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Fluorine 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:

Bromine (Br) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Compound 3 (ML299) Bound Human Phospholipase D2 Catalytic Domain, PDB code: 6ohs:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ohs

Go back to Fluorine Binding Sites List in 6ohs
Fluorine 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 Fluorine with other atoms in the F 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:F1001

b:92.4
occ:1.00
 F1 A:MJY1001 0.0 92.4 1.0
C21 A:MJY1001 1.4 83.7 1.0
C20 A:MJY1001 2.3 81.8 1.0
C22 A:MJY1001 2.4 78.3 1.0
C19 A:MJY1001 3.6 79.6 1.0
C17 A:MJY1001 3.6 73.4 1.0
CB A:ALA440 3.7 46.4 1.0
CZ A:PHE402 3.8 54.8 1.0
CE2 A:PHE402 4.0 54.5 1.0
C18 A:MJY1001 4.1 77.4 1.0
O A:LEU438 4.1 46.6 1.0
NH1 A:ARG777 4.3 53.6 1.0
NE1 A:TRP364 4.6 49.7 1.0
CD1 A:LEU409 4.8 63.2 1.0
N4 A:MJY1001 4.8 65.1 1.0
CA A:ALA440 4.8 48.6 1.0
N A:ALA440 4.9 48.5 1.0
C A:TRP439 4.9 45.9 1.0
CE1 A:PHE402 4.9 55.9 1.0
C23 A:MJY1001 5.0 63.3 1.0

Fluorine binding site 2 out of 4 in 6ohs

Go back to Fluorine Binding Sites List in 6ohs
Fluorine 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 Fluorine with other atoms in the F 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:F1001

b:64.9
occ:1.00
 F1 B:MJY1001 0.0 64.9 1.0
C21 B:MJY1001 1.4 71.9 1.0
C22 B:MJY1001 2.3 77.4 1.0
C20 B:MJY1001 2.4 74.6 1.0
CB B:ALA440 3.3 29.8 1.0
C19 B:MJY1001 3.6 76.6 1.0
C17 B:MJY1001 3.6 84.1 1.0
NH1 B:ARG777 4.0 48.5 1.0
CZ B:PHE402 4.1 52.4 1.0
O B:LEU438 4.1 35.4 1.0
C18 B:MJY1001 4.1 80.1 1.0
CE2 B:PHE402 4.1 51.1 1.0
CA B:ALA440 4.4 31.2 1.0
N B:ALA440 4.4 33.8 1.0
NE1 B:TRP364 4.4 31.2 1.0
C B:TRP439 4.6 36.1 1.0
N4 B:MJY1001 4.8 88.5 1.0
CZ B:ARG777 4.8 46.8 1.0
CD1 B:LEU409 4.8 40.0 1.0
O B:TRP439 4.9 34.0 1.0

Fluorine binding site 3 out of 4 in 6ohs

Go back to Fluorine Binding Sites List in 6ohs
Fluorine 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 Fluorine with other atoms in the F 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:F1001

b:94.7
occ:1.00
 F1 C:MJY1001 0.0 94.7 1.0
C21 C:MJY1001 1.4 92.2 1.0
C20 C:MJY1001 2.3 90.7 1.0
C22 C:MJY1001 2.4 92.0 1.0
C19 C:MJY1001 3.6 88.8 1.0
C17 C:MJY1001 3.6 87.9 1.0
NH1 C:ARG777 4.1 58.6 1.0
C18 C:MJY1001 4.1 85.9 1.0
O C:LEU438 4.3 62.6 1.0
CZ C:ARG777 4.5 59.4 1.0
NH2 C:ARG777 4.6 61.3 1.0
N4 C:MJY1001 4.8 91.6 1.0
CB C:ALA440 4.9 62.1 1.0

Fluorine binding site 4 out of 4 in 6ohs

Go back to Fluorine Binding Sites List in 6ohs
Fluorine 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 Fluorine with other atoms in the F 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:F1001

b:75.9
occ:1.00
 F1 D:MJY1001 0.0 75.9 1.0
C21 D:MJY1001 1.4 75.5 1.0
C22 D:MJY1001 2.3 74.2 1.0
C20 D:MJY1001 2.3 74.6 1.0
CB D:ALA440 3.1 52.6 1.0
CZ D:PHE402 3.1 58.7 1.0
CE2 D:PHE402 3.3 57.5 1.0
C19 D:MJY1001 3.6 72.2 1.0
C17 D:MJY1001 3.6 75.7 1.0
NE1 D:TRP364 4.0 63.1 1.0
C18 D:MJY1001 4.1 73.3 1.0
CE1 D:PHE402 4.1 60.5 1.0
CA D:ALA440 4.2 52.7 1.0
CD1 D:LEU409 4.3 84.5 1.0
CD2 D:PHE402 4.4 59.3 1.0
N D:ALA440 4.5 56.2 1.0
O D:LEU438 4.5 57.8 1.0
NH1 D:ARG777 4.6 36.5 1.0
C D:TRP439 4.7 58.8 1.0
O D:TRP439 4.7 60.2 1.0
N4 D:MJY1001 4.8 71.6 1.0
CE2 D:TRP364 4.8 63.1 1.0
CZ2 D:TRP364 4.9 63.9 1.0
CD1 D:TRP364 5.0 61.2 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: Tue Jul 15 14:12:17 2025

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