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Fluorine in PDB 3zns: HDAC7 Bound with Tfmo Inhibitor TMP942

Enzymatic activity of HDAC7 Bound with Tfmo Inhibitor TMP942

All present enzymatic activity of HDAC7 Bound with Tfmo Inhibitor TMP942:
3.5.1.98;

Protein crystallography data

The structure of HDAC7 Bound with Tfmo Inhibitor TMP942, PDB code: 3zns was solved by M.Lobera, K.P.Madauss, D.T.Pohlhaus, R.P.Trump, M.A.Nolan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.71 / 2.45
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 81.570, 81.570, 150.101, 90.00, 90.00, 120.00
R / Rfree (%) 18.619 / 22.496

Other elements in 3zns:

The structure of HDAC7 Bound with Tfmo Inhibitor TMP942 also contains other interesting chemical elements:

Potassium (K) 6 atoms
Zinc (Zn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the HDAC7 Bound with Tfmo Inhibitor TMP942 (pdb code 3zns). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the HDAC7 Bound with Tfmo Inhibitor TMP942, PDB code: 3zns:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3zns

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Fluorine binding site 1 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1900

b:64.5
occ:1.00
 F01 A:NU71900 0.0 64.5 1.0
C02 A:NU71900 1.3 65.4 1.0
F03 A:NU71900 2.1 65.4 1.0
F04 A:NU71900 2.2 65.9 1.0
C05 A:NU71900 2.3 65.3 1.0
O09 A:NU71900 3.0 65.1 1.0
CA A:GLY841 3.2 29.8 1.0
CG A:PRO667 3.3 27.1 1.0
CB A:PRO667 3.3 27.0 1.0
N A:GLY841 3.4 29.8 1.0
N06 A:NU71900 3.4 65.7 1.0
C A:GLU840 3.7 29.6 1.0
O A:GLU840 3.9 29.5 1.0
C35 A:NU71900 4.2 66.0 1.0
C34 A:NU71900 4.2 65.6 1.0
N08 A:NU71900 4.2 65.3 1.0
ZN A:ZN101 4.3 32.4 1.0
OD2 A:ASP707 4.3 28.2 1.0
C07 A:NU71900 4.4 65.0 1.0
CA A:GLU840 4.5 29.6 1.0
CD A:PRO667 4.6 26.9 1.0
NE2 A:HIS669 4.6 26.9 1.0
C A:GLY841 4.6 30.0 1.0
CB A:GLU840 4.6 29.7 1.0
O A:GLY678 4.8 28.5 1.0
CA A:PRO667 4.9 27.2 1.0
CD2 A:HIS669 4.9 27.7 1.0
SG A:CYS680 5.0 28.3 1.0

Fluorine binding site 2 out of 9 in 3zns

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Fluorine binding site 2 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1900

b:65.4
occ:1.00
 F03 A:NU71900 0.0 65.4 1.0
C02 A:NU71900 1.3 65.4 1.0
F01 A:NU71900 2.1 64.5 1.0
F04 A:NU71900 2.2 65.9 1.0
C05 A:NU71900 2.3 65.3 1.0
N06 A:NU71900 2.8 65.7 1.0
CD2 A:HIS670 3.0 30.5 1.0
NE2 A:HIS669 3.4 26.9 1.0
O A:GLY678 3.4 28.5 1.0
NE2 A:HIS670 3.4 30.8 1.0
SG A:CYS680 3.5 28.3 1.0
CD2 A:HIS669 3.5 27.7 1.0
O09 A:NU71900 3.6 65.1 1.0
CG A:PRO667 3.8 27.1 1.0
CB A:PRO667 3.8 27.0 1.0
CG A:HIS670 4.1 29.9 1.0
C07 A:NU71900 4.1 65.0 1.0
N08 A:NU71900 4.5 65.3 1.0
CE1 A:HIS670 4.6 30.8 1.0
ZN A:ZN101 4.6 32.4 1.0
C A:GLY678 4.6 28.8 1.0
CE1 A:HIS669 4.7 27.3 1.0
CB A:HIS670 4.8 29.1 1.0
ND1 A:HIS670 4.9 31.1 1.0
CG A:HIS669 4.9 28.0 1.0
OD2 A:ASP707 4.9 28.2 1.0
N A:GLY841 5.0 29.8 1.0
OE1 A:GLU840 5.0 31.0 1.0
CB A:PHE679 5.0 28.4 1.0

Fluorine binding site 3 out of 9 in 3zns

Go back to Fluorine Binding Sites List in 3zns
Fluorine binding site 3 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1900

b:65.9
occ:1.00
 F04 A:NU71900 0.0 65.9 1.0
C02 A:NU71900 1.3 65.4 1.0
F03 A:NU71900 2.2 65.4 1.0
F01 A:NU71900 2.2 64.5 1.0
C05 A:NU71900 2.3 65.3 1.0
ZN A:ZN101 2.7 32.4 1.0
NE2 A:HIS669 2.8 26.9 1.0
OD2 A:ASP707 2.8 28.2 1.0
O09 A:NU71900 2.9 65.1 1.0
N06 A:NU71900 3.3 65.7 1.0
CG A:ASP707 3.4 28.8 1.0
OD1 A:ASP707 3.5 28.8 1.0
N A:GLY841 3.6 29.8 1.0
CD2 A:HIS669 3.6 27.7 1.0
CA A:GLY841 3.7 29.8 1.0
CE1 A:HIS669 3.7 27.3 1.0
NE2 A:HIS670 3.9 30.8 1.0
OD2 A:ASP801 4.1 29.0 1.0
N08 A:NU71900 4.1 65.3 1.0
CB A:GLU840 4.2 29.7 1.0
CD2 A:HIS670 4.2 30.5 1.0
ND1 A:HIS709 4.3 27.4 1.0
C07 A:NU71900 4.3 65.0 1.0
C A:GLU840 4.3 29.6 1.0
CB A:ASP707 4.7 28.6 1.0
CB A:PRO667 4.7 27.0 1.0
CG A:HIS669 4.7 28.0 1.0
ND1 A:HIS669 4.8 27.3 1.0
CA A:GLU840 4.8 29.6 1.0
CE1 A:HIS670 4.9 30.8 1.0
CB A:HIS709 4.9 27.8 1.0
CG A:HIS709 4.9 27.9 1.0

Fluorine binding site 4 out of 9 in 3zns

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Fluorine binding site 4 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1900

b:64.9
occ:1.00
 F01 B:NU71900 0.0 64.9 1.0
C02 B:NU71900 1.3 66.4 1.0
F03 B:NU71900 2.1 65.5 1.0
F04 B:NU71900 2.2 66.7 1.0
C05 B:NU71900 2.3 67.0 1.0
O09 B:NU71900 2.9 67.4 1.0
CA B:GLY841 3.0 29.6 1.0
N B:GLY841 3.2 29.8 1.0
N06 B:NU71900 3.5 67.5 1.0
C B:GLU840 3.6 29.7 1.0
CG B:PRO667 3.6 26.1 1.0
CB B:PRO667 3.7 26.1 1.0
O B:GLU840 3.8 29.7 1.0
ZN B:ZN101 4.0 34.6 1.0
N08 B:NU71900 4.2 67.0 1.0
OD2 B:ASP707 4.2 26.2 1.0
C35 B:NU71900 4.4 72.1 1.0
C B:GLY841 4.5 29.7 1.0
C07 B:NU71900 4.5 67.5 1.0
C34 B:NU71900 4.5 71.8 1.0
CA B:GLU840 4.6 29.8 1.0
NE2 B:HIS669 4.6 30.1 1.0
CB B:GLU840 4.7 30.0 1.0
OD2 B:ASP801 4.8 26.8 1.0
CD2 B:HIS669 4.9 29.6 1.0
N B:GLY842 4.9 29.8 1.0
CD B:PRO667 4.9 26.5 1.0
O B:GLY678 4.9 28.1 1.0

Fluorine binding site 5 out of 9 in 3zns

Go back to Fluorine Binding Sites List in 3zns
Fluorine binding site 5 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1900

b:65.5
occ:1.00
 F03 B:NU71900 0.0 65.5 1.0
C02 B:NU71900 1.3 66.4 1.0
F01 B:NU71900 2.1 64.9 1.0
F04 B:NU71900 2.2 66.7 1.0
C05 B:NU71900 2.3 67.0 1.0
N06 B:NU71900 2.8 67.5 1.0
O B:GLY678 3.1 28.1 1.0
CD2 B:HIS670 3.2 27.7 1.0
SG B:CYS680 3.4 28.6 1.0
O09 B:NU71900 3.6 67.4 1.0
NE2 B:HIS670 3.7 27.5 1.0
CG B:PRO667 3.7 26.1 1.0
CB B:PRO667 3.8 26.1 1.0
NE2 B:HIS669 4.0 30.1 1.0
CD2 B:HIS669 4.0 29.6 1.0
C07 B:NU71900 4.1 67.5 1.0
CG B:HIS670 4.3 27.9 1.0
C B:GLY678 4.4 28.0 1.0
CB B:PHE679 4.4 27.7 1.0
N08 B:NU71900 4.5 67.0 1.0
ZN B:ZN101 4.7 34.6 1.0
CE1 B:HIS670 4.8 28.0 1.0
CD2 B:PHE679 4.8 28.4 1.0
CB B:HIS670 5.0 27.4 1.0

Fluorine binding site 6 out of 9 in 3zns

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Fluorine binding site 6 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1900

b:66.7
occ:1.00
 F04 B:NU71900 0.0 66.7 1.0
C02 B:NU71900 1.3 66.4 1.0
F01 B:NU71900 2.2 64.9 1.0
F03 B:NU71900 2.2 65.5 1.0
C05 B:NU71900 2.3 67.0 1.0
NE2 B:HIS669 2.7 30.1 1.0
ZN B:ZN101 2.7 34.6 1.0
O09 B:NU71900 3.1 67.4 1.0
N06 B:NU71900 3.2 67.5 1.0
CD2 B:HIS669 3.4 29.6 1.0
OD2 B:ASP707 3.4 26.2 1.0
NE2 B:HIS670 3.5 27.5 1.0
OD1 B:ASP707 3.6 27.8 1.0
CE1 B:HIS669 3.7 29.9 1.0
CG B:ASP707 3.7 27.5 1.0
CD2 B:HIS670 3.8 27.7 1.0
N B:GLY841 4.0 29.8 1.0
CA B:GLY841 4.1 29.6 1.0
ND1 B:HIS709 4.1 27.8 1.0
N08 B:NU71900 4.2 67.0 1.0
OD2 B:ASP801 4.2 26.8 1.0
C07 B:NU71900 4.3 67.5 1.0
CE1 B:HIS670 4.4 28.0 1.0
CG B:HIS669 4.6 28.5 1.0
CB B:HIS709 4.6 27.5 1.0
CB B:GLU840 4.6 30.0 1.0
CG B:HIS709 4.7 27.6 1.0
ND1 B:HIS669 4.7 29.7 1.0
C B:GLU840 4.7 29.7 1.0
CG B:HIS670 4.8 27.9 1.0
CB B:ASP707 4.9 27.7 1.0
CE1 B:HIS709 4.9 27.5 1.0
CB B:PRO667 4.9 26.1 1.0

Fluorine binding site 7 out of 9 in 3zns

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Fluorine binding site 7 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1900

b:84.0
occ:1.00
 F01 C:NU71900 0.0 84.0 1.0
C02 C:NU71900 1.3 84.1 1.0
F03 C:NU71900 2.2 83.3 1.0
F04 C:NU71900 2.2 84.1 1.0
C05 C:NU71900 2.3 84.2 1.0
O09 C:NU71900 2.8 84.0 1.0
CA C:GLY841 2.9 33.5 1.0
N C:GLY841 2.9 33.4 1.0
C C:GLU840 3.3 33.3 1.0
N06 C:NU71900 3.6 84.2 1.0
OD2 C:ASP707 3.6 31.6 1.0
O C:GLU840 3.7 33.1 1.0
CB C:PRO667 3.7 29.2 1.0
ZN C:ZN101 3.7 32.4 1.0
CG C:PRO667 3.8 29.1 1.0
N08 C:NU71900 4.2 84.3 1.0
CA C:GLU840 4.2 33.4 1.0
CB C:GLU840 4.2 33.5 1.0
NE2 C:HIS669 4.3 31.2 1.0
C C:GLY841 4.4 33.6 1.0
C34 C:NU71900 4.4 86.0 1.0
C07 C:NU71900 4.5 84.1 1.0
C33 C:NU71900 4.5 86.1 1.0
CG C:ASP707 4.6 31.7 1.0
OD2 C:ASP801 4.6 31.9 1.0
CD2 C:HIS669 4.7 31.5 1.0
OE1 C:GLU840 4.9 35.2 1.0
N C:GLY842 4.9 33.7 1.0
OD1 C:ASP707 5.0 31.8 1.0

Fluorine binding site 8 out of 9 in 3zns

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Fluorine binding site 8 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1900

b:83.3
occ:1.00
 F03 C:NU71900 0.0 83.3 1.0
C02 C:NU71900 1.3 84.1 1.0
F01 C:NU71900 2.2 84.0 1.0
F04 C:NU71900 2.2 84.1 1.0
C05 C:NU71900 2.3 84.2 1.0
N06 C:NU71900 2.8 84.2 1.0
CG C:PRO667 3.0 29.1 1.0
O C:GLY678 3.3 33.4 1.0
CB C:PRO667 3.5 29.2 1.0
O09 C:NU71900 3.5 84.0 1.0
CB C:PHE679 3.8 33.2 1.0
SG C:CYS680 3.9 33.3 1.0
CD2 C:HIS670 3.9 31.5 1.0
C07 C:NU71900 4.1 84.1 1.0
C33 C:NU71900 4.3 86.1 1.0
NE2 C:HIS670 4.4 31.4 1.0
N08 C:NU71900 4.4 84.3 1.0
CD C:PRO667 4.4 29.3 1.0
C C:GLY678 4.4 33.6 1.0
CD2 C:PHE679 4.5 33.5 1.0
C34 C:NU71900 4.6 86.0 1.0
CG C:PHE679 4.6 33.5 1.0
C C:PHE679 4.7 33.1 1.0
CA C:PHE679 4.7 33.3 1.0
NE2 C:HIS669 4.7 31.2 1.0
O C:PHE679 4.7 33.0 1.0
CD2 C:HIS669 4.8 31.5 1.0
CA C:PRO667 4.9 29.3 1.0
CA C:GLY841 4.9 33.5 1.0
N C:GLY841 5.0 33.4 1.0

Fluorine binding site 9 out of 9 in 3zns

Go back to Fluorine Binding Sites List in 3zns
Fluorine binding site 9 out of 9 in the HDAC7 Bound with Tfmo Inhibitor TMP942


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of HDAC7 Bound with Tfmo Inhibitor TMP942 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1900

b:84.1
occ:1.00
 F04 C:NU71900 0.0 84.1 1.0
C02 C:NU71900 1.3 84.1 1.0
F03 C:NU71900 2.2 83.3 1.0
F01 C:NU71900 2.2 84.0 1.0
C05 C:NU71900 2.3 84.2 1.0
NE2 C:HIS669 2.7 31.2 1.0
CD2 C:HIS670 3.0 31.5 1.0
N06 C:NU71900 3.0 84.2 1.0
NE2 C:HIS670 3.0 31.4 1.0
CD2 C:HIS669 3.1 31.5 1.0
O09 C:NU71900 3.4 84.0 1.0
ZN C:ZN101 3.6 32.4 1.0
CE1 C:HIS669 3.9 31.2 1.0
OD2 C:ASP707 3.9 31.6 1.0
CE1 C:HIS670 4.2 31.1 1.0
CG C:HIS670 4.2 31.4 1.0
C07 C:NU71900 4.2 84.1 1.0
N08 C:NU71900 4.4 84.3 1.0
CG C:HIS669 4.4 30.9 1.0
CB C:PRO667 4.4 29.2 1.0
SG C:CYS680 4.4 33.3 1.0
O C:GLY678 4.5 33.4 1.0
CG C:ASP707 4.5 31.7 1.0
OD1 C:ASP707 4.6 31.8 1.0
N C:GLY841 4.6 33.4 1.0
CG C:PRO667 4.6 29.1 1.0
OE1 C:GLU840 4.7 35.2 1.0
ND1 C:HIS670 4.8 31.2 1.0
ND1 C:HIS669 4.8 30.6 1.0
CB C:GLU840 4.8 33.5 1.0
CA C:GLY841 4.8 33.5 1.0

Reference:

M.Lobera, K.P.Madauss, D.T.Pohlhaus, Q.G.Wright, M.Trocha, D.R.Schmidt, E.Baloglu, R.P.Trump, M.S.Head, G.A.Hofmann, M.Murray-Thompson, B.Schwartz, S.Chakravorty, Z.Wu, P.K.Mander, L.Kruidenier, R.A.Reid, W.Burkhart, B.J.Turunen, J.X.Rong, C.Wagner, M.B.Moyer, C.Wells, X.Hong, J.T.Moore, J.D.Williams, D.Soler, S.Ghosh, M.A.Nolan. Selective Class Iia Histone Deacetylase Inhibition Via A Non-Chelating Zinc Binding Group Nat.Chem.Biol. V. 9 319 2013.
ISSN: ISSN 1552-4450
PubMed: 23524983
DOI: 10.1038/NCHEMBIO.1223
Page generated: Wed Jul 31 23:47:33 2024

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