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Bromine in PDB 6ohs: Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain

Enzymatic activity of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain

All present enzymatic activity of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain:
3.1.4.4;

Protein crystallography data

The structure of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain, PDB code: 6ohs was solved by C.M.Metrick, J.V.Chodaparambil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.17 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.060, 132.317, 114.611, 90.00, 100.01, 90.00
R / Rfree (%) 27.8 / 31.9

Other elements in 6ohs:

The structure of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain (pdb code 6ohs). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain, PDB code: 6ohs:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in 6ohs

Go back to Bromine Binding Sites List in 6ohs
Bromine binding site 1 out of 4 in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br1001

b:0.8
occ:1.00
 BR1 A:MJY1001 0.0 0.8 1.0
C11 A:MJY1001 1.9 0.4 1.0
C10 A:MJY1001 2.8 0.4 1.0
C12 A:MJY1001 2.9 0.8 1.0
OD2 A:ASP518 3.1 0.4 1.0
OD1 A:ASP518 3.2 0.4 1.0
N A:GLY410 3.4 83.0 1.0
CG A:ASP518 3.6 0.2 1.0
C A:GLY410 3.6 71.4 1.0
CG2 A:ILE411 3.6 49.6 1.0
N A:ILE411 3.7 68.2 1.0
CA A:GLY410 3.8 78.4 1.0
O A:GLY410 3.9 68.8 1.0
C9 A:MJY1001 4.1 0.9 1.0
C13 A:MJY1001 4.1 0.4 1.0
CA A:ILE411 4.3 65.1 1.0
CD2 A:LEU409 4.3 65.7 1.0
C A:LEU409 4.6 78.8 1.0
CB A:ILE411 4.6 49.9 1.0
CB A:LEU409 4.6 67.5 1.0
C8 A:MJY1001 4.7 0.6 1.0
CA A:LEU409 4.7 69.3 1.0
CB A:TRP519 4.8 64.8 1.0
O A:TRP519 4.8 65.6 1.0
N A:TRP519 4.8 83.8 1.0
CE3 A:TRP519 4.9 51.9 1.0

Bromine binding site 2 out of 4 in 6ohs

Go back to Bromine Binding Sites List in 6ohs
Bromine binding site 2 out of 4 in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br1001

b:0.6
occ:1.00
 BR1 B:MJY1001 0.0 0.6 1.0
C11 B:MJY1001 1.9 0.3 1.0
C12 B:MJY1001 2.8 0.2 1.0
C10 B:MJY1001 2.9 0.1 1.0
C B:GLY410 3.7 59.6 1.0
O B:GLY410 3.7 68.5 1.0
CB B:TRP519 3.8 43.5 1.0
CG2 B:ILE411 3.9 46.7 1.0
N B:ILE411 4.0 54.7 1.0
O B:TRP519 4.1 53.8 1.0
N B:TRP519 4.1 51.5 1.0
C13 B:MJY1001 4.1 0.2 1.0
C9 B:MJY1001 4.1 0.8 1.0
CA B:GLY410 4.1 54.9 1.0
N B:GLY410 4.2 50.3 1.0
CE3 B:TRP519 4.2 37.4 1.0
CA B:ILE411 4.3 52.7 1.0
CA B:TRP519 4.4 47.9 1.0
C B:TRP519 4.6 50.4 1.0
C8 B:MJY1001 4.7 0.5 1.0
CG B:TRP519 4.7 40.1 1.0
CB B:ILE411 4.7 46.6 1.0
CD2 B:TRP519 4.8 38.1 1.0
CB B:ASP518 5.0 64.2 1.0

Bromine binding site 3 out of 4 in 6ohs

Go back to Bromine Binding Sites List in 6ohs
Bromine binding site 3 out of 4 in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br1001

b:0.0
occ:1.00
 BR1 C:MJY1001 0.0 0.0 1.0
C11 C:MJY1001 1.9 0.6 1.0
C10 C:MJY1001 2.8 0.1 1.0
C12 C:MJY1001 2.8 0.2 1.0
OD2 C:ASP518 3.1 0.6 1.0
N C:GLY410 3.2 0.0 1.0
C C:GLY410 3.3 0.3 1.0
OD1 C:ASP518 3.4 0.8 1.0
N C:ILE411 3.4 98.5 1.0
CG2 C:ILE411 3.4 93.7 1.0
CA C:GLY410 3.5 0.4 1.0
CG C:ASP518 3.6 0.5 1.0
O C:GLY410 3.7 0.3 1.0
CA C:ILE411 4.1 92.7 1.0
C9 C:MJY1001 4.1 0.5 1.0
C13 C:MJY1001 4.1 1.0 1.0
C C:LEU409 4.3 0.2 1.0
CB C:ILE411 4.4 93.1 1.0
CD2 C:LEU409 4.4 0.8 1.0
CB C:LEU409 4.5 0.1 1.0
CA C:LEU409 4.6 0.9 1.0
C8 C:MJY1001 4.7 0.5 1.0
O C:TRP519 4.7 80.0 1.0
CB C:TRP519 4.8 82.3 1.0
N C:TRP519 4.8 88.0 1.0
CE3 C:TRP519 5.0 85.3 1.0

Bromine binding site 4 out of 4 in 6ohs

Go back to Bromine Binding Sites List in 6ohs
Bromine binding site 4 out of 4 in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br1001

b:0.7
occ:1.00
 BR1 D:MJY1001 0.0 0.7 1.0
C11 D:MJY1001 1.9 0.1 1.0
C12 D:MJY1001 2.8 0.1 1.0
C10 D:MJY1001 2.9 0.9 1.0
OD1 D:ASP518 3.2 96.8 1.0
OD2 D:ASP518 3.6 97.6 1.0
CE3 D:TRP519 3.7 72.7 1.0
CG D:ASP518 3.8 94.4 1.0
CG2 D:ILE411 3.8 73.2 1.0
C D:GLY410 4.0 0.8 1.0
O D:GLY410 4.0 0.5 1.0
CB D:TRP519 4.0 81.0 1.0
C13 D:MJY1001 4.1 0.4 1.0
N D:ILE411 4.1 96.0 1.0
C9 D:MJY1001 4.2 0.2 1.0
N D:TRP519 4.3 81.0 1.0
CA D:ILE411 4.4 83.6 1.0
CD2 D:TRP519 4.5 75.3 1.0
N D:GLY410 4.5 95.0 1.0
CA D:GLY410 4.5 0.3 1.0
CZ3 D:TRP519 4.6 71.4 1.0
CG D:TRP519 4.6 78.9 1.0
C8 D:MJY1001 4.7 0.8 1.0
CB D:ILE411 4.7 75.3 1.0
CA D:TRP519 4.7 82.3 1.0
CZ3 D:TRP365 4.8 45.6 1.0
O D:TRP519 4.8 86.1 1.0
CH2 D:TRP365 4.9 47.2 1.0

Reference:

C.M.Metrick, E.A.Peterson, J.C.Santoro, I.J.Enyedy, P.Murugan, T.Chen, K.Michelsen, M.Cullivan, K.A.Spilker, P.R.Kumar, T.L.May-Dracka, J.V.Chodaparambil. Human Pld Structures Enable Drug Design and Characterization of Isoenzyme Selectivity. Nat.Chem.Biol. 2020.
ISSN: ESSN 1552-4469
PubMed: 32042197
DOI: 10.1038/S41589-019-0458-4
Page generated: Thu Jul 11 02:21:06 2024

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