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Chlorine in PDB 6hu1: Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10

Enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10

All present enzymatic activity of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10:
3.5.1.98;

Protein crystallography data

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10, PDB code: 6hu1 was solved by T.B.Shaik, M.Marek, C.Romier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.08 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 71.220, 71.190, 99.030, 78.27, 75.65, 85.73
R / Rfree (%) 16 / 20.5

Other elements in 6hu1:

The structure of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 also contains other interesting chemical elements:

Potassium (K) 8 atoms
Zinc (Zn) 4 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 (pdb code 6hu1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10, PDB code: 6hu1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6hu1

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Chlorine binding site 1 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:97.8
occ:1.00
 CL1 A:GT2504 0.0 97.8 1.0
C5 A:GT2504 1.7 87.3 1.0
C4 A:GT2504 2.7 86.7 1.0
C6 A:GT2504 2.7 81.0 1.0
O14 A:GT2504 2.8 70.2 1.0
C2 A:GT2504 3.1 70.3 1.0
CD1 A:TYR341 3.3 40.5 1.0
CG A:TYR341 3.6 37.3 1.0
CE1 A:TYR341 3.8 40.8 1.0
C3 A:GT2504 4.0 88.5 1.0
CB A:TYR341 4.0 30.3 1.0
C7 A:GT2504 4.0 83.9 1.0
CE A:LYS20 4.1 46.8 1.0
CD2 A:TYR341 4.3 35.8 1.0
N1 A:GT2504 4.4 61.4 1.0
C8 A:GT2504 4.5 85.6 1.0
CZ A:TYR341 4.5 35.8 1.0
CE2 A:TYR341 4.7 31.8 1.0
NZ A:LYS20 4.9 52.7 1.0

Chlorine binding site 2 out of 12 in 6hu1

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Chlorine binding site 2 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:92.5
occ:1.00
 CL2 A:GT2504 0.0 92.5 1.0
C3 A:GT2504 1.7 88.5 1.0
C8 A:GT2504 2.7 85.6 1.0
C4 A:GT2504 2.7 86.7 1.0
CB A:PRO291 3.6 28.9 1.0
O A:PRO291 3.8 27.8 1.0
C7 A:GT2504 4.0 83.9 1.0
C5 A:GT2504 4.0 87.3 1.0
C A:PRO291 4.0 30.5 1.0
CG A:PRO291 4.3 27.4 1.0
CA A:PRO291 4.5 17.2 1.0
N A:HIS292 4.5 28.6 1.0
C6 A:GT2504 4.5 81.0 1.0
CA A:HIS292 5.0 30.6 1.0

Chlorine binding site 3 out of 12 in 6hu1

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Chlorine binding site 3 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:71.7
occ:1.00
 CL3 A:GT2504 0.0 71.7 1.0
C20 A:GT2504 1.7 63.6 1.0
C21 A:GT2504 2.7 60.6 1.0
C19 A:GT2504 2.7 61.0 1.0
N1 A:GT2504 3.0 61.4 1.0
OD2 A:ASP100 3.7 74.9 1.0
C2 A:GT2504 3.8 70.3 1.0
C16 A:GT2504 4.0 60.2 1.0
C18 A:GT2504 4.0 60.9 1.0
O14 A:GT2504 4.1 70.2 1.0
CG A:ASP100 4.4 68.0 1.0
C17 A:GT2504 4.5 57.7 1.0
CG A:PHE216 4.7 23.3 1.0
OD1 A:ASP100 4.8 72.6 1.0
CB A:PHE216 4.9 24.0 1.0
C6 A:GT2504 4.9 81.0 1.0
CD2 A:PHE216 5.0 24.0 1.0
CD1 A:PHE216 5.0 22.8 1.0
NZ A:LYS20 5.0 52.7 1.0

Chlorine binding site 4 out of 12 in 6hu1

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Chlorine binding site 4 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:98.7
occ:1.00
 CL1 B:GT2504 0.0 98.7 1.0
C5 B:GT2504 1.7 96.4 1.0
C4 B:GT2504 2.7 96.3 1.0
C6 B:GT2504 2.7 91.6 1.0
O14 B:GT2504 2.9 86.2 1.0
NZ B:LYS20 3.0 54.4 1.0
CD1 B:TYR341 3.1 40.8 1.0
C2 B:GT2504 3.1 82.8 1.0
CG B:TYR341 3.3 34.8 1.0
CB B:TYR341 3.7 21.9 1.0
CE1 B:TYR341 3.7 40.6 1.0
C3 B:GT2504 4.0 97.1 1.0
C7 B:GT2504 4.0 92.7 1.0
CD2 B:TYR341 4.1 40.5 1.0
CE B:LYS20 4.3 53.5 1.0
N1 B:GT2504 4.3 72.2 1.0
CZ B:TYR341 4.4 38.2 1.0
C8 B:GT2504 4.5 94.8 1.0
CE2 B:TYR341 4.6 35.3 1.0
CE1 B:HIS292 5.0 28.0 1.0

Chlorine binding site 5 out of 12 in 6hu1

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Chlorine binding site 5 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:0.5
occ:1.00
 CL2 B:GT2504 0.0 0.5 1.0
C3 B:GT2504 1.7 97.1 1.0
C4 B:GT2504 2.7 96.3 1.0
C8 B:GT2504 2.7 94.8 1.0
O B:HOH768 3.9 55.5 1.0
C5 B:GT2504 4.0 96.4 1.0
C7 B:GT2504 4.0 92.7 1.0
CB B:PRO291 4.0 27.8 1.0
O B:PRO291 4.1 26.2 1.0
C B:PRO291 4.4 21.6 1.0
C6 B:GT2504 4.5 91.6 1.0
CG B:PRO291 4.7 27.6 1.0
CA B:PRO291 4.9 25.6 1.0

Chlorine binding site 6 out of 12 in 6hu1

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Chlorine binding site 6 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:63.1
occ:1.00
 CL3 B:GT2504 0.0 63.1 1.0
C20 B:GT2504 1.7 55.8 1.0
C21 B:GT2504 2.7 44.0 1.0
C19 B:GT2504 2.7 60.0 1.0
O A:HOH606 2.9 52.9 1.0
N1 B:GT2504 3.0 72.2 1.0
OD1 A:ASP50 3.4 62.9 1.0
C2 B:GT2504 3.8 82.8 1.0
C16 B:GT2504 4.0 45.8 1.0
C18 B:GT2504 4.0 54.9 1.0
O14 B:GT2504 4.1 86.2 1.0
OD1 B:ASP100 4.2 75.4 1.0
O A:HOH658 4.3 45.0 1.0
C17 B:GT2504 4.5 53.1 1.0
CG A:ASP50 4.6 59.7 1.0
CG B:ASP100 4.7 75.0 1.0
C6 B:GT2504 4.8 91.6 1.0
C7 B:GT2504 4.9 92.7 1.0
CG B:PHE216 4.9 20.1 1.0
OD2 A:ASP50 5.0 66.8 1.0

Chlorine binding site 7 out of 12 in 6hu1

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Chlorine binding site 7 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:90.2
occ:1.00
 CL1 C:GT2504 0.0 90.2 1.0
C5 C:GT2504 1.7 83.8 1.0
C4 C:GT2504 2.7 83.4 1.0
C6 C:GT2504 2.7 76.5 1.0
NZ C:LYS20 2.8 56.4 1.0
O14 C:GT2504 2.9 70.8 1.0
C2 C:GT2504 3.1 69.6 1.0
CD1 C:TYR341 3.2 41.4 1.0
O C:HOH769 3.2 57.9 1.0
CE C:LYS20 3.4 49.6 1.0
CG C:TYR341 3.5 36.3 1.0
CB C:TYR341 3.8 29.0 1.0
CE1 C:TYR341 3.8 41.8 1.0
C3 C:GT2504 4.0 83.1 1.0
C7 C:GT2504 4.0 75.7 1.0
CD2 C:TYR341 4.4 28.0 1.0
N1 C:GT2504 4.4 67.4 1.0
C8 C:GT2504 4.5 77.7 1.0
CD C:LYS20 4.5 40.1 1.0
CZ C:TYR341 4.6 39.7 1.0
CE2 C:TYR341 4.9 26.6 1.0

Chlorine binding site 8 out of 12 in 6hu1

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Chlorine binding site 8 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


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 Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:86.4
occ:1.00
 CL2 C:GT2504 0.0 86.4 1.0
C3 C:GT2504 1.7 83.1 1.0
C4 C:GT2504 2.7 83.4 1.0
C8 C:GT2504 2.7 77.7 1.0
CB C:PRO291 3.7 21.6 1.0
O C:PRO291 3.9 24.3 1.0
C5 C:GT2504 4.0 83.8 1.0
C7 C:GT2504 4.0 75.7 1.0
C C:PRO291 4.3 24.2 1.0
C6 C:GT2504 4.5 76.5 1.0
CA C:PRO291 4.6 19.8 1.0
CG C:PRO291 4.8 24.2 1.0
N C:HIS292 5.0 23.1 1.0

Chlorine binding site 9 out of 12 in 6hu1

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Chlorine binding site 9 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl504

b:72.7
occ:1.00
 CL3 C:GT2504 0.0 72.7 1.0
C20 C:GT2504 1.7 66.3 1.0
C21 C:GT2504 2.7 56.5 1.0
C19 C:GT2504 2.7 63.7 1.0
N1 C:GT2504 3.0 67.4 1.0
OD1 D:ASP50 3.4 54.3 1.0
C2 C:GT2504 3.7 69.6 1.0
CZ C:PHE151 3.7 39.1 0.5
O14 C:GT2504 3.8 70.8 1.0
C16 C:GT2504 4.0 54.6 1.0
C18 C:GT2504 4.0 60.9 1.0
CE2 C:PHE151 4.1 37.4 0.5
O C:HOH635 4.1 42.2 1.0
OD2 C:ASP100 4.1 81.8 1.0
CG D:ASP50 4.5 54.2 1.0
C17 C:GT2504 4.5 56.0 1.0
CG C:ASP100 4.6 77.3 1.0
CE1 C:PHE151 4.7 33.9 0.5
OD1 C:ASP100 4.7 81.5 1.0
C6 C:GT2504 4.8 76.5 1.0
C7 C:GT2504 4.9 75.7 1.0

Chlorine binding site 10 out of 12 in 6hu1

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Chlorine binding site 10 out of 12 in the Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of Schistosoma Mansoni HDAC8 Complexed with A Benzohydroxamate Inhibitor 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl504

b:75.4
occ:0.78
 CL1 D:GT2504 0.0 75.4 0.8
C5 D:GT2504 1.7 67.3 0.8
C4 D:GT2504 2.7 66.8 0.8
C6 D:GT2504 2.7 63.8 0.8
O14 D:GT2504 2.7 55.8 0.8
NZ D:LYS20 2.8 58.9 1.0
C2 D:GT2504 3.1 52.8 0.8
CD1 D:TYR341 3.2 33.9 1.0
CG D:TYR341 3.5 32.5 1.0
CE D:LYS20 3.7 50.8 1.0
CE1 D:TYR341 3.8 34.9 1.0
CB D:TYR341 3.9 23.4 1.0
C3 D:GT2504 3.9 71.8 0.8
C7 D:GT2504 4.0 67.2 0.8
CD2 D:TYR341 4.3 35.0 1.0
C8 D:GT2504 4.5 68.5 0.8
N1 D:GT2504 4.5 46.8 0.8
CZ D:TYR341 4.5 33.6 1.0
CE2 D:TYR341 4.8 37.2 1.0

Reference:

M.Marek, T.B.Shaik, T.Heimburg, A.Chakrabarti, J.Lancelot, E.Ramos-Morales, C.Da Veiga, D.Kalinin, J.Melesina, D.Robaa, K.Schmidtkunz, T.Suzuki, R.Holl, E.Ennifar, R.J.Pierce, M.Jung, W.Sippl, C.Romier. Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. V. 61 10000 2018.
ISSN: ISSN 1520-4804
PubMed: 30347148
DOI: 10.1021/ACS.JMEDCHEM.8B01087
Page generated: Sun Jul 28 01:10:26 2024

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