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Chlorine in PDB 4i9n: Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122

Enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122

All present enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122, PDB code: 4i9n was solved by T.Zhou, A.Kohlmann, Z.G.Stephan, F.Li, L.Commodore, M.T.Greenfield, W.C.Shakespeare, X.Zhu, D.C.Dalgarno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 84.040, 139.815, 138.934, 90.00, 94.57, 90.00
R / Rfree (%) 22 / 26.4

Other elements in 4i9n:

The structure of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 (pdb code 4i9n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122, PDB code: 4i9n:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4i9n

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Chlorine binding site 1 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:17.1
occ:1.00
CL3 A:1E6401 0.0 17.1 1.0
C18 A:1E6401 1.7 29.9 1.0
C17 A:1E6401 2.7 28.3 1.0
C19 A:1E6401 2.8 30.4 1.0
O22 A:1E6401 3.1 32.8 1.0
CB A:ALA95 3.4 23.3 1.0
CA A:GLY26 3.5 20.6 1.0
N A:GLY26 3.6 22.0 1.0
OD2 A:ASP51 3.7 26.7 1.0
CG A:ASP51 3.9 29.8 1.0
CG1 A:VAL25 3.9 18.8 1.0
CA A:ASP51 3.9 28.4 1.0
C20 A:1E6401 4.1 30.3 1.0
C16 A:1E6401 4.1 31.0 1.0
O A:VAL50 4.2 27.4 1.0
CA A:ALA95 4.2 24.8 1.0
OD1 A:ASP51 4.2 31.6 1.0
C23 A:1E6401 4.3 34.0 1.0
C A:VAL25 4.3 22.6 1.0
C27 A:1E6401 4.3 34.2 1.0
CB A:ASP51 4.4 28.0 1.0
O A:HOH517 4.5 23.4 1.0
CD1 A:ILE119 4.5 23.3 1.0
C21 A:1E6401 4.6 28.7 1.0
N A:VAL52 4.7 28.2 1.0
N A:ASP51 4.8 28.4 1.0
C A:ASP51 4.8 29.0 1.0
O28 A:1E6401 4.8 31.3 1.0
O A:VAL25 4.8 22.4 1.0
C A:VAL50 4.8 28.0 1.0
C24 A:1E6401 4.9 33.7 1.0
O A:HOH523 4.9 27.4 1.0
C A:GLY26 4.9 20.3 1.0
N A:ALA95 4.9 22.9 1.0

Chlorine binding site 2 out of 8 in 4i9n

Go back to Chlorine Binding Sites List in 4i9n
Chlorine binding site 2 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:3.6
occ:1.00
CL3 B:1E6401 0.0 3.6 1.0
C18 B:1E6401 1.7 20.1 1.0
C17 B:1E6401 2.7 21.0 1.0
C19 B:1E6401 2.8 19.9 1.0
O22 B:1E6401 3.1 23.4 1.0
CB B:ALA95 3.5 24.0 1.0
CA B:GLY26 3.5 18.6 1.0
N B:GLY26 3.5 18.6 1.0
CA B:ASP51 3.7 22.8 1.0
CG B:ASP51 3.7 23.7 1.0
OD2 B:ASP51 3.8 23.5 1.0
OD1 B:ASP51 3.9 23.7 1.0
CG1 B:VAL25 3.9 15.0 1.0
O B:VAL50 4.0 20.4 1.0
C20 B:1E6401 4.0 23.9 1.0
C16 B:1E6401 4.1 24.0 1.0
CB B:ASP51 4.2 23.5 1.0
CD1 B:ILE119 4.2 24.0 1.0
CA B:ALA95 4.2 25.4 1.0
C B:VAL25 4.3 17.9 1.0
C23 B:1E6401 4.4 28.7 1.0
N B:VAL52 4.4 24.9 1.0
C B:ASP51 4.5 23.8 1.0
C27 B:1E6401 4.6 31.5 1.0
N B:ASP51 4.6 21.8 1.0
C21 B:1E6401 4.6 23.0 1.0
C B:VAL50 4.7 20.4 1.0
O B:VAL25 4.8 16.9 1.0
C B:GLY26 4.9 20.6 1.0
N B:ALA95 4.9 25.1 1.0

Chlorine binding site 3 out of 8 in 4i9n

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Chlorine binding site 3 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:18.1
occ:1.00
CL3 C:1E6401 0.0 18.1 1.0
C18 C:1E6401 1.7 29.2 1.0
C17 C:1E6401 2.7 31.6 1.0
C19 C:1E6401 2.8 30.6 1.0
O22 C:1E6401 3.1 33.7 1.0
CA C:GLY26 3.5 21.3 1.0
CB C:ALA95 3.6 26.3 1.0
N C:GLY26 3.6 19.2 1.0
CA C:ASP51 3.7 27.8 1.0
CG C:ASP51 3.7 26.6 1.0
CG1 C:VAL25 3.8 19.4 1.0
O C:VAL50 3.9 29.3 1.0
OD1 C:ASP51 3.9 28.3 1.0
OD2 C:ASP51 3.9 25.0 1.0
C20 C:1E6401 4.1 31.4 1.0
C16 C:1E6401 4.1 32.5 1.0
CB C:ASP51 4.1 26.6 1.0
C C:VAL25 4.3 19.1 1.0
CD1 C:ILE119 4.3 24.8 1.0
CA C:ALA95 4.4 29.0 1.0
C23 C:1E6401 4.4 37.6 1.0
C C:ASP51 4.5 28.5 1.0
N C:VAL52 4.5 29.4 1.0
N C:ASP51 4.5 27.4 1.0
C C:VAL50 4.6 27.4 1.0
C21 C:1E6401 4.6 32.1 1.0
O C:VAL25 4.7 20.9 1.0
O C:HOH534 4.9 34.5 1.0
C27 C:1E6401 4.9 36.9 1.0
C C:GLY26 4.9 22.8 1.0

Chlorine binding site 4 out of 8 in 4i9n

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Chlorine binding site 4 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:17.9
occ:1.00
CL3 D:1E6401 0.0 17.9 1.0
C18 D:1E6401 1.7 29.2 1.0
C17 D:1E6401 2.7 31.7 1.0
C19 D:1E6401 2.8 31.0 1.0
O22 D:1E6401 3.1 35.3 1.0
OD2 D:ASP51 3.4 32.9 1.0
CG D:ASP51 3.5 31.6 1.0
CB D:ALA95 3.5 27.8 1.0
CA D:ASP51 3.7 28.5 1.0
OD1 D:ASP51 3.7 33.0 1.0
CA D:GLY26 3.8 26.3 1.0
N D:GLY26 3.9 25.1 1.0
CG1 D:VAL25 4.0 21.9 1.0
O D:VAL50 4.1 24.2 1.0
C20 D:1E6401 4.1 33.5 1.0
C16 D:1E6401 4.1 33.0 1.0
CB D:ASP51 4.1 29.0 1.0
C23 D:1E6401 4.3 35.0 1.0
CA D:ALA95 4.3 27.8 1.0
N D:VAL52 4.4 28.4 1.0
C D:ASP51 4.4 28.7 1.0
O D:HOH535 4.4 24.6 1.0
C D:VAL25 4.5 24.1 1.0
CD1 D:ILE119 4.6 26.4 1.0
N D:ASP51 4.6 25.3 1.0
C21 D:1E6401 4.6 34.0 1.0
C27 D:1E6401 4.7 34.1 1.0
C D:VAL50 4.7 25.1 1.0
O D:VAL25 4.9 23.6 1.0
O28 D:1E6401 4.9 34.9 1.0

Chlorine binding site 5 out of 8 in 4i9n

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Chlorine binding site 5 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:22.1
occ:1.00
CL3 E:1E6401 0.0 22.1 1.0
C18 E:1E6401 1.7 31.2 1.0
C17 E:1E6401 2.7 31.5 1.0
C19 E:1E6401 2.8 33.0 1.0
O22 E:1E6401 3.1 35.0 1.0
CA E:GLY26 3.5 21.0 1.0
N E:GLY26 3.6 21.6 1.0
CG E:ASP51 3.7 29.8 1.0
OD1 E:ASP51 3.7 30.4 1.0
CA E:ASP51 3.8 28.2 1.0
OD2 E:ASP51 3.8 25.6 1.0
CB E:ALA95 3.8 32.2 1.0
CG1 E:VAL25 3.9 22.0 1.0
C20 E:1E6401 4.1 34.7 1.0
C16 E:1E6401 4.1 33.3 1.0
O E:VAL50 4.2 30.7 1.0
CB E:ASP51 4.2 28.6 1.0
CA E:ALA95 4.3 33.7 1.0
C E:VAL25 4.3 22.9 1.0
C23 E:1E6401 4.3 37.1 1.0
CD1 E:ILE119 4.6 29.6 1.0
N E:VAL52 4.6 29.4 1.0
C E:ASP51 4.6 29.1 1.0
C21 E:1E6401 4.6 34.4 1.0
C27 E:1E6401 4.6 39.5 1.0
O E:VAL25 4.7 23.5 1.0
N E:ASP51 4.8 29.1 1.0
C E:VAL50 4.9 30.0 1.0
C E:GLY26 4.9 22.6 1.0
N E:ALA95 5.0 32.6 1.0

Chlorine binding site 6 out of 8 in 4i9n

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Chlorine binding site 6 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:14.4
occ:1.00
CL3 F:1E6401 0.0 14.4 1.0
C18 F:1E6401 1.7 27.2 1.0
C17 F:1E6401 2.7 28.3 1.0
C19 F:1E6401 2.8 29.4 1.0
O22 F:1E6401 3.1 31.2 1.0
OD2 F:ASP51 3.3 38.4 1.0
CA F:GLY26 3.4 22.6 1.0
N F:GLY26 3.6 21.9 1.0
CB F:ALA95 3.8 29.5 1.0
CG F:ASP51 3.8 36.4 1.0
CA F:ASP51 3.9 34.3 1.0
O F:VAL50 3.9 33.2 1.0
C20 F:1E6401 4.1 32.9 1.0
C16 F:1E6401 4.1 32.3 1.0
C23 F:1E6401 4.3 32.3 1.0
CA F:ALA95 4.3 31.1 1.0
CG1 F:VAL25 4.3 21.4 1.0
CB F:ASP51 4.4 34.7 1.0
C F:VAL25 4.4 22.0 1.0
OD1 F:ASP51 4.4 40.4 1.0
N F:VAL52 4.6 35.8 1.0
C F:VAL50 4.6 31.9 1.0
C21 F:1E6401 4.7 35.5 1.0
C F:ASP51 4.7 35.4 1.0
N F:ASP51 4.7 32.2 1.0
C F:GLY26 4.8 23.0 1.0
C27 F:1E6401 4.8 30.1 1.0
O F:VAL25 4.8 23.0 1.0
CD1 F:ILE119 4.8 37.3 1.0
N F:ALA95 5.0 30.2 1.0

Chlorine binding site 7 out of 8 in 4i9n

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Chlorine binding site 7 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl401

b:13.8
occ:1.00
CL3 G:1E6401 0.0 13.8 1.0
C18 G:1E6401 1.7 23.4 1.0
C17 G:1E6401 2.7 23.2 1.0
C19 G:1E6401 2.8 24.2 1.0
O22 G:1E6401 3.1 25.8 1.0
CB G:ALA95 3.4 31.4 1.0
CA G:GLY26 3.6 23.1 1.0
N G:GLY26 3.6 23.9 1.0
CG1 G:VAL25 3.7 24.2 1.0
CA G:ASP51 3.8 28.7 1.0
CG G:ASP51 3.8 30.2 1.0
OD2 G:ASP51 3.9 30.5 1.0
OD1 G:ASP51 4.0 30.0 1.0
C20 G:1E6401 4.1 27.5 1.0
C16 G:1E6401 4.1 28.1 1.0
O G:VAL50 4.1 27.4 1.0
CA G:ALA95 4.1 32.8 1.0
C G:VAL25 4.3 24.6 1.0
CD1 G:ILE119 4.3 23.6 1.0
CB G:ASP51 4.3 28.6 1.0
O G:HOH522 4.4 25.1 1.0
C23 G:1E6401 4.5 26.8 1.0
N G:VAL52 4.5 28.8 1.0
C G:ASP51 4.6 29.0 1.0
C21 G:1E6401 4.6 28.0 1.0
C27 G:1E6401 4.7 25.9 1.0
O G:VAL25 4.7 22.1 1.0
N G:ASP51 4.8 27.6 1.0
C G:VAL50 4.8 25.6 1.0
CB G:VAL25 5.0 23.8 1.0
N G:ALA95 5.0 27.5 1.0

Chlorine binding site 8 out of 8 in 4i9n

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Chlorine binding site 8 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Rabbit Ldha in Complex with AP28161 and AP28122 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl401

b:11.1
occ:1.00
CL3 H:1E6401 0.0 11.1 1.0
C18 H:1E6401 1.7 21.7 1.0
C17 H:1E6401 2.7 22.3 1.0
C19 H:1E6401 2.8 25.6 1.0
O22 H:1E6401 3.1 28.8 1.0
CB H:ALA95 3.4 26.2 1.0
CA H:GLY26 3.5 20.2 1.0
N H:GLY26 3.6 21.5 1.0
CG H:ASP51 3.6 23.0 1.0
OD2 H:ASP51 3.6 21.2 1.0
CA H:ASP51 3.8 21.2 1.0
OD1 H:ASP51 3.8 22.2 1.0
CG1 H:VAL25 3.8 18.7 1.0
C20 H:1E6401 4.1 27.5 1.0
O H:VAL50 4.1 18.2 1.0
C16 H:1E6401 4.1 27.2 1.0
CB H:ASP51 4.1 21.4 1.0
CD1 H:ILE119 4.2 22.1 1.0
CA H:ALA95 4.2 27.2 1.0
C H:VAL25 4.3 22.1 1.0
C23 H:1E6401 4.5 32.9 1.0
N H:VAL52 4.6 20.8 1.0
C H:ASP51 4.6 21.5 1.0
C21 H:1E6401 4.6 28.2 1.0
C27 H:1E6401 4.6 34.6 1.0
N H:ASP51 4.7 21.7 1.0
C H:VAL50 4.7 20.2 1.0
O H:VAL25 4.8 23.3 1.0
C H:GLY26 4.9 20.8 1.0
N H:ALA95 5.0 24.5 1.0

Reference:

A.Kohlmann, S.G.Zech, F.Li, T.Zhou, R.M.Squillace, L.Commodore, M.T.Greenfield, X.Lu, D.P.Miller, W.S.Huang, J.Qi, R.M.Thomas, Y.Wang, S.Zhang, R.Dodd, S.Liu, R.Xu, Y.Xu, J.J.Miret, V.Rivera, T.Clackson, W.C.Shakespeare, X.Zhu, D.C.Dalgarno. Fragment Growing and Linking Lead to Novel Nanomolar Lactate Dehydrogenase Inhibitors. J.Med.Chem. V. 56 1023 2013.
ISSN: ISSN 0022-2623
PubMed: 23302067
DOI: 10.1021/JM3014844
Page generated: Sun Jul 21 16:28:28 2024

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