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Fluorine in PDB 6ohr: Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain

Enzymatic activity of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain

All present enzymatic activity of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain:
3.1.4.4;

Protein crystallography data

The structure of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain, PDB code: 6ohr 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) 48.36 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 93.039, 155.106, 273.560, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 24.7

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain (pdb code 6ohr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain, PDB code: 6ohr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6ohr

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Fluorine binding site 1 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 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 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:67.8
occ:1.00
 F1 A:MKG1101 0.0 67.8 1.0
C12 A:MKG1101 1.4 57.0 1.0
C11 A:MKG1101 2.3 56.2 1.0
C13 A:MKG1101 2.3 49.1 1.0
CA A:GLY428 3.3 57.4 1.0
C10 A:MKG1101 3.6 56.0 1.0
C14 A:MKG1101 3.6 46.9 1.0
C A:GLY428 3.9 55.2 1.0
C9 A:MKG1101 4.1 51.3 1.0
O A:GLY428 4.2 69.6 1.0
N A:GLY428 4.3 54.7 1.0
N A:ILE429 4.6 46.6 1.0
CH2 A:TRP382 4.8 42.2 1.0
CZ2 A:TRP382 4.9 41.2 1.0

Fluorine binding site 2 out of 12 in 6ohr

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Fluorine binding site 2 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 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 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:71.5
occ:1.00
 F2 A:MKG1101 0.0 71.5 1.0
C22 A:MKG1101 1.4 49.8 1.0
C21 A:MKG1101 2.3 44.4 1.0
C23 A:MKG1101 2.3 40.9 1.0
CD A:ARG879 3.5 46.2 1.0
ND2 A:ASN877 3.5 37.0 1.0
C20 A:MKG1101 3.6 41.9 1.0
C18 A:MKG1101 3.6 43.0 1.0
CE2 A:PHE745 3.7 40.6 1.0
CD2 A:PHE745 4.0 38.9 1.0
C19 A:MKG1101 4.1 51.0 1.0
NE A:ARG879 4.2 49.3 1.0
CG A:ARG879 4.3 57.9 1.0
CB A:ARG879 4.4 47.1 1.0
CG A:ASN877 4.4 45.0 1.0
CD1 A:ILE804 4.5 43.4 1.0
CZ A:PHE745 4.6 39.2 1.0
O A:TRP1035 4.7 60.2 1.0
C17 A:MKG1101 4.9 37.0 1.0
O2 A:MKG1101 4.9 46.3 1.0
C1 A:MKG1101 4.9 44.0 1.0

Fluorine binding site 3 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 3 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 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 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:54.6
occ:1.00
 F1 B:MKG1101 0.0 54.6 1.0
C12 B:MKG1101 1.4 49.0 1.0
C13 B:MKG1101 2.3 47.9 1.0
C11 B:MKG1101 2.3 44.3 1.0
CA B:GLY428 2.9 51.2 1.0
C B:GLY428 3.4 50.9 1.0
C14 B:MKG1101 3.6 40.3 1.0
C10 B:MKG1101 3.6 47.0 1.0
O B:GLY428 3.7 52.8 1.0
N B:GLY428 4.1 46.6 1.0
C9 B:MKG1101 4.1 41.1 1.0
N B:ILE429 4.2 50.0 1.0
CG1 B:ILE429 4.9 46.6 1.0

Fluorine binding site 4 out of 12 in 6ohr

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Fluorine binding site 4 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 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 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:56.6
occ:1.00
 F2 B:MKG1101 0.0 56.6 1.0
C22 B:MKG1101 1.4 47.9 1.0
C21 B:MKG1101 2.3 39.8 1.0
C23 B:MKG1101 2.3 36.0 1.0
ND2 B:ASN877 3.4 44.8 1.0
CE2 B:PHE745 3.5 36.7 1.0
C20 B:MKG1101 3.6 34.2 1.0
C18 B:MKG1101 3.6 32.9 1.0
CD2 B:PHE745 3.8 35.4 1.0
CD B:ARG879 4.0 36.8 1.0
C19 B:MKG1101 4.1 38.2 1.0
CD1 B:ILE804 4.1 43.2 1.0
CZ B:PHE745 4.3 42.6 1.0
NE B:ARG879 4.4 33.4 1.0
CG B:ASN877 4.4 34.9 1.0
O B:TRP1035 4.6 50.0 1.0
CG B:PHE745 4.8 36.3 1.0
CB B:ARG879 4.8 34.9 1.0
C17 B:MKG1101 4.9 38.0 1.0
OXT B:THR1036 4.9 51.2 1.0
O2 B:MKG1101 4.9 40.2 1.0
C1 B:MKG1101 5.0 40.1 1.0

Fluorine binding site 5 out of 12 in 6ohr

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Fluorine binding site 5 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:52.0
occ:1.00
 F1 C:MKG1101 0.0 52.0 1.0
C12 C:MKG1101 1.4 46.6 1.0
C11 C:MKG1101 2.3 44.8 1.0
C13 C:MKG1101 2.3 42.8 1.0
CA C:GLY428 3.1 55.3 1.0
C10 C:MKG1101 3.6 43.1 1.0
C14 C:MKG1101 3.6 37.4 1.0
C C:GLY428 3.6 48.4 1.0
N C:GLY428 4.0 58.7 1.0
O C:GLY428 4.1 46.8 1.0
C9 C:MKG1101 4.1 39.7 1.0
N C:ILE429 4.3 49.1 1.0
CG1 C:ILE429 4.8 50.1 1.0

Fluorine binding site 6 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 6 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1101

b:60.7
occ:1.00
 F2 C:MKG1101 0.0 60.7 1.0
C22 C:MKG1101 1.4 45.0 1.0
C21 C:MKG1101 2.3 42.5 1.0
C23 C:MKG1101 2.3 36.0 1.0
ND2 C:ASN877 3.2 39.7 1.0
CE2 C:PHE745 3.5 32.4 1.0
C20 C:MKG1101 3.6 32.5 1.0
C18 C:MKG1101 3.6 38.8 1.0
CD C:ARG879 3.7 35.8 1.0
CD2 C:PHE745 3.9 35.0 1.0
C19 C:MKG1101 4.1 35.5 1.0
NE C:ARG879 4.1 35.2 1.0
CG C:ASN877 4.2 39.3 1.0
CZ C:PHE745 4.2 34.3 1.0
CB C:ARG879 4.4 35.9 1.0
O C:TRP1035 4.5 39.9 1.0
CD1 C:ILE804 4.5 28.0 1.0
CG C:ARG879 4.7 38.6 1.0
OD1 C:ASN877 4.8 38.5 1.0
C17 C:MKG1101 4.9 37.7 1.0
ND2 C:ASN875 4.9 34.5 1.0
OXT C:THR1036 4.9 53.8 1.0
O2 C:MKG1101 5.0 34.3 1.0
CG C:PHE745 5.0 34.9 1.0
C1 C:MKG1101 5.0 32.9 1.0

Fluorine binding site 7 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 7 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1101

b:55.4
occ:1.00
 F1 D:MKG1101 0.0 55.4 1.0
C12 D:MKG1101 1.4 45.5 1.0
C11 D:MKG1101 2.3 41.2 1.0
C13 D:MKG1101 2.3 42.7 1.0
CA D:GLY428 3.1 53.1 1.0
C10 D:MKG1101 3.6 45.3 1.0
C14 D:MKG1101 3.6 46.2 1.0
C D:GLY428 3.6 53.6 1.0
O D:GLY428 4.0 63.6 1.0
N D:GLY428 4.1 56.7 1.0
C9 D:MKG1101 4.1 46.4 1.0
N D:ILE429 4.3 47.9 1.0
CG1 D:ILE429 4.7 40.3 1.0

Fluorine binding site 8 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 8 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1101

b:74.3
occ:1.00
 F2 D:MKG1101 0.0 74.3 1.0
C22 D:MKG1101 1.4 44.6 1.0
C21 D:MKG1101 2.3 37.5 1.0
C23 D:MKG1101 2.3 35.7 1.0
ND2 D:ASN877 3.5 41.2 1.0
C20 D:MKG1101 3.6 33.9 1.0
C18 D:MKG1101 3.6 38.3 1.0
CE2 D:PHE745 3.7 34.7 1.0
CD D:ARG879 3.7 33.8 1.0
NE D:ARG879 4.0 40.0 1.0
CD2 D:PHE745 4.1 43.7 1.0
C19 D:MKG1101 4.1 40.7 1.0
CD1 D:ILE804 4.1 48.3 1.0
OXT D:THR1036 4.3 55.4 1.0
CG D:ASN877 4.5 41.2 1.0
CZ D:PHE745 4.5 43.6 1.0
O D:TRP1035 4.6 48.8 1.0
CB D:ARG879 4.6 46.2 1.0
O D:VAL1034 4.8 56.6 1.0
CG D:ARG879 4.8 36.7 1.0
C17 D:MKG1101 4.9 43.8 1.0
O2 D:MKG1101 5.0 41.1 1.0

Fluorine binding site 9 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 9 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:92.7
occ:1.00
 F1 E:MKG1101 0.0 92.7 1.0
C12 E:MKG1101 1.4 89.1 1.0
C11 E:MKG1101 2.3 91.6 1.0
C13 E:MKG1101 2.3 86.0 1.0
CA E:GLY428 3.1 93.8 1.0
C10 E:MKG1101 3.6 85.0 1.0
C14 E:MKG1101 3.6 83.8 1.0
N E:GLY428 4.0 90.3 1.0
C E:GLY428 4.0 97.2 1.0
C9 E:MKG1101 4.1 79.7 1.0
O E:GLY428 4.5 95.6 1.0
N E:ILE429 4.8 95.9 1.0

Fluorine binding site 10 out of 12 in 6ohr

Go back to Fluorine Binding Sites List in 6ohr
Fluorine binding site 10 out of 12 in the Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Compound 5 Bound Human Phospholipase D1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1101

b:70.2
occ:1.00
 F2 E:MKG1101 0.0 70.2 1.0
C22 E:MKG1101 1.4 73.8 1.0
C23 E:MKG1101 2.3 70.7 1.0
C21 E:MKG1101 2.3 77.9 1.0
ND2 E:ASN877 2.6 61.1 1.0
CE2 E:PHE745 3.6 69.3 1.0
C20 E:MKG1101 3.6 76.4 1.0
C18 E:MKG1101 3.6 74.7 1.0
CD2 E:PHE745 3.8 58.8 1.0
CG E:ASN877 3.9 56.5 1.0
CD E:ARG879 3.9 66.2 1.0
C19 E:MKG1101 4.1 76.6 1.0
CD1 E:ILE804 4.1 75.8 1.0
OXT E:THR1036 4.2 85.4 1.0
ND2 E:ASN875 4.4 56.6 1.0
CB E:ARG879 4.4 62.8 1.0
CZ E:PHE745 4.5 72.0 1.0
OD1 E:ASN877 4.5 62.0 1.0
CG E:ARG879 4.8 61.3 1.0
C17 E:MKG1101 4.9 70.0 1.0
CG E:PHE745 4.9 57.8 1.0
O2 E:MKG1101 4.9 72.7 1.0
C1 E:MKG1101 4.9 70.8 1.0
CB E:ASN877 4.9 52.5 1.0
O E:VAL1034 5.0 81.2 1.0
NE E:ARG879 5.0 71.2 1.0
O E:TRP1035 5.0 81.0 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 Aug 1 23:38:37 2024

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