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Fluorine in PDB 6ohp: Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain

Enzymatic activity of Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain

All present enzymatic activity of Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain:
3.1.4.4;

Protein crystallography data

The structure of Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain, PDB code: 6ohp 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) 48.29 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.186, 132.509, 114.638, 90.00, 100.34, 90.00
R / Rfree (%) 24 / 27.6

Other elements in 6ohp:

The structure of Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Compound 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain (pdb code 6ohp). 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 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain, PDB code: 6ohp:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6ohp

Go back to Fluorine Binding Sites List in 6ohp
Fluorine binding site 1 out of 4 in the Structure of Compound 1 (Halopemide) 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 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:44.1
occ:1.00
 F20 A:MJV1001 0.0 44.1 1.0
C19 A:MJV1001 1.3 43.2 1.0
C18 A:MJV1001 2.4 40.1 1.0
C21 A:MJV1001 2.4 43.9 1.0
O A:GLY410 3.2 48.7 1.0
C A:GLY410 3.4 49.6 1.0
O A:LEU409 3.6 77.6 1.0
C17 A:MJV1001 3.7 40.5 1.0
C22 A:MJV1001 3.7 44.0 1.0
CA A:GLY410 3.7 56.3 1.0
O A:TRP519 3.8 46.5 1.0
CB A:TRP519 3.8 38.5 1.0
N A:TRP519 3.9 46.9 1.0
N A:ILE411 4.1 48.2 1.0
C16 A:MJV1001 4.2 39.6 1.0
CA A:TRP519 4.3 44.4 1.0
C A:LEU409 4.4 70.4 1.0
C A:TRP519 4.4 46.9 1.0
N A:GLY410 4.5 63.1 1.0
CE3 A:TRP519 4.5 32.4 1.0
CB A:ASP518 4.6 52.5 1.0
CA A:ILE411 4.7 46.5 1.0
CG A:ASP518 4.8 57.5 1.0
CG A:TRP519 4.9 32.5 1.0
C A:ASP518 4.9 49.7 1.0

Fluorine binding site 2 out of 4 in 6ohp

Go back to Fluorine Binding Sites List in 6ohp
Fluorine binding site 2 out of 4 in the Structure of Compound 1 (Halopemide) 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 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:45.5
occ:1.00
 F20 B:MJV1001 0.0 45.5 1.0
C19 B:MJV1001 1.3 44.6 1.0
C21 B:MJV1001 2.4 42.1 1.0
C18 B:MJV1001 2.4 40.8 1.0
O B:LEU409 2.9 74.7 1.0
O B:GLY410 3.3 52.1 1.0
CA B:GLY410 3.4 55.7 1.0
C B:GLY410 3.4 50.9 1.0
C22 B:MJV1001 3.7 41.2 1.0
C17 B:MJV1001 3.7 40.8 1.0
C B:LEU409 3.8 67.0 1.0
O B:TRP519 3.8 40.8 1.0
N B:TRP519 3.9 42.8 1.0
CB B:TRP519 4.0 35.0 1.0
N B:GLY410 4.0 60.0 1.0
N B:ILE411 4.2 48.7 1.0
C16 B:MJV1001 4.2 41.4 1.0
CA B:TRP519 4.3 37.3 1.0
CB B:ASP518 4.4 56.5 1.0
C B:TRP519 4.5 38.2 1.0
CG B:ASP518 4.7 60.9 1.0
CE3 B:TRP519 4.7 30.8 1.0
C B:ASP518 4.8 51.2 1.0
CA B:ILE411 5.0 46.1 1.0

Fluorine binding site 3 out of 4 in 6ohp

Go back to Fluorine Binding Sites List in 6ohp
Fluorine binding site 3 out of 4 in the Structure of Compound 1 (Halopemide) 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 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1001

b:70.6
occ:1.00
 F20 C:MJV1001 0.0 70.6 1.0
C19 C:MJV1001 1.3 69.5 1.0
C18 C:MJV1001 2.4 68.2 1.0
C21 C:MJV1001 2.4 69.4 1.0
O C:LEU409 2.8 90.1 1.0
C C:GLY410 3.2 80.2 1.0
O C:GLY410 3.2 81.9 1.0
CA C:GLY410 3.2 82.7 1.0
O C:TRP519 3.5 59.9 1.0
C C:LEU409 3.6 88.3 1.0
C22 C:MJV1001 3.7 69.6 1.0
C17 C:MJV1001 3.7 68.1 1.0
N C:GLY410 3.8 84.8 1.0
N C:ILE411 3.9 75.7 1.0
N C:TRP519 4.0 51.2 1.0
CB C:TRP519 4.1 49.2 1.0
C16 C:MJV1001 4.2 67.5 1.0
C C:TRP519 4.3 58.0 1.0
CA C:TRP519 4.4 52.0 1.0
CB C:ASP518 4.4 67.4 1.0
CA C:ILE411 4.7 71.6 1.0
CG C:ASP518 4.7 75.0 1.0
C C:ASP518 4.9 55.7 1.0
CA C:LEU409 4.9 88.6 1.0

Fluorine binding site 4 out of 4 in 6ohp

Go back to Fluorine Binding Sites List in 6ohp
Fluorine binding site 4 out of 4 in the Structure of Compound 1 (Halopemide) 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 1 (Halopemide) Bound Human Phospholipase D2 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1001

b:92.2
occ:1.00
 F20 D:MJV1001 0.0 92.2 1.0
C19 D:MJV1001 1.3 90.2 1.0
C21 D:MJV1001 2.4 88.8 1.0
C18 D:MJV1001 2.4 88.2 1.0
O D:LEU409 2.8 84.0 1.0
C D:GLY410 3.1 77.4 1.0
O D:GLY410 3.1 79.6 1.0
CA D:GLY410 3.1 78.7 1.0
O D:TRP519 3.5 61.8 1.0
C D:LEU409 3.5 81.4 1.0
C22 D:MJV1001 3.6 86.1 1.0
C17 D:MJV1001 3.7 85.0 1.0
N D:GLY410 3.7 79.5 1.0
N D:ILE411 3.8 71.8 1.0
CB D:TRP519 3.9 57.7 1.0
N D:TRP519 4.1 59.2 1.0
C16 D:MJV1001 4.2 81.3 1.0
C D:TRP519 4.3 61.5 1.0
CA D:TRP519 4.3 58.5 1.0
CB D:ASP518 4.6 66.1 1.0
CA D:ILE411 4.6 66.4 1.0
CA D:LEU409 4.9 80.7 1.0
CG D:ASP518 4.9 71.1 1.0
CG2 D:ILE411 4.9 61.2 1.0
C D:ASP518 5.0 58.3 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 14:11:21 2025

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