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Fluorine in PDB 8ig0: Crystal Structure of Menin in Complex with Ds-1594B

Protein crystallography data

The structure of Crystal Structure of Menin in Complex with Ds-1594B, PDB code: 8ig0 was solved by M.Suzuki, T.Yoneyama, E.Imai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 141.576, 70.151, 144.426, 90, 91.47, 90
R / Rfree (%) 21.2 / 26.6

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Menin in Complex with Ds-1594B (pdb code 8ig0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Menin in Complex with Ds-1594B, PDB code: 8ig0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 8ig0

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Fluorine binding site 1 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F700

b:44.5
occ:1.00
 F3 A:7IX700 0.0 44.5 1.0
C21 A:7IX700 1.3 47.0 1.0
F1 A:7IX700 2.1 54.9 1.0
F2 A:7IX700 2.2 46.9 1.0
C20 A:7IX700 2.3 43.6 1.0
O A:HIS181 2.8 46.4 1.0
C A:HIS181 2.8 39.9 1.0
CA A:HIS181 3.2 41.6 1.0
N A:HIS181 3.2 41.4 1.0
N A:ALA182 3.4 35.9 1.0
CB A:ALA182 3.6 32.1 1.0
C18 A:7IX700 3.6 40.0 1.0
CB A:SER155 3.6 44.6 1.0
C A:ASP180 3.7 44.9 1.0
CA A:ALA182 4.0 34.7 1.0
O A:ASP180 4.2 52.7 1.0
OG A:SER155 4.4 48.1 1.0
CA A:ASP180 4.4 46.3 1.0
C19 A:7IX700 4.5 36.1 1.0
S1 A:7IX700 4.6 40.4 1.0
CA A:SER155 4.7 46.6 1.0
CB A:HIS181 4.7 42.7 1.0
CD2 A:LEU177 4.8 44.6 1.0
N A:ASP180 4.8 46.5 1.0

Fluorine binding site 2 out of 12 in 8ig0

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Fluorine binding site 2 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F700

b:54.9
occ:1.00
 F1 A:7IX700 0.0 54.9 1.0
C21 A:7IX700 1.3 47.0 1.0
F3 A:7IX700 2.1 44.5 1.0
F2 A:7IX700 2.2 46.9 1.0
C20 A:7IX700 2.4 43.6 1.0
C18 A:7IX700 3.0 40.0 1.0
CB A:SER155 3.2 44.6 1.0
S1 A:7IX700 3.2 40.4 1.0
CD2 A:LEU177 3.3 44.6 1.0
CE1 A:PHE238 3.4 41.0 1.0
CB A:ALA182 3.7 32.1 1.0
OG A:SER155 3.7 48.1 1.0
CZ A:PHE238 3.8 40.0 1.0
O A:HIS181 3.8 46.4 1.0
C19 A:7IX700 4.1 36.1 1.0
C A:HIS181 4.3 39.9 1.0
CD1 A:PHE238 4.5 44.0 1.0
CA A:SER155 4.5 46.6 1.0
CA A:ALA182 4.6 34.7 1.0
CG A:LEU177 4.6 45.3 1.0
C17 A:7IX700 4.6 35.6 1.0
N A:ALA182 4.7 35.9 1.0
CB A:LEU177 4.9 42.1 1.0
C15 A:7IX700 4.9 35.9 1.0

Fluorine binding site 3 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 3 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F700

b:46.9
occ:1.00
 F2 A:7IX700 0.0 46.9 1.0
C21 A:7IX700 1.3 47.0 1.0
F1 A:7IX700 2.2 54.9 1.0
F3 A:7IX700 2.2 44.5 1.0
C20 A:7IX700 2.3 43.6 1.0
C18 A:7IX700 2.6 40.0 1.0
C19 A:7IX700 3.1 36.1 1.0
CB A:SER155 3.7 44.6 1.0
S1 A:7IX700 3.7 40.4 1.0
OG A:SER155 3.7 48.1 1.0
S A:DMS702 3.9 103.4 1.0
C15 A:7IX700 4.1 35.9 1.0
C1 A:DMS702 4.4 83.5 1.0
C17 A:7IX700 4.5 35.6 1.0
CE1 A:PHE238 4.7 41.0 1.0
C2 A:DMS702 4.7 93.8 1.0
O A:HIS181 4.8 46.4 1.0
N A:HIS181 4.8 41.4 1.0
C A:ASP180 4.9 44.9 1.0
CA A:ASP180 5.0 46.3 1.0

Fluorine binding site 4 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 4 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F700

b:40.2
occ:1.00
 F3 B:7IX700 0.0 40.2 1.0
C21 B:7IX700 1.4 46.2 1.0
F1 B:7IX700 2.2 55.3 1.0
F2 B:7IX700 2.3 45.9 1.0
C20 B:7IX700 2.4 39.5 1.0
O B:HIS181 2.8 51.8 1.0
C B:HIS181 2.9 47.8 1.0
CA B:HIS181 3.3 43.6 1.0
N B:HIS181 3.3 46.1 1.0
N B:ALA182 3.5 48.3 1.0
CB B:SER155 3.5 53.7 1.0
CB B:ALA182 3.6 45.4 1.0
C18 B:7IX700 3.7 34.9 1.0
C B:ASP180 3.8 53.6 1.0
CA B:ALA182 4.0 50.1 1.0
OG B:SER155 4.3 55.4 1.0
O B:ASP180 4.4 60.4 1.0
CA B:ASP180 4.4 50.3 1.0
CA B:SER155 4.5 53.8 1.0
C19 B:7IX700 4.7 31.9 1.0
S1 B:7IX700 4.7 33.5 1.0
N B:ASP180 4.8 47.2 1.0
CB B:HIS181 4.8 38.7 1.0

Fluorine binding site 5 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 5 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F700

b:55.3
occ:1.00
 F1 B:7IX700 0.0 55.3 1.0
C21 B:7IX700 1.3 46.2 1.0
F3 B:7IX700 2.2 40.2 1.0
F2 B:7IX700 2.2 45.9 1.0
C20 B:7IX700 2.3 39.5 1.0
C18 B:7IX700 2.9 34.9 1.0
S1 B:7IX700 3.1 33.5 1.0
CD2 B:LEU177 3.4 46.9 1.0
CB B:SER155 3.5 53.7 1.0
O B:HIS181 3.5 51.8 1.0
CB B:ALA182 3.7 45.4 1.0
CE1 B:PHE238 3.8 66.0 1.0
OG B:SER155 4.1 55.4 1.0
C19 B:7IX700 4.1 31.9 1.0
C B:HIS181 4.2 47.8 1.0
CZ B:PHE238 4.4 65.6 1.0
CA B:ALA182 4.5 50.1 1.0
C17 B:7IX700 4.6 28.8 1.0
N B:ALA182 4.6 48.3 1.0
CG B:LEU177 4.7 49.0 1.0
CD1 B:PHE238 4.8 64.6 1.0
CA B:SER155 4.8 53.8 1.0
C15 B:7IX700 4.9 30.1 1.0
N B:HIS181 5.0 46.1 1.0

Fluorine binding site 6 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 6 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F700

b:45.9
occ:1.00
 F2 B:7IX700 0.0 45.9 1.0
C21 B:7IX700 1.4 46.2 1.0
F1 B:7IX700 2.2 55.3 1.0
F3 B:7IX700 2.3 40.2 1.0
C20 B:7IX700 2.3 39.5 1.0
C18 B:7IX700 2.7 34.9 1.0
C19 B:7IX700 3.3 31.9 1.0
CB B:SER155 3.4 53.7 1.0
OG B:SER155 3.4 55.4 1.0
S1 B:7IX700 3.8 33.5 1.0
S B:DMS702 4.0 101.3 1.0
C1 B:DMS702 4.0 92.4 1.0
C15 B:7IX700 4.3 30.1 1.0
C17 B:7IX700 4.6 28.8 1.0
C2 B:DMS702 4.7 94.0 1.0
O B:HIS181 4.7 51.8 1.0
CA B:SER155 4.8 53.8 1.0
CE1 B:PHE238 4.8 66.0 1.0

Fluorine binding site 7 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 7 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:38.7
occ:1.00
 F3 C:7IX700 0.0 38.7 1.0
C21 C:7IX700 1.3 44.0 1.0
F1 C:7IX700 2.1 50.9 1.0
F2 C:7IX700 2.3 43.4 1.0
C20 C:7IX700 2.3 42.3 1.0
O C:HIS181 2.7 46.1 1.0
C C:HIS181 2.8 43.4 1.0
N C:HIS181 3.1 46.7 1.0
CA C:HIS181 3.2 43.0 1.0
C C:ASP180 3.5 48.7 1.0
N C:ALA182 3.5 42.2 1.0
C18 C:7IX700 3.6 40.5 1.0
CB C:ALA182 3.6 35.5 1.0
O C:ASP180 3.7 52.9 1.0
CB C:SER155 4.0 51.3 1.0
CA C:ALA182 4.1 40.0 1.0
CA C:ASP180 4.3 49.6 1.0
C19 C:7IX700 4.4 37.8 1.0
OG C:SER155 4.6 55.1 1.0
N C:ASP180 4.6 48.3 1.0
CB C:HIS181 4.7 41.0 1.0
S1 C:7IX700 4.8 39.9 1.0
CA C:SER155 5.0 51.4 1.0

Fluorine binding site 8 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 8 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:50.9
occ:1.00
 F1 C:7IX700 0.0 50.9 1.0
C21 C:7IX700 1.3 44.0 1.0
F3 C:7IX700 2.1 38.7 1.0
F2 C:7IX700 2.2 43.4 1.0
C20 C:7IX700 2.4 42.3 1.0
CB C:SER155 3.1 51.3 1.0
C18 C:7IX700 3.1 40.5 1.0
CB C:ALA182 3.5 35.5 1.0
S1 C:7IX700 3.6 39.9 1.0
CE1 C:PHE238 3.6 52.5 1.0
OG C:SER155 3.7 55.1 1.0
CD2 C:LEU177 3.7 40.6 1.0
O C:HIS181 3.7 46.1 1.0
CZ C:PHE238 3.9 50.6 1.0
C19 C:7IX700 4.2 37.8 1.0
C C:HIS181 4.2 43.4 1.0
CA C:SER155 4.4 51.4 1.0
CA C:ALA182 4.5 40.0 1.0
C2 C:DMS702 4.6 108.6 1.0
N C:ALA182 4.6 42.2 1.0
CD1 C:PHE238 4.8 53.4 1.0
C17 C:7IX700 4.9 37.3 1.0
CG C:LEU177 5.0 41.0 1.0

Fluorine binding site 9 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 9 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F700

b:43.4
occ:1.00
 F2 C:7IX700 0.0 43.4 1.0
C21 C:7IX700 1.3 44.0 1.0
F1 C:7IX700 2.2 50.9 1.0
F3 C:7IX700 2.3 38.7 1.0
C20 C:7IX700 2.3 42.3 1.0
C18 C:7IX700 2.6 40.5 1.0
C19 C:7IX700 3.0 37.8 1.0
S C:DMS702 3.7 115.8 1.0
OG C:SER155 3.8 55.1 1.0
S1 C:7IX700 3.9 39.9 1.0
C2 C:DMS702 3.9 108.6 1.0
CB C:SER155 3.9 51.3 1.0
C15 C:7IX700 4.1 39.4 1.0
C17 C:7IX700 4.5 37.3 1.0
C1 C:DMS702 4.6 108.5 1.0
O C:HIS181 4.7 46.1 1.0
C C:ASP180 4.7 48.7 1.0
CE1 C:PHE238 4.8 52.5 1.0
N C:HIS181 4.9 46.7 1.0
CA C:ASP180 5.0 49.6 1.0
O C:ASP180 5.0 52.9 1.0
O C:DMS702 5.0 98.0 1.0
C13 C:7IX700 5.0 42.4 1.0

Fluorine binding site 10 out of 12 in 8ig0

Go back to Fluorine Binding Sites List in 8ig0
Fluorine binding site 10 out of 12 in the Crystal Structure of Menin in Complex with Ds-1594B


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Menin in Complex with Ds-1594B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F700

b:45.0
occ:1.00
 F3 D:7IX700 0.0 45.0 1.0
C21 D:7IX700 1.3 43.4 1.0
F1 D:7IX700 2.1 47.0 1.0
F2 D:7IX700 2.2 40.9 1.0
C20 D:7IX700 2.3 39.3 1.0
O D:HIS181 2.9 52.5 1.0
C D:HIS181 3.1 43.8 1.0
N D:HIS181 3.2 44.4 1.0
CA D:HIS181 3.3 39.9 1.0
C D:ASP180 3.4 51.2 1.0
C18 D:7IX700 3.6 33.6 1.0
O D:ASP180 3.7 57.6 1.0
CB D:SER155 3.8 46.4 1.0
CB D:ALA182 3.8 31.3 1.0
N D:ALA182 3.8 38.7 1.0
CA D:ASP180 4.2 51.0 1.0
OG D:SER155 4.4 46.0 1.0
CA D:ALA182 4.4 36.4 1.0
C19 D:7IX700 4.4 30.4 1.0
N D:ASP180 4.5 49.4 1.0
S1 D:7IX700 4.7 32.8 1.0
CA D:SER155 4.8 48.9 1.0
CB D:HIS181 4.8 36.9 1.0

Reference:

M.Numata, N.Haginoya, M.Shiroishi, T.Hirata, A.Sato-Otsubo, K.Yoshikawa, Y.Takata, R.Nagase, Y.Kashimoto, M.Suzuki, N.Schulte, G.Polier, A.Kurimoto, Y.Tomoe, A.Toyota, T.Yoneyama, E.Imai, K.Watanabe, T.Hamada, R.Kanada, J.Watanabe, Y.Kagoshima, E.Tokumaru, K.Murata, T.Baba, T.Shinozaki, M.Ohtsuka, K.Goto, T.Karibe, T.Deguchi, Y.Gocho, M.Yoshida, D.Tomizawa, M.Kato, S.Tsutsumi, M.Kitagawa, Y.Abe. A Novel Menin-MLL1 Inhibitor, Ds-1594A, Prevents the Progression of Acute Leukemia with Rearranged MLL1 or Mutated NPM1. Cancer Cell Int V. 23 36 2023.
ISSN: ISSN 1475-2867
PubMed: 36841758
DOI: 10.1186/S12935-023-02877-Y
Page generated: Wed Jul 16 05:36:24 2025

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