Atomistry » Chlorine » PDB 4i1y-4ibc » 4i9h
Atomistry »
  Chlorine »
    PDB 4i1y-4ibc »
      4i9h »

Chlorine in PDB 4i9h: Crystal Structure of Rabbit Ldha in Complex with AP28669

Enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with AP28669

All present enzymatic activity of Crystal Structure of Rabbit Ldha in Complex with AP28669:
1.1.1.27;

Protein crystallography data

The structure of Crystal Structure of Rabbit Ldha in Complex with AP28669, PDB code: 4i9h was solved by T.Zhou, Z.G.Stephan, A.Kohlmann, 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 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.866, 139.690, 138.810, 90.00, 94.43, 90.00
R / Rfree (%) 20.7 / 24.3

Other elements in 4i9h:

The structure of Crystal Structure of Rabbit Ldha in Complex with AP28669 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 AP28669 (pdb code 4i9h). 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 AP28669, PDB code: 4i9h:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 1 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:22.2
occ:1.00
CL4 A:1E4401 0.0 22.2 1.0
C5 A:1E4401 1.7 36.5 1.0
C6 A:1E4401 2.6 35.3 1.0
C4 A:1E4401 2.8 38.7 1.0
O9 A:1E4401 3.4 44.0 1.0
CA A:ASP51 3.6 31.4 1.0
N A:GLY26 3.6 30.4 1.0
CB A:ALA95 3.6 33.9 1.0
CA A:GLY26 3.7 29.9 1.0
CG1 A:VAL25 3.7 27.5 1.0
CG A:ASP51 3.8 34.1 1.0
C10 A:1E4401 3.8 44.9 1.0
OD2 A:ASP51 3.9 32.6 1.0
O A:VAL50 3.9 30.5 1.0
OD1 A:ASP51 4.0 32.9 1.0
C1 A:1E4401 4.0 39.9 1.0
C3 A:1E4401 4.1 38.6 1.0
CB A:ASP51 4.2 31.4 1.0
N A:VAL52 4.3 31.2 1.0
O A:HOH521 4.3 30.5 1.0
C A:ASP51 4.3 31.9 1.0
CD1 A:ILE119 4.3 32.8 1.0
C A:VAL25 4.4 28.7 1.0
N A:ASP51 4.4 32.6 1.0
C A:VAL50 4.5 32.0 1.0
CA A:ALA95 4.5 32.4 1.0
C2 A:1E4401 4.6 38.7 1.0
O A:VAL25 4.9 27.0 1.0
OH A:TYR82 5.0 28.2 1.0

Chlorine binding site 2 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 2 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:14.4
occ:1.00
CL4 B:1E4401 0.0 14.4 1.0
C5 B:1E4401 1.7 31.4 1.0
C6 B:1E4401 2.6 33.4 1.0
C4 B:1E4401 2.8 34.0 1.0
O9 B:1E4401 3.4 38.3 1.0
N B:GLY26 3.5 28.8 1.0
CB B:ALA95 3.5 30.6 1.0
CA B:GLY26 3.5 27.1 1.0
CG1 B:VAL25 3.6 26.8 1.0
CA B:ASP51 3.6 29.5 1.0
O B:VAL50 3.8 29.1 1.0
CG B:ASP51 3.8 29.1 1.0
OD2 B:ASP51 3.9 30.8 1.0
OD1 B:ASP51 4.0 31.6 1.0
C1 B:1E4401 4.0 36.2 1.0
C10 B:1E4401 4.0 44.0 1.0
C3 B:1E4401 4.1 36.8 1.0
C B:VAL25 4.2 28.3 1.0
CB B:ASP51 4.3 29.8 1.0
CD1 B:ILE119 4.3 27.6 1.0
C B:ASP51 4.4 30.1 1.0
N B:VAL52 4.4 30.7 1.0
CA B:ALA95 4.4 29.8 1.0
C B:VAL50 4.5 29.4 1.0
N B:ASP51 4.5 30.6 1.0
C2 B:1E4401 4.6 35.9 1.0
O B:HOH512 4.7 30.2 1.0
O B:VAL25 4.7 27.2 1.0
CB B:VAL25 4.8 28.3 1.0
CA B:VAL25 4.9 27.8 1.0
C B:GLY26 4.9 27.9 1.0
O50 B:1E4401 5.0 43.9 1.0

Chlorine binding site 3 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 3 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:27.1
occ:1.00
CL4 C:1E4401 0.0 27.1 1.0
C5 C:1E4401 1.7 39.6 1.0
C6 C:1E4401 2.6 38.9 1.0
C4 C:1E4401 2.8 40.0 1.0
O9 C:1E4401 3.4 44.0 1.0
CA C:ASP51 3.5 33.2 1.0
N C:GLY26 3.6 29.7 1.0
CB C:ALA95 3.7 33.1 1.0
CG1 C:VAL25 3.7 30.1 1.0
CA C:GLY26 3.7 30.1 1.0
CG C:ASP51 3.8 32.9 1.0
O C:VAL50 3.8 33.3 1.0
C10 C:1E4401 3.8 45.1 1.0
OD2 C:ASP51 3.9 32.4 1.0
C1 C:1E4401 4.0 42.2 1.0
OD1 C:ASP51 4.0 35.3 1.0
C3 C:1E4401 4.1 40.1 1.0
CB C:ASP51 4.1 32.4 1.0
CD1 C:ILE119 4.2 33.7 1.0
C C:ASP51 4.3 33.5 1.0
N C:VAL52 4.3 34.9 1.0
C C:VAL25 4.3 29.2 1.0
N C:ASP51 4.4 32.5 1.0
C C:VAL50 4.4 32.2 1.0
C2 C:1E4401 4.6 41.9 1.0
CA C:ALA95 4.6 35.1 1.0
OH C:TYR82 4.9 32.6 1.0
O C:VAL25 4.9 28.9 1.0
CB C:VAL25 5.0 31.6 1.0
O50 C:1E4401 5.0 46.3 1.0
CA C:VAL25 5.0 30.2 1.0

Chlorine binding site 4 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 4 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:25.6
occ:1.00
CL4 D:1E4401 0.0 25.6 1.0
C5 D:1E4401 1.7 37.9 1.0
C6 D:1E4401 2.6 39.2 1.0
C4 D:1E4401 2.9 40.5 1.0
C10 D:1E4401 3.5 48.0 1.0
CB D:ALA95 3.5 30.9 1.0
O9 D:1E4401 3.6 43.0 1.0
CA D:GLY26 3.6 32.4 1.0
CA D:ASP51 3.6 36.3 1.0
N D:GLY26 3.7 31.7 1.0
OD2 D:ASP51 3.7 34.5 1.0
CG D:ASP51 3.8 36.3 1.0
CG1 D:VAL25 3.9 30.9 1.0
C1 D:1E4401 4.0 41.5 1.0
O D:VAL50 4.0 32.5 1.0
OD1 D:ASP51 4.1 37.9 1.0
C3 D:1E4401 4.1 40.9 1.0
CB D:ASP51 4.2 35.3 1.0
O D:HOH530 4.3 30.6 1.0
C D:VAL25 4.3 30.6 1.0
CD1 D:ILE119 4.3 33.0 1.0
N D:VAL52 4.3 36.0 1.0
CA D:ALA95 4.4 31.9 1.0
C D:ASP51 4.4 35.5 1.0
N D:ASP51 4.5 32.3 1.0
C2 D:1E4401 4.6 42.1 1.0
C D:VAL50 4.6 32.9 1.0
O D:VAL25 4.7 31.3 1.0
O50 D:1E4401 5.0 44.0 1.0
C11 D:1E4401 5.0 49.0 1.0

Chlorine binding site 5 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 5 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl401

b:28.9
occ:1.00
CL4 E:1E4401 0.0 28.9 1.0
C5 E:1E4401 1.7 40.5 1.0
C6 E:1E4401 2.6 39.4 1.0
C4 E:1E4401 2.8 40.2 1.0
O9 E:1E4401 3.4 43.5 1.0
N E:GLY26 3.5 28.6 1.0
CA E:ASP51 3.6 37.9 1.0
CG1 E:VAL25 3.6 31.4 1.0
CA E:GLY26 3.6 29.4 1.0
O E:VAL50 3.7 37.4 1.0
OD2 E:ASP51 3.7 40.3 1.0
CG E:ASP51 3.8 41.7 1.0
C10 E:1E4401 4.0 45.2 1.0
C1 E:1E4401 4.0 41.9 1.0
CB E:ALA95 4.0 37.9 1.0
C3 E:1E4401 4.1 42.6 1.0
CB E:ASP51 4.1 38.0 1.0
OD1 E:ASP51 4.1 43.5 1.0
C E:VAL25 4.2 29.2 1.0
CD1 E:ILE119 4.2 33.7 1.0
C E:ASP51 4.3 37.9 1.0
C E:VAL50 4.4 37.4 1.0
N E:ASP51 4.4 37.0 1.0
N E:VAL52 4.4 37.4 1.0
C2 E:1E4401 4.6 42.4 1.0
CA E:ALA95 4.6 38.2 1.0
O E:VAL25 4.8 28.0 1.0
OH E:TYR82 4.8 34.4 1.0
CB E:VAL25 4.8 32.3 1.0
CA E:VAL25 4.8 30.0 1.0
O50 E:1E4401 4.9 39.5 1.0
C E:GLY26 5.0 29.7 1.0

Chlorine binding site 6 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 6 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl401

b:30.6
occ:1.00
CL4 F:1E4401 0.0 30.6 1.0
C5 F:1E4401 1.7 41.4 1.0
C6 F:1E4401 2.6 43.2 1.0
C4 F:1E4401 2.9 43.2 1.0
C10 F:1E4401 3.5 49.1 1.0
O9 F:1E4401 3.6 44.8 1.0
CB F:ALA95 3.6 34.3 1.0
N F:GLY26 3.6 31.2 1.0
CA F:GLY26 3.6 31.7 1.0
OD2 F:ASP51 3.7 36.7 1.0
CA F:ASP51 3.7 36.1 1.0
CG F:ASP51 3.8 36.3 1.0
CG1 F:VAL25 3.8 35.0 1.0
O F:VAL50 3.9 36.9 1.0
OD1 F:ASP51 4.0 36.8 1.0
C1 F:1E4401 4.0 45.1 1.0
C3 F:1E4401 4.1 44.5 1.0
C F:VAL25 4.3 30.9 1.0
CB F:ASP51 4.3 35.6 1.0
CD1 F:ILE119 4.3 41.3 1.0
CA F:ALA95 4.3 35.2 1.0
N F:VAL52 4.4 35.9 1.0
C F:ASP51 4.5 36.6 1.0
C F:VAL50 4.6 35.0 1.0
C2 F:1E4401 4.6 46.4 1.0
N F:ASP51 4.6 35.2 1.0
O F:VAL25 4.7 31.5 1.0
O50 F:1E4401 4.9 47.2 1.0
C11 F:1E4401 5.0 51.1 1.0

Chlorine binding site 7 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 7 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl401

b:23.9
occ:1.00
CL4 G:1E4401 0.0 23.9 1.0
C5 G:1E4401 1.7 36.3 1.0
C6 G:1E4401 2.6 38.7 1.0
C4 G:1E4401 2.9 36.9 1.0
N G:GLY26 3.3 29.9 1.0
CA G:ASP51 3.4 32.2 1.0
O9 G:1E4401 3.5 40.4 1.0
CA G:GLY26 3.5 29.7 1.0
CG1 G:VAL25 3.6 30.4 1.0
OD2 G:ASP51 3.6 31.5 1.0
CG G:ASP51 3.6 34.1 1.0
O G:VAL50 3.7 29.5 1.0
C10 G:1E4401 3.8 44.6 1.0
CB G:ALA95 3.8 30.5 1.0
C1 G:1E4401 4.0 42.8 1.0
CB G:ASP51 4.0 31.6 1.0
OD1 G:ASP51 4.0 33.5 1.0
C3 G:1E4401 4.1 38.4 1.0
C G:VAL25 4.1 32.0 1.0
C G:ASP51 4.2 32.4 1.0
N G:VAL52 4.2 33.5 1.0
N G:ASP51 4.3 30.6 1.0
CD1 G:ILE119 4.3 32.9 1.0
C G:VAL50 4.3 29.9 1.0
CA G:ALA95 4.5 30.7 1.0
C2 G:1E4401 4.6 41.9 1.0
O G:VAL25 4.8 30.6 1.0
CB G:VAL25 4.8 30.7 1.0
CA G:VAL25 4.8 30.4 1.0
C G:GLY26 4.9 30.8 1.0

Chlorine binding site 8 out of 8 in 4i9h

Go back to Chlorine Binding Sites List in 4i9h
Chlorine binding site 8 out of 8 in the Crystal Structure of Rabbit Ldha in Complex with AP28669


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 AP28669 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl401

b:22.0
occ:1.00
CL4 H:1E4401 0.0 22.0 1.0
C5 H:1E4401 1.7 35.8 1.0
C6 H:1E4401 2.6 36.1 1.0
C4 H:1E4401 2.8 37.8 1.0
O9 H:1E4401 3.5 39.4 1.0
N H:GLY26 3.5 28.6 1.0
CB H:ALA95 3.5 31.6 1.0
CA H:ASP51 3.6 29.1 1.0
CG1 H:VAL25 3.6 29.7 1.0
CA H:GLY26 3.6 28.0 1.0
CG H:ASP51 3.8 31.4 1.0
O H:VAL50 3.8 27.2 1.0
OD2 H:ASP51 3.9 32.5 1.0
C1 H:1E4401 4.0 40.9 1.0
C10 H:1E4401 4.0 42.5 1.0
OD1 H:ASP51 4.0 31.3 1.0
C3 H:1E4401 4.1 39.1 1.0
CB H:ASP51 4.2 29.2 1.0
C H:VAL25 4.2 30.2 1.0
CD1 H:ILE119 4.3 25.8 1.0
C H:ASP51 4.3 29.2 1.0
N H:VAL52 4.4 29.9 1.0
CA H:ALA95 4.4 33.3 1.0
N H:ASP51 4.4 26.9 1.0
C H:VAL50 4.5 28.1 1.0
O H:HOH521 4.5 36.0 1.0
C2 H:1E4401 4.6 40.9 1.0
CB H:VAL25 4.8 30.9 1.0
O H:VAL25 4.9 30.4 1.0
CA H:VAL25 4.9 28.0 1.0
C H:GLY26 5.0 27.6 1.0
OH H:TYR82 5.0 29.1 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: Sat Dec 12 10:45:01 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy