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Chlorine in PDB 4i9u: Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256

Enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256

All present enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256, PDB code: 4i9u was solved by T.Zhou, A.Kohlmann, Z.G.Stephan, L.Commodore, M.T.Greenfield, 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 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.690, 138.740, 138.170, 90.00, 94.82, 90.00
R / Rfree (%) 22.2 / 27.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256 (pdb code 4i9u). 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 A Fragment Inhibitor AP26256, PDB code: 4i9u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4i9u

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Chlorine binding site 1 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:13.0
occ:1.00
CL3 A:1E7401 0.0 13.0 1.0
C24 A:1E7401 1.8 25.3 1.0
C25 A:1E7401 2.8 25.0 1.0
C23 A:1E7401 2.8 26.6 1.0
N A:GLY26 3.3 24.4 1.0
CA A:GLY26 3.3 24.7 1.0
O A:VAL50 3.5 31.6 1.0
OD1 A:ASP51 3.5 37.8 1.0
CA A:ASP51 3.5 33.8 1.0
CG A:ASP51 3.5 36.3 1.0
CG1 A:VAL25 3.6 21.9 1.0
CB A:ALA95 3.7 22.4 1.0
OD2 A:ASP51 3.9 36.5 1.0
C A:VAL25 3.9 23.9 1.0
CB A:ASP51 4.0 33.6 1.0
C26 A:1E7401 4.1 24.6 1.0
C3 A:1E7401 4.2 28.7 1.0
C A:VAL50 4.3 30.2 1.0
CD1 A:ILE119 4.3 30.1 1.0
O A:VAL25 4.4 23.9 1.0
N A:ASP51 4.4 32.2 1.0
C A:ASP51 4.4 33.9 1.0
CA A:ALA95 4.5 21.7 1.0
O A:HOH535 4.6 25.6 1.0
N A:VAL52 4.6 33.5 1.0
CA A:VAL25 4.7 23.2 1.0
C A:GLY26 4.7 26.6 1.0
C27 A:1E7401 4.7 27.6 1.0
CB A:VAL25 4.7 24.3 1.0
OH A:TYR82 4.9 30.8 1.0

Chlorine binding site 2 out of 8 in 4i9u

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Chlorine binding site 2 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:17.2
occ:1.00
CL3 B:1E7401 0.0 17.2 1.0
C24 B:1E7401 1.7 24.5 1.0
C25 B:1E7401 2.8 25.5 1.0
C23 B:1E7401 2.8 25.8 1.0
N B:GLY26 3.2 16.1 1.0
CA B:ASP51 3.2 25.6 1.0
O B:VAL50 3.4 20.4 1.0
CG1 B:VAL25 3.4 14.9 1.0
OD2 B:ASP51 3.4 27.6 1.0
CA B:GLY26 3.4 16.2 1.0
CG B:ASP51 3.5 27.6 1.0
CB B:ASP51 3.7 26.8 1.0
C B:VAL25 3.9 15.7 1.0
CB B:ALA95 3.9 22.0 1.0
N B:ASP51 4.0 25.0 1.0
C B:VAL50 4.0 21.8 1.0
C26 B:1E7401 4.1 24.4 1.0
OD1 B:ASP51 4.1 28.7 1.0
C3 B:1E7401 4.2 26.1 1.0
CD1 B:ILE119 4.2 27.6 1.0
C B:ASP51 4.3 26.7 1.0
N B:VAL52 4.4 26.4 1.0
O B:VAL25 4.5 15.6 1.0
CA B:VAL25 4.5 15.1 1.0
CB B:VAL25 4.6 17.2 1.0
OH B:TYR82 4.6 28.1 1.0
CA B:ALA95 4.7 23.0 1.0
C27 B:1E7401 4.7 26.1 1.0
C B:GLY26 4.7 19.1 1.0

Chlorine binding site 3 out of 8 in 4i9u

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Chlorine binding site 3 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:17.6
occ:1.00
CL3 C:1E7401 0.0 17.6 1.0
C24 C:1E7401 1.8 22.1 1.0
C25 C:1E7401 2.7 23.2 1.0
C23 C:1E7401 2.8 26.2 1.0
CA C:GLY26 3.4 25.7 1.0
N C:GLY26 3.4 22.5 1.0
CA C:ASP51 3.4 26.2 1.0
CG1 C:VAL25 3.5 24.3 1.0
OD2 C:ASP51 3.5 27.1 1.0
O C:VAL50 3.6 24.4 1.0
CB C:ALA95 3.7 28.3 1.0
CG C:ASP51 3.8 27.4 1.0
CD1 C:ILE119 3.9 31.2 1.0
CB C:ASP51 4.0 26.1 1.0
C C:VAL25 4.0 23.5 1.0
C26 C:1E7401 4.1 25.8 1.0
C3 C:1E7401 4.2 27.0 1.0
N C:ASP51 4.2 26.5 1.0
C C:VAL50 4.2 25.6 1.0
C C:ASP51 4.4 27.4 1.0
CA C:ALA95 4.4 29.7 1.0
N C:VAL52 4.5 28.4 1.0
OD1 C:ASP51 4.6 29.0 1.0
O C:VAL25 4.6 23.6 1.0
OH C:TYR82 4.7 27.7 1.0
C27 C:1E7401 4.7 26.9 1.0
CB C:VAL25 4.7 24.1 1.0
CA C:VAL25 4.7 23.6 1.0
C C:GLY26 4.8 27.4 1.0

Chlorine binding site 4 out of 8 in 4i9u

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Chlorine binding site 4 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:11.3
occ:1.00
CL3 D:1E7401 0.0 11.3 1.0
C24 D:1E7401 1.7 22.2 1.0
C25 D:1E7401 2.7 23.3 1.0
C23 D:1E7401 2.8 24.7 1.0
N D:GLY26 3.3 19.9 1.0
CA D:GLY26 3.4 20.4 1.0
CA D:ASP51 3.5 27.6 1.0
O D:VAL50 3.6 26.8 1.0
CG1 D:VAL25 3.6 17.6 1.0
CB D:ALA95 3.8 26.9 1.0
CG D:ASP51 3.8 27.3 1.0
OD2 D:ASP51 3.8 28.1 1.0
C D:VAL25 3.8 20.0 1.0
CD1 D:ILE119 4.0 28.1 1.0
C26 D:1E7401 4.1 24.8 1.0
OD1 D:ASP51 4.1 28.1 1.0
CB D:ASP51 4.2 27.7 1.0
C3 D:1E7401 4.2 25.4 1.0
C D:VAL50 4.2 26.5 1.0
N D:ASP51 4.2 27.9 1.0
O D:VAL25 4.3 21.4 1.0
C D:ASP51 4.5 27.4 1.0
CA D:ALA95 4.6 28.0 1.0
CA D:VAL25 4.6 19.4 1.0
OH D:TYR82 4.7 27.5 1.0
C27 D:1E7401 4.7 25.1 1.0
N D:VAL52 4.7 28.5 1.0
CB D:VAL25 4.7 20.7 1.0
CG2 D:VAL50 4.8 26.3 1.0
C D:GLY26 4.8 21.0 1.0

Chlorine binding site 5 out of 8 in 4i9u

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Chlorine binding site 5 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:19.6
occ:1.00
CL3 E:1E7401 0.0 19.6 1.0
C24 E:1E7401 1.8 29.1 1.0
C25 E:1E7401 2.8 29.9 1.0
C23 E:1E7401 2.8 30.2 1.0
CA E:GLY26 3.3 27.7 1.0
N E:GLY26 3.3 25.6 1.0
CG1 E:VAL25 3.5 28.8 1.0
O E:VAL50 3.5 30.3 1.0
CA E:ASP51 3.6 34.1 1.0
CD1 E:ILE119 3.7 24.9 1.0
OD2 E:ASP51 3.8 36.9 1.0
CB E:ALA95 3.9 37.7 1.0
CG E:ASP51 3.9 37.4 1.0
C E:VAL25 4.0 25.6 1.0
C26 E:1E7401 4.1 31.7 1.0
C3 E:1E7401 4.2 31.6 1.0
CB E:ASP51 4.2 35.9 1.0
C E:VAL50 4.3 30.9 1.0
N E:ASP51 4.3 32.2 1.0
CA E:ALA95 4.4 37.0 1.0
OD1 E:ASP51 4.4 40.0 1.0
C E:ASP51 4.4 34.7 1.0
O E:VAL25 4.5 24.0 1.0
N E:VAL52 4.6 36.1 1.0
C27 E:1E7401 4.7 32.4 1.0
CB E:VAL25 4.7 26.7 1.0
CA E:VAL25 4.7 26.2 1.0
OH E:TYR82 4.7 25.0 1.0
C E:GLY26 4.7 29.3 1.0
N E:ALA95 4.9 35.1 1.0

Chlorine binding site 6 out of 8 in 4i9u

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Chlorine binding site 6 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:26.4
occ:1.00
CL3 F:1E7401 0.0 26.4 1.0
C24 F:1E7401 1.8 32.5 1.0
C25 F:1E7401 2.8 35.1 1.0
C23 F:1E7401 2.8 33.7 1.0
O F:VAL50 3.1 41.0 1.0
N F:GLY26 3.2 23.9 1.0
CA F:GLY26 3.3 23.3 1.0
OD2 F:ASP51 3.5 40.0 1.0
CA F:ASP51 3.6 41.3 1.0
CG1 F:VAL25 3.6 23.1 1.0
CB F:ALA95 3.7 29.5 1.0
CG F:ASP51 3.9 41.0 1.0
C F:VAL25 3.9 22.9 1.0
C F:VAL50 4.1 39.9 1.0
C26 F:1E7401 4.1 36.0 1.0
CB F:ASP51 4.2 40.7 1.0
C3 F:1E7401 4.2 36.0 1.0
N F:ASP51 4.3 41.0 1.0
C F:ASP51 4.4 41.7 1.0
O F:VAL25 4.5 22.8 1.0
CA F:ALA95 4.5 29.5 1.0
N F:VAL52 4.5 41.0 1.0
OD1 F:ASP51 4.6 41.2 1.0
CA F:VAL25 4.6 22.2 1.0
C F:GLY26 4.6 24.4 1.0
C27 F:1E7401 4.7 36.3 1.0
CD1 F:ILE119 4.7 45.2 1.0
CB F:VAL25 4.7 21.6 1.0
OH F:TYR82 4.9 46.6 1.0
N F:VAL27 4.9 23.7 1.0

Chlorine binding site 7 out of 8 in 4i9u

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Chlorine binding site 7 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl401

b:28.4
occ:1.00
CL3 G:1E7401 0.0 28.4 1.0
C24 G:1E7401 1.8 31.1 1.0
C25 G:1E7401 2.8 29.9 1.0
C23 G:1E7401 2.8 32.2 1.0
N G:GLY26 3.2 25.6 1.0
CG1 G:VAL25 3.4 24.9 1.0
CA G:GLY26 3.5 26.8 1.0
CA G:ASP51 3.5 32.2 1.0
O G:VAL50 3.5 28.7 1.0
CG G:ASP51 3.6 32.5 1.0
OD2 G:ASP51 3.7 33.5 1.0
CB G:ALA95 3.7 29.6 1.0
OD1 G:ASP51 3.9 32.6 1.0
C G:VAL25 3.9 24.8 1.0
CB G:ASP51 4.0 32.6 1.0
C26 G:1E7401 4.1 30.1 1.0
C3 G:1E7401 4.2 31.6 1.0
C G:VAL50 4.3 28.8 1.0
CD1 G:ILE119 4.3 31.7 1.0
N G:ASP51 4.4 30.2 1.0
C G:ASP51 4.4 33.6 1.0
CA G:ALA95 4.4 31.3 1.0
N G:VAL52 4.5 33.9 1.0
O G:HOH504 4.5 19.8 1.0
CA G:VAL25 4.5 23.5 1.0
CB G:VAL25 4.6 23.5 1.0
O G:VAL25 4.7 23.7 1.0
C27 G:1E7401 4.7 31.1 1.0
C G:GLY26 4.8 28.4 1.0

Chlorine binding site 8 out of 8 in 4i9u

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Chlorine binding site 8 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with A Fragment Inhibitor AP26256


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 A Fragment Inhibitor AP26256 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl401

b:14.8
occ:1.00
CL3 H:1E7401 0.0 14.8 1.0
C24 H:1E7401 1.7 22.3 1.0
C25 H:1E7401 2.7 22.4 1.0
C23 H:1E7401 2.8 25.1 1.0
N H:GLY26 3.2 26.8 1.0
O H:VAL50 3.4 27.5 1.0
CA H:GLY26 3.4 25.7 1.0
CA H:ASP51 3.4 27.2 1.0
CG1 H:VAL25 3.4 26.0 1.0
CG H:ASP51 3.7 26.1 1.0
CB H:ALA95 3.9 25.0 1.0
OD1 H:ASP51 3.9 21.9 1.0
OD2 H:ASP51 3.9 25.3 1.0
C H:VAL25 4.0 27.8 1.0
CB H:ASP51 4.0 26.1 1.0
C26 H:1E7401 4.1 24.7 1.0
O H:HOH522 4.1 33.8 1.0
C H:VAL50 4.1 26.0 1.0
C3 H:1E7401 4.2 28.1 1.0
N H:ASP51 4.2 26.4 1.0
C H:ASP51 4.4 27.7 1.0
CD1 H:ILE119 4.4 35.6 1.0
N H:VAL52 4.5 28.9 1.0
O H:VAL25 4.6 29.0 1.0
CA H:VAL25 4.6 26.7 1.0
OH H:TYR82 4.7 29.3 1.0
CB H:VAL25 4.7 28.1 1.0
C27 H:1E7401 4.7 27.4 1.0
CA H:ALA95 4.8 25.7 1.0
C H:GLY26 4.8 26.4 1.0
CG2 H:VAL50 4.8 25.5 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 16:29:16 2024

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