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Fluorine in PDB 5w8j: Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29

Enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29

All present enzymatic activity of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29, PDB code: 5w8j was solved by C.M.Lukacs, A.Moulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.12 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.530, 80.770, 121.090, 90.00, 118.23, 90.00
R / Rfree (%) 14.5 / 16.9

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 (pdb code 5w8j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29, PDB code: 5w8j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5w8j

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Fluorine binding site 1 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:43.3
occ:1.00
 F20 A:9Y7501 0.0 43.3 1.0
C19 A:9Y7501 1.3 41.9 1.0
C21 A:9Y7501 2.3 39.8 1.0
C18 A:9Y7501 2.3 40.7 1.0
F23 A:9Y7501 2.7 40.9 1.0
OE1 A:GLN99 2.7 50.4 1.0
CD A:GLN99 3.0 44.8 1.0
CB A:GLN99 3.1 37.6 1.0
CG A:LEU108 3.3 26.2 1.0
CD1 A:LEU108 3.3 31.0 1.0
CG A:GLN99 3.5 40.6 1.0
C17 A:9Y7501 3.6 38.1 1.0
C22 A:9Y7501 3.7 35.0 1.0
CB A:LEU108 3.7 29.9 1.0
NE2 A:GLN99 3.8 41.5 1.0
C16 A:9Y7501 4.1 31.2 1.0
CA A:GLN99 4.2 35.5 1.0
N A:GLN99 4.5 36.5 1.0
CD2 A:LEU108 4.6 27.1 1.0
CA A:ARG105 4.9 32.4 1.0

Fluorine binding site 2 out of 12 in 5w8j

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Fluorine binding site 2 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:40.9
occ:1.00
 F23 A:9Y7501 0.0 40.9 1.0
C21 A:9Y7501 1.3 39.8 1.0
C19 A:9Y7501 2.3 41.9 1.0
C22 A:9Y7501 2.4 35.0 1.0
F20 A:9Y7501 2.7 43.3 1.0
CG A:PRO138 3.4 20.4 1.0
CD A:PRO138 3.4 20.3 1.0
CB A:PRO138 3.5 17.1 1.0
C18 A:9Y7501 3.6 40.7 1.0
C16 A:9Y7501 3.6 31.2 1.0
CD1 A:LEU108 4.0 31.0 1.0
C17 A:9Y7501 4.1 38.1 1.0
N A:PRO138 4.2 16.9 1.0
C32 A:9Y7501 4.4 23.9 1.0
CA A:PRO138 4.4 16.5 1.0
C33 A:9Y7501 4.6 25.3 1.0
CG2 A:VAL109 4.7 28.1 1.0
OE1 A:GLN99 4.7 50.4 1.0
CG A:LEU108 4.9 26.2 1.0
CB A:ARG105 4.9 37.5 1.0
C15 A:9Y7501 4.9 22.4 1.0
C08 A:9Y7501 5.0 22.2 1.0

Fluorine binding site 3 out of 12 in 5w8j

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Fluorine binding site 3 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:26.4
occ:1.00
 F20 A:9Y7502 0.0 26.4 1.0
C19 A:9Y7502 1.3 26.7 1.0
C21 A:9Y7502 2.3 23.3 1.0
C18 A:9Y7502 2.3 22.6 1.0
F23 A:9Y7502 2.7 25.0 1.0
OH A:TYR82 2.8 43.0 1.0
CG1 A:VAL25 3.2 12.6 1.0
CG1 A:VAL50 3.5 16.8 1.0
C17 A:9Y7502 3.6 22.8 1.0
C22 A:9Y7502 3.6 20.2 1.0
O A:HOH777 3.7 28.4 1.0
CA A:ASP51 3.8 12.0 1.0
CZ A:TYR82 3.9 32.1 1.0
CG1 A:ILE119 4.0 14.4 1.0
O A:VAL50 4.0 13.2 1.0
C16 A:9Y7502 4.1 19.6 1.0
C A:VAL50 4.1 13.2 1.0
N A:ASP51 4.1 11.7 1.0
CD1 A:ILE119 4.1 14.8 1.0
C A:ASP51 4.2 16.3 1.0
CB A:VAL50 4.5 15.1 1.0
CE2 A:TYR82 4.5 22.2 1.0
CB A:VAL25 4.6 11.2 1.0
N A:VAL52 4.7 16.0 1.0
CE1 A:TYR82 4.7 31.4 1.0
CG1 A:VAL52 4.7 21.7 1.0
O A:ASP51 4.8 17.5 1.0
OD1 A:ASP51 4.8 18.0 1.0
N A:GLY26 4.8 11.1 1.0
CB A:ASP51 4.9 14.7 1.0
CG2 A:ILE119 5.0 14.7 1.0
CA A:VAL50 5.0 12.9 1.0

Fluorine binding site 4 out of 12 in 5w8j

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Fluorine binding site 4 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:25.0
occ:1.00
 F23 A:9Y7502 0.0 25.0 1.0
C21 A:9Y7502 1.3 23.3 1.0
C22 A:9Y7502 2.3 20.2 1.0
C19 A:9Y7502 2.4 26.7 1.0
F20 A:9Y7502 2.7 26.4 1.0
OD1 A:ASP51 3.1 18.0 1.0
CG A:ASP51 3.2 16.1 1.0
CB A:ALA95 3.3 14.9 1.0
N A:GLY26 3.4 11.1 1.0
CA A:GLY26 3.4 12.9 1.0
CA A:ASP51 3.5 12.0 1.0
CG1 A:VAL25 3.6 12.6 1.0
C18 A:9Y7502 3.6 22.6 1.0
C16 A:9Y7502 3.6 19.6 1.0
OD2 A:ASP51 3.7 15.1 1.0
O A:VAL50 3.7 13.2 1.0
CB A:ASP51 3.8 14.7 1.0
O A:HOH800 3.9 30.6 1.0
C17 A:9Y7502 4.1 22.8 1.0
C A:VAL25 4.2 11.8 1.0
C A:VAL50 4.4 13.2 1.0
N A:ASP51 4.4 11.7 1.0
C A:ASP51 4.5 16.3 1.0
N A:VAL52 4.5 16.0 1.0
CA A:ALA95 4.5 13.5 1.0
CD1 A:ILE119 4.6 14.8 1.0
O A:HOH696 4.6 25.5 1.0
O A:HOH772 4.7 21.8 1.0
C A:GLY26 4.8 11.6 1.0
O A:VAL25 4.8 13.3 1.0
C15 A:9Y7502 4.8 21.7 1.0
CB A:VAL25 4.8 11.2 1.0
CA A:VAL25 4.9 10.9 1.0
N14 A:9Y7502 5.0 22.8 1.0

Fluorine binding site 5 out of 12 in 5w8j

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Fluorine binding site 5 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:25.0
occ:1.00
 F20 B:9Y7402 0.0 25.0 1.0
C19 B:9Y7402 1.3 21.5 1.0
C21 B:9Y7402 2.3 18.2 1.0
C18 B:9Y7402 2.4 21.3 1.0
F23 B:9Y7402 2.6 21.5 1.0
OH B:TYR82 2.9 42.3 1.0
CG1 B:VAL25 3.3 11.7 1.0
C17 B:9Y7402 3.6 17.8 1.0
C22 B:9Y7402 3.6 15.7 1.0
O B:HOH662 3.7 22.1 1.0
CG1 B:VAL50 3.7 15.2 1.0
CA B:ASP51 3.7 13.1 1.0
CZ B:TYR82 3.9 31.2 1.0
O B:VAL50 4.1 12.7 1.0
N B:ASP51 4.1 11.9 1.0
CD1 B:ILE119 4.1 13.9 1.0
C16 B:9Y7402 4.1 18.7 1.0
C B:ASP51 4.2 15.1 1.0
CG1 B:ILE119 4.2 12.4 1.0
C B:VAL50 4.2 11.2 1.0
CE1 B:TYR82 4.5 29.3 1.0
N B:VAL52 4.5 13.0 1.0
CB B:VAL50 4.6 14.7 1.0
CG1 B:VAL52 4.6 20.2 1.0
CE2 B:TYR82 4.7 27.8 1.0
O B:ASP51 4.8 16.5 1.0
CB B:VAL25 4.8 11.1 1.0
CB B:ALA95 4.9 10.8 1.0
OD1 B:ASP51 4.9 21.3 1.0
CB B:ASP51 4.9 13.1 1.0
N B:GLY26 5.0 10.6 1.0

Fluorine binding site 6 out of 12 in 5w8j

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Fluorine binding site 6 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:21.5
occ:1.00
 F23 B:9Y7402 0.0 21.5 1.0
C21 B:9Y7402 1.3 18.2 1.0
C19 B:9Y7402 2.3 21.5 1.0
C22 B:9Y7402 2.3 15.7 1.0
F20 B:9Y7402 2.6 25.0 1.0
CG B:ASP51 3.2 18.5 1.0
OD1 B:ASP51 3.2 21.3 1.0
CA B:ASP51 3.3 13.1 1.0
CB B:ALA95 3.3 10.8 1.0
N B:GLY26 3.5 10.6 1.0
CA B:GLY26 3.5 10.8 1.0
OD2 B:ASP51 3.5 13.8 1.0
C18 B:9Y7402 3.6 21.3 1.0
O B:VAL50 3.6 12.7 1.0
C16 B:9Y7402 3.6 18.7 1.0
CB B:ASP51 3.7 13.1 1.0
CG1 B:VAL25 3.8 11.7 1.0
O B:HOH621 3.9 37.8 1.0
C17 B:9Y7402 4.1 17.8 1.0
N B:ASP51 4.2 11.9 1.0
C B:VAL25 4.2 10.3 1.0
C B:ASP51 4.2 15.1 1.0
N B:VAL52 4.3 13.0 1.0
C B:VAL50 4.3 11.2 1.0
CA B:ALA95 4.5 8.2 1.0
O B:HOH582 4.7 24.4 1.0
O B:HOH667 4.7 20.3 1.0
CD1 B:ILE119 4.7 13.9 1.0
C B:GLY26 4.8 11.9 1.0
C15 B:9Y7402 4.8 20.8 1.0
O B:VAL25 4.9 11.2 1.0
CA B:VAL25 4.9 8.8 1.0
CB B:VAL25 5.0 11.1 1.0

Fluorine binding site 7 out of 12 in 5w8j

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Fluorine binding site 7 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:34.1
occ:1.00
 F20 C:9Y7402 0.0 34.1 1.0
C19 C:9Y7402 1.3 32.9 1.0
C18 C:9Y7402 2.3 31.0 1.0
C21 C:9Y7402 2.4 33.5 1.0
F23 C:9Y7402 2.7 40.4 1.0
CD1 C:LEU108 3.0 19.7 1.0
OE1 C:GLN99 3.2 26.9 1.0
CG C:LEU108 3.3 14.8 1.0
CD C:GLN99 3.5 25.8 1.0
CB C:GLN99 3.6 17.8 1.0
C17 C:9Y7402 3.6 23.1 1.0
C22 C:9Y7402 3.7 29.5 1.0
CG C:GLN99 3.8 20.5 1.0
CB C:LEU108 3.8 15.2 1.0
C16 C:9Y7402 4.1 21.8 1.0
NE2 C:GLN99 4.2 22.1 1.0
CD C:PRO138 4.3 14.8 1.0
CG C:ARG105 4.5 34.4 1.0
O C:HOH681 4.5 37.4 1.0
CA C:GLN99 4.5 16.7 1.0
CG C:PRO138 4.6 19.7 1.0
CD2 C:LEU108 4.6 17.4 1.0
N C:GLN99 4.7 17.9 1.0
CA C:ARG105 4.7 22.4 1.0
O C:HOH557 4.8 42.9 1.0
O C:HOH727 4.9 34.8 1.0
CB C:ARG105 5.0 28.0 1.0
NE C:ARG105 5.0 39.8 1.0

Fluorine binding site 8 out of 12 in 5w8j

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Fluorine binding site 8 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:40.4
occ:1.00
 F23 C:9Y7402 0.0 40.4 1.0
C21 C:9Y7402 1.3 33.5 1.0
O C:HOH557 2.3 42.9 1.0
C22 C:9Y7402 2.4 29.5 1.0
C19 C:9Y7402 2.4 32.9 1.0
F20 C:9Y7402 2.7 34.1 1.0
O C:HOH727 3.1 34.8 1.0
CD1 C:LEU108 3.3 19.7 1.0
N C:GLN99 3.4 17.9 1.0
C18 C:9Y7402 3.6 31.0 1.0
C16 C:9Y7402 3.6 21.8 1.0
CG C:LEU108 3.7 14.8 1.0
CB C:GLN99 3.8 17.8 1.0
O C:ASN137 3.9 18.6 1.0
C17 C:9Y7402 4.1 23.1 1.0
CD C:PRO138 4.1 14.8 1.0
CA C:GLN99 4.2 16.7 1.0
C C:ARG98 4.2 17.5 1.0
O C:ALA97 4.2 21.4 1.0
O C:HOH698 4.2 40.9 1.0
CA C:ARG98 4.2 19.8 1.0
C C:ASN137 4.3 17.3 1.0
CD2 C:LEU108 4.3 17.4 1.0
O C:HOH681 4.3 37.4 1.0
N C:PRO138 4.5 14.8 1.0
OE1 C:GLN99 4.7 26.9 1.0
C15 C:9Y7402 4.9 19.5 1.0
CB C:ASN137 4.9 18.2 1.0
CG C:GLN99 4.9 20.5 1.0

Fluorine binding site 9 out of 12 in 5w8j

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Fluorine binding site 9 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:21.6
occ:1.00
 F20 C:9Y7403 0.0 21.6 1.0
C19 C:9Y7403 1.3 21.8 1.0
C18 C:9Y7403 2.3 19.1 1.0
C21 C:9Y7403 2.3 22.4 1.0
F23 C:9Y7403 2.7 31.6 1.0
OH C:TYR82 3.3 40.1 1.0
CG1 C:VAL25 3.3 14.5 1.0
CG1 C:VAL50 3.6 16.2 1.0
C17 C:9Y7403 3.6 18.8 1.0
CA C:ASP51 3.6 12.6 1.0
C22 C:9Y7403 3.6 19.0 1.0
O C:HOH665 3.8 30.4 1.0
O C:VAL50 4.0 13.5 1.0
N C:ASP51 4.0 13.4 1.0
C C:VAL50 4.1 12.8 1.0
C16 C:9Y7403 4.1 17.4 1.0
C C:ASP51 4.1 17.6 1.0
CG1 C:ILE119 4.1 15.7 1.0
CD1 C:ILE119 4.2 17.0 1.0
CZ C:TYR82 4.3 33.9 1.0
N C:VAL52 4.4 14.7 1.0
CB C:VAL50 4.5 14.7 1.0
CG1 C:VAL52 4.6 18.6 1.0
OD1 C:ASP51 4.7 21.4 1.0
O C:ASP51 4.7 19.7 1.0
CB C:VAL25 4.7 10.9 1.0
CB C:ASP51 4.8 15.1 1.0
N C:GLY26 4.8 10.7 1.0
CE2 C:TYR82 4.9 27.2 1.0
CG C:ASP51 4.9 21.8 1.0
CA C:VAL50 4.9 11.3 1.0
CB C:ALA95 5.0 16.8 1.0

Fluorine binding site 10 out of 12 in 5w8j

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Fluorine binding site 10 out of 12 in the Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Lactate Dehydrogenase A in Complex with Inhibitor Compound 29 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:31.6
occ:1.00
 F23 C:9Y7403 0.0 31.6 1.0
C21 C:9Y7403 1.3 22.4 1.0
C19 C:9Y7403 2.3 21.8 1.0
C22 C:9Y7403 2.4 19.0 1.0
F20 C:9Y7403 2.7 21.6 1.0
OD1 C:ASP51 3.1 21.4 1.0
CB C:ALA95 3.2 16.8 1.0
CG C:ASP51 3.3 21.8 1.0
O C:HOH701 3.6 33.4 1.0
C18 C:9Y7403 3.6 19.1 1.0
C16 C:9Y7403 3.6 17.4 1.0
OD2 C:ASP51 3.6 17.8 1.0
CA C:GLY26 3.7 10.8 1.0
CA C:ASP51 3.7 12.6 1.0
N C:GLY26 3.7 10.7 1.0
CG1 C:VAL25 3.8 14.5 1.0
CB C:ASP51 4.0 15.1 1.0
O C:VAL50 4.0 13.5 1.0
C17 C:9Y7403 4.1 18.8 1.0
O C:HOH565 4.2 31.1 1.0
C C:VAL25 4.4 11.3 1.0
CA C:ALA95 4.5 12.8 1.0
N C:VAL52 4.5 14.7 1.0
C C:ASP51 4.6 17.6 1.0
O C:HOH676 4.6 26.4 1.0
CD1 C:ILE119 4.6 17.0 1.0
N C:ASP51 4.6 13.4 1.0
C C:VAL50 4.7 12.8 1.0
C15 C:9Y7403 4.9 19.4 1.0
O C:VAL25 5.0 12.4 1.0

Reference:

G.Rai, K.R.Brimacombe, B.T.Mott, D.J.Urban, X.Hu, S.M.Yang, T.D.Lee, D.M.Cheff, J.Kouznetsova, G.A.Benavides, K.Pohida, E.J.Kuenstner, D.K.Luci, C.M.Lukacs, D.R.Davies, D.M.Dranow, H.Zhu, G.Sulikowski, W.J.Moore, G.M.Stott, A.J.Flint, M.D.Hall, V.M.Darley-Usmar, L.M.Neckers, C.V.Dang, A.G.Waterson, A.Simeonov, A.Jadhav, D.J.Maloney. Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (Ldh). J. Med. Chem. V. 60 9184 2017.
ISSN: ISSN 1520-4804
PubMed: 29120638
DOI: 10.1021/ACS.JMEDCHEM.7B00941
Page generated: Tue Jul 15 08:50:45 2025

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