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Chlorine 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:

Fluorine (F) 4 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 4 in 6ohp

Go back to Chlorine Binding Sites List in 6ohp
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1001

b:59.5
occ:1.00
 CL A:MJV1001 0.0 59.5 1.0
C28 A:MJV1001 1.9 53.1 1.0
C27 A:MJV1001 2.8 49.6 1.0
C01 A:MJV1001 2.8 48.6 1.0
NH1 A:ARG777 3.4 44.2 1.0
CB A:ALA440 3.6 33.0 1.0
O A:LEU438 3.9 46.9 1.0
CZ A:ARG777 4.1 50.4 1.0
C26 A:MJV1001 4.1 45.0 1.0
C02 A:MJV1001 4.2 45.1 1.0
NH2 A:ARG777 4.4 55.6 1.0
CD1 A:LEU409 4.6 65.6 1.0
NE1 A:TRP364 4.6 28.1 1.0
CZ A:PHE402 4.7 35.7 1.0
N A:ALA440 4.7 36.7 1.0
C25 A:MJV1001 4.7 43.6 1.0
OD2 A:ASP784 4.7 53.2 1.0
CA A:ALA440 4.7 37.7 1.0
CE2 A:PHE402 4.7 39.1 1.0
NE A:ARG777 4.9 50.0 1.0
C A:TRP439 4.9 39.6 1.0
OD1 A:ASP784 5.0 53.1 1.0

Chlorine binding site 2 out of 4 in 6ohp

Go back to Chlorine Binding Sites List in 6ohp
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1001

b:60.9
occ:1.00
 CL B:MJV1001 0.0 60.9 1.0
C28 B:MJV1001 1.9 47.2 1.0
C27 B:MJV1001 2.8 46.9 1.0
C01 B:MJV1001 2.8 44.6 1.0
NH1 B:ARG777 2.9 34.3 1.0
CB B:ALA440 3.4 39.4 1.0
O B:LEU438 3.4 39.5 1.0
CZ B:ARG777 3.9 38.0 1.0
C26 B:MJV1001 4.1 43.9 1.0
N B:ALA440 4.2 38.1 1.0
C02 B:MJV1001 4.2 42.6 1.0
OD2 B:ASP784 4.2 55.6 1.0
OD1 B:ASP784 4.3 61.3 1.0
NH2 B:ARG777 4.4 38.0 1.0
CA B:ALA440 4.4 42.0 1.0
C B:TRP439 4.4 38.1 1.0
C B:LEU438 4.5 38.5 1.0
CA B:TRP439 4.7 38.4 1.0
C25 B:MJV1001 4.7 43.2 1.0
NE B:ARG777 4.7 34.3 1.0
CG B:ASP784 4.7 57.7 1.0
CZ B:PHE402 4.9 46.9 1.0
CD B:ARG777 4.9 32.2 1.0
NE1 B:TRP364 5.0 31.0 1.0
O B:TRP439 5.0 39.9 1.0

Chlorine binding site 3 out of 4 in 6ohp

Go back to Chlorine Binding Sites List in 6ohp
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1001

b:89.1
occ:1.00
 CL C:MJV1001 0.0 89.1 1.0
C28 C:MJV1001 1.9 75.9 1.0
C27 C:MJV1001 2.8 71.0 1.0
C01 C:MJV1001 2.8 69.2 1.0
NH1 C:ARG777 3.1 50.6 1.0
CB C:ALA440 3.4 57.4 1.0
CZ C:ARG777 3.8 50.8 1.0
O C:LEU438 3.9 52.6 1.0
C26 C:MJV1001 4.1 67.1 1.0
C02 C:MJV1001 4.2 64.4 1.0
OD2 C:ASP784 4.3 49.4 1.0
NH2 C:ARG777 4.4 51.3 1.0
N C:ALA440 4.4 58.5 1.0
CA C:ALA440 4.5 57.8 1.0
NE1 C:TRP364 4.5 51.1 1.0
NE C:ARG777 4.5 51.9 1.0
OD1 C:ASP784 4.6 52.4 1.0
C25 C:MJV1001 4.7 62.2 1.0
C C:TRP439 4.7 56.4 1.0
CD C:ARG777 4.8 50.6 1.0
CG C:ASP784 4.9 50.4 1.0
CZ C:PHE402 4.9 65.8 1.0
C C:LEU438 5.0 52.0 1.0

Chlorine binding site 4 out of 4 in 6ohp

Go back to Chlorine Binding Sites List in 6ohp
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1001

b:0.4
occ:1.00
 CL D:MJV1001 0.0 0.4 1.0
C28 D:MJV1001 1.9 86.5 1.0
C27 D:MJV1001 2.8 80.4 1.0
C01 D:MJV1001 2.8 79.3 1.0
NH1 D:ARG777 2.9 41.3 1.0
O D:LEU438 3.4 56.0 1.0
CB D:ALA440 3.4 60.8 1.0
CG B:MET926 3.7 0.6 1.0
CZ D:ARG777 3.8 45.5 1.0
C26 D:MJV1001 4.1 75.4 1.0
NH2 D:ARG777 4.2 43.3 1.0
N D:ALA440 4.2 58.3 1.0
C02 D:MJV1001 4.2 73.6 1.0
SD B:MET926 4.3 0.5 1.0
C D:TRP439 4.4 58.5 1.0
CA D:ALA440 4.4 59.1 1.0
C D:LEU438 4.4 54.0 1.0
OD1 D:ASP784 4.5 71.5 1.0
OD2 D:ASP784 4.5 69.2 1.0
CA D:TRP439 4.6 56.8 1.0
CZ D:PHE402 4.7 66.5 1.0
NE D:ARG777 4.7 49.2 1.0
C25 D:MJV1001 4.7 70.7 1.0
O D:TRP439 4.8 56.5 1.0
N D:TRP439 5.0 55.9 1.0
CG D:ASP784 5.0 68.9 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: Mon Jul 29 12:41:16 2024

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