 in 5jsm

Go back to Chlorine Binding Sites List in 5jsm
Chlorine binding site 3 out of 3 in the BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of BRAFV600E Kinase Domain in Complex with Chemically Linked Vemurafenib Inhibitor Vem-3-Vem within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl802

b:54.2
occ:1.00
 O A:HOH960 2.8 39.5 1.0
N1 A:BEN804 2.8 28.8 1.0
O D:PHE516 3.0 33.6 1.0
HN1 A:BEN804 3.2 34.5 1.0
HN22 A:BEN804 3.4 43.6 1.0
CZ3 D:TRP450 3.5 26.3 1.0
CH2 D:TRP450 3.7 37.0 1.0
CD2 D:LEU515 3.8 39.2 1.0
CA D:MET517 3.8 29.6 1.0
C A:BEN804 3.8 28.2 1.0
CH2 A:TRP476 3.9 36.6 1.0
N2 A:BEN804 4.0 36.4 1.0
C D:PHE516 4.1 33.0 1.0
CZ2 A:TRP476 4.1 41.0 1.0
CG D:LEU515 4.1 40.5 1.0
CD1 D:LEU515 4.2 33.7 1.0
O D:HOH928 4.2 44.9 1.0
CG D:MET517 4.3 34.7 1.0
O D:HOH947 4.4 41.0 1.0
N D:MET517 4.5 28.0 1.0
CB D:MET517 4.5 27.2 1.0
NH2 D:ARG509 4.5 35.8 1.0
C D:MET517 4.6 25.5 1.0
O D:MET517 4.6 31.2 1.0
CE3 D:TRP450 4.8 36.1 1.0
HN21 A:BEN804 4.8 43.6 1.0

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 Inactive Braf(V600E) Conformation. Acs Chem.Biol. V. 11 2876 2016.
ISSN: ESSN 1554-8937
PubMed: 27571413
DOI: 10.1021/ACSCHEMBIO.6B00529
Page generated: Sat Dec 12 11:54:13 2020

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