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Fluorine in PDB 6o0h: Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143

Enzymatic activity of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143

All present enzymatic activity of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143:
2.3.3.8;

Other elements in 6o0h:

The structure of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 (pdb code 6o0h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143, PDB code: 6o0h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6o0h

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Fluorine binding site 1 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:41.8
occ:1.00
 F1 A:LBG2001 0.0 41.8 1.0
C5 A:LBG2001 1.3 41.8 1.0
C6 A:LBG2001 2.3 41.8 1.0
C4 A:LBG2001 2.3 41.8 1.0
O A:ARG378 2.6 44.8 1.0
N1 A:LBG2001 2.7 41.8 1.0
C A:ARG378 3.1 44.8 1.0
CA A:ARG379 3.2 41.7 1.0
N A:ARG379 3.4 41.7 1.0
C7 A:LBG2001 3.5 41.8 1.0
C15 A:LBG2001 3.6 41.8 1.0
CG1 A:VAL377 3.7 51.1 1.0
CZ A:PHE354 3.8 34.3 1.0
O1 A:LBG2001 3.9 41.8 1.0
CB A:ARG379 3.9 41.7 1.0
C8 A:LBG2001 4.1 41.8 1.0
CE1 A:PHE354 4.1 34.3 1.0
S1 A:LBG2001 4.2 41.8 1.0
C2 A:LBG2001 4.2 41.8 1.0
N A:ARG378 4.2 44.8 1.0
CA A:ARG378 4.3 44.8 1.0
C3 A:LBG2001 4.4 41.8 1.0
C A:ARG379 4.4 41.7 1.0
F2 A:LBG2001 4.6 41.8 1.0
O3 A:LBG2001 4.7 41.8 1.0
N A:GLY380 4.7 38.1 1.0
CA A:GLY341 4.8 45.8 1.0
CE2 A:PHE354 4.9 34.3 1.0
O A:ILE340 4.9 50.6 1.0

Fluorine binding site 2 out of 8 in 6o0h

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Fluorine binding site 2 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2001

b:41.8
occ:1.00
 F2 A:LBG2001 0.0 41.8 1.0
C7 A:LBG2001 1.3 41.8 1.0
C6 A:LBG2001 2.3 41.8 1.0
C8 A:LBG2001 2.3 41.8 1.0
C9 A:LBG2001 2.7 41.8 1.0
C14 A:LBG2001 3.1 41.8 1.0
CD1 A:ILE357 3.2 42.8 1.0
C5 A:LBG2001 3.5 41.8 1.0
CG2 A:ILE340 3.6 50.6 1.0
C15 A:LBG2001 3.6 41.8 1.0
C10 A:LBG2001 3.6 41.8 1.0
C4 A:LBG2001 4.1 41.8 1.0
C13 A:LBG2001 4.2 41.8 1.0
CE1 A:PHE354 4.3 34.3 1.0
CG1 A:ILE357 4.3 42.8 1.0
CB A:ILE357 4.4 42.8 1.0
CG2 A:ILE357 4.5 42.8 1.0
CD1 A:PHE354 4.5 34.3 1.0
C11 A:LBG2001 4.5 41.8 1.0
CZ A:PHE354 4.6 34.3 1.0
F1 A:LBG2001 4.6 41.8 1.0
C12 A:LBG2001 4.8 41.8 1.0
CB A:ILE340 5.0 50.6 1.0

Fluorine binding site 3 out of 8 in 6o0h

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Fluorine binding site 3 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:40.7
occ:1.00
 F1 B:LBG2001 0.0 40.7 1.0
C5 B:LBG2001 1.3 40.7 1.0
C6 B:LBG2001 2.3 40.7 1.0
C4 B:LBG2001 2.3 40.7 1.0
O B:ARG378 2.6 44.0 1.0
N1 B:LBG2001 2.7 40.7 1.0
C B:ARG378 3.1 44.0 1.0
CA B:ARG379 3.2 41.0 1.0
N B:ARG379 3.4 41.0 1.0
C7 B:LBG2001 3.5 40.7 1.0
C15 B:LBG2001 3.6 40.7 1.0
CG1 B:VAL377 3.7 51.8 1.0
CZ B:PHE354 3.8 34.5 1.0
O1 B:LBG2001 3.9 40.7 1.0
CB B:ARG379 3.9 41.0 1.0
C8 B:LBG2001 4.1 40.7 1.0
CE1 B:PHE354 4.1 34.5 1.0
S1 B:LBG2001 4.2 40.7 1.0
C2 B:LBG2001 4.2 40.7 1.0
N B:ARG378 4.2 44.0 1.0
CA B:ARG378 4.3 44.0 1.0
C3 B:LBG2001 4.4 40.7 1.0
C B:ARG379 4.4 41.0 1.0
F2 B:LBG2001 4.6 40.7 1.0
O3 B:LBG2001 4.7 40.7 1.0
N B:GLY380 4.7 37.4 1.0
CA B:GLY341 4.8 46.0 1.0
CE2 B:PHE354 4.9 34.5 1.0
O B:ILE340 4.9 50.9 1.0
C B:VAL377 5.0 51.8 1.0

Fluorine binding site 4 out of 8 in 6o0h

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Fluorine binding site 4 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2001

b:40.7
occ:1.00
 F2 B:LBG2001 0.0 40.7 1.0
C7 B:LBG2001 1.3 40.7 1.0
C6 B:LBG2001 2.3 40.7 1.0
C8 B:LBG2001 2.3 40.7 1.0
C9 B:LBG2001 2.7 40.7 1.0
C14 B:LBG2001 3.1 40.7 1.0
CD1 B:ILE357 3.2 42.5 1.0
C5 B:LBG2001 3.5 40.7 1.0
CG2 B:ILE340 3.6 50.9 1.0
C15 B:LBG2001 3.6 40.7 1.0
C10 B:LBG2001 3.6 40.7 1.0
C4 B:LBG2001 4.1 40.7 1.0
C13 B:LBG2001 4.2 40.7 1.0
CE1 B:PHE354 4.3 34.5 1.0
CG1 B:ILE357 4.3 42.5 1.0
CB B:ILE357 4.4 42.5 1.0
CG2 B:ILE357 4.5 42.5 1.0
CD1 B:PHE354 4.5 34.5 1.0
C11 B:LBG2001 4.5 40.7 1.0
CZ B:PHE354 4.6 34.5 1.0
F1 B:LBG2001 4.6 40.7 1.0
C12 B:LBG2001 4.8 40.7 1.0
CB B:ILE340 5.0 50.9 1.0

Fluorine binding site 5 out of 8 in 6o0h

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Fluorine binding site 5 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:41.4
occ:1.00
 F1 C:LBG2001 0.0 41.4 1.0
C5 C:LBG2001 1.3 41.4 1.0
C6 C:LBG2001 2.3 41.4 1.0
C4 C:LBG2001 2.3 41.4 1.0
O C:ARG378 2.6 45.2 1.0
N1 C:LBG2001 2.7 41.4 1.0
C C:ARG378 3.1 45.2 1.0
CA C:ARG379 3.2 42.0 1.0
N C:ARG379 3.4 42.0 1.0
C7 C:LBG2001 3.5 41.4 1.0
C15 C:LBG2001 3.6 41.4 1.0
CG1 C:VAL377 3.7 51.4 1.0
CZ C:PHE354 3.8 33.9 1.0
O1 C:LBG2001 3.9 41.4 1.0
CB C:ARG379 3.9 42.0 1.0
C8 C:LBG2001 4.1 41.4 1.0
CE1 C:PHE354 4.1 33.9 1.0
S1 C:LBG2001 4.2 41.4 1.0
C2 C:LBG2001 4.2 41.4 1.0
N C:ARG378 4.2 45.2 1.0
CA C:ARG378 4.3 45.2 1.0
C3 C:LBG2001 4.4 41.4 1.0
C C:ARG379 4.4 42.0 1.0
F2 C:LBG2001 4.6 41.4 1.0
O3 C:LBG2001 4.7 41.4 1.0
N C:GLY380 4.7 39.1 1.0
CA C:GLY341 4.8 46.4 1.0
CE2 C:PHE354 4.9 33.9 1.0
O C:ILE340 4.9 50.1 1.0
C C:VAL377 5.0 51.4 1.0

Fluorine binding site 6 out of 8 in 6o0h

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Fluorine binding site 6 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2001

b:41.4
occ:1.00
 F2 C:LBG2001 0.0 41.4 1.0
C7 C:LBG2001 1.3 41.4 1.0
C6 C:LBG2001 2.3 41.4 1.0
C8 C:LBG2001 2.3 41.4 1.0
C9 C:LBG2001 2.7 41.4 1.0
C14 C:LBG2001 3.1 41.4 1.0
CD1 C:ILE357 3.2 40.4 1.0
C5 C:LBG2001 3.5 41.4 1.0
CG2 C:ILE340 3.6 50.1 1.0
C15 C:LBG2001 3.6 41.4 1.0
C10 C:LBG2001 3.6 41.4 1.0
C4 C:LBG2001 4.1 41.4 1.0
C13 C:LBG2001 4.2 41.4 1.0
CE1 C:PHE354 4.3 33.9 1.0
CG1 C:ILE357 4.3 40.4 1.0
CB C:ILE357 4.4 40.4 1.0
CG2 C:ILE357 4.5 40.4 1.0
CD1 C:PHE354 4.5 33.9 1.0
C11 C:LBG2001 4.5 41.4 1.0
CZ C:PHE354 4.6 33.9 1.0
F1 C:LBG2001 4.6 41.4 1.0
C12 C:LBG2001 4.8 41.4 1.0
CB C:ILE340 5.0 50.1 1.0

Fluorine binding site 7 out of 8 in 6o0h

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Fluorine binding site 7 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2001

b:40.5
occ:1.00
 F1 D:LBG2001 0.0 40.5 1.0
C5 D:LBG2001 1.3 40.5 1.0
C6 D:LBG2001 2.3 40.5 1.0
C4 D:LBG2001 2.3 40.5 1.0
O D:ARG378 2.6 44.8 1.0
N1 D:LBG2001 2.7 40.5 1.0
C D:ARG378 3.1 44.8 1.0
CA D:ARG379 3.2 41.4 1.0
N D:ARG379 3.4 41.4 1.0
C7 D:LBG2001 3.5 40.5 1.0
C15 D:LBG2001 3.6 40.5 1.0
CG1 D:VAL377 3.7 51.5 1.0
CZ D:PHE354 3.8 33.3 1.0
O1 D:LBG2001 3.9 40.5 1.0
CB D:ARG379 3.9 41.4 1.0
C8 D:LBG2001 4.1 40.5 1.0
CE1 D:PHE354 4.1 33.3 1.0
S1 D:LBG2001 4.2 40.5 1.0
C2 D:LBG2001 4.2 40.5 1.0
N D:ARG378 4.2 44.8 1.0
CA D:ARG378 4.3 44.8 1.0
C3 D:LBG2001 4.4 40.5 1.0
C D:ARG379 4.4 41.4 1.0
F2 D:LBG2001 4.6 40.5 1.0
O3 D:LBG2001 4.7 40.5 1.0
N D:GLY380 4.7 37.3 1.0
CA D:GLY341 4.8 45.4 1.0
CE2 D:PHE354 4.9 33.3 1.0
O D:ILE340 4.9 49.6 1.0
C D:VAL377 5.0 51.5 1.0

Fluorine binding site 8 out of 8 in 6o0h

Go back to Fluorine Binding Sites List in 6o0h
Fluorine binding site 8 out of 8 in the Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cryo-Em Structure of Human Atp-Citrate Lyase in Complex with Inhibitor Ndi-091143 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F2001

b:40.5
occ:1.00
 F2 D:LBG2001 0.0 40.5 1.0
C7 D:LBG2001 1.3 40.5 1.0
C6 D:LBG2001 2.3 40.5 1.0
C8 D:LBG2001 2.3 40.5 1.0
C9 D:LBG2001 2.7 40.5 1.0
C14 D:LBG2001 3.1 40.5 1.0
CD1 D:ILE357 3.2 41.2 1.0
C5 D:LBG2001 3.5 40.5 1.0
CG2 D:ILE340 3.6 49.6 1.0
C15 D:LBG2001 3.6 40.5 1.0
C10 D:LBG2001 3.6 40.5 1.0
C4 D:LBG2001 4.1 40.5 1.0
C13 D:LBG2001 4.2 40.5 1.0
CE1 D:PHE354 4.3 33.3 1.0
CG1 D:ILE357 4.3 41.2 1.0
CB D:ILE357 4.4 41.2 1.0
CG2 D:ILE357 4.5 41.2 1.0
CD1 D:PHE354 4.5 33.3 1.0
C11 D:LBG2001 4.5 40.5 1.0
CZ D:PHE354 4.6 33.3 1.0
F1 D:LBG2001 4.6 40.5 1.0
C12 D:LBG2001 4.8 40.5 1.0
CB D:ILE340 5.0 49.6 1.0

Reference:

J.Wei, S.Leit, J.Kuai, E.Therrien, S.Rafi, H.J.Harwood Jr., B.Delabarre, L.Tong. An Allosteric Mechanism For Potent Inhibition of Human Atp-Citrate Lyase. Nature V. 568 566 2019.
ISSN: ESSN 1476-4687
PubMed: 30944472
DOI: 10.1038/S41586-019-1094-6
Page generated: Thu Aug 1 23:17:09 2024

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