Fluorine in PDB 8out: Crystal Structure of Dlk in Complex with Compound 22

Enzymatic activity of Crystal Structure of Dlk in Complex with Compound 22

All present enzymatic activity of Crystal Structure of Dlk in Complex with Compound 22:
2.7.11.25;

Protein crystallography data

The structure of Crystal Structure of Dlk in Complex with Compound 22, PDB code: 8out was solved by M.Zebisch, O.Akkermans, J.J.Barker, J.B.Cross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.37 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.043, 38.888, 62.691, 90, 108.73, 90
R / Rfree (%) 19.3 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Dlk in Complex with Compound 22 (pdb code 8out). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of Dlk in Complex with Compound 22, PDB code: 8out:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 8out

Go back to Fluorine Binding Sites List in 8out
Fluorine binding site 1 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.4
occ:1.00
 F6 A:W3C501 0.0 29.4 1.0
C11 A:W3C501 1.4 28.9 1.0
C12 A:W3C501 2.6 28.7 1.0
C13 A:W3C501 2.6 28.8 1.0
C10 A:W3C501 2.6 28.7 1.0
H6 A:W3C501 3.1 35.6 1.0
H8 A:W3C501 3.1 35.2 1.0
H10 A:W3C501 3.1 34.6 1.0
H5 A:W3C501 3.1 36.2 1.0
H9 A:W3C501 3.1 34.5 1.0
H7 A:W3C501 3.1 35.9 1.0
C9 A:W3C501 3.2 28.8 1.0
O A:ALA194 4.3 27.5 1.0
N3 A:W3C501 4.7 28.5 1.0
O A:VAL131 4.8 29.3 1.0

Fluorine binding site 2 out of 7 in 8out

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Fluorine binding site 2 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.9
occ:1.00
 F5 A:W3C501 0.0 28.9 1.0
C8 A:W3C501 1.3 29.1 1.0
F4 A:W3C501 2.1 29.1 1.0
F3 A:W3C501 2.1 29.4 1.0
C7 A:W3C501 2.4 29.0 1.0
H4 A:W3C501 2.4 33.2 1.0
O1 A:W3C501 2.7 29.2 1.0
C6 A:W3C501 3.0 28.5 1.0
N2 A:W3C501 3.2 28.2 1.0
H A:W3C501 3.3 34.3 1.0
N A:GLY134 3.3 27.6 1.0
CG2 A:VAL139 3.3 26.9 1.0
O A:HOH639 3.3 22.1 1.0
C A:SER133 3.4 28.4 1.0
O A:GLY132 3.4 28.0 1.0
C A:GLY132 3.5 28.3 1.0
N A:SER133 3.6 28.0 1.0
CA A:SER133 3.7 28.3 0.6
CA A:SER133 3.7 28.3 0.4
O A:SER133 3.9 28.8 1.0
O A:HOH652 3.9 18.2 1.0
CA A:GLY134 3.9 27.6 1.0
CB A:VAL139 3.9 26.6 1.0
N3 A:W3C501 4.1 28.5 1.0
CA A:GLY132 4.3 28.7 1.0
C5 A:W3C501 4.4 28.1 1.0
O A:GLY137 4.5 24.8 1.0
H12 A:W3C501 4.5 31.2 1.0
H6 A:W3C501 4.6 35.6 1.0
N A:VAL139 4.7 25.3 1.0
OE1 A:GLN197 4.7 33.5 1.0
C14 A:W3C501 4.8 28.2 1.0
CG1 A:VAL139 4.9 27.0 1.0
N A:GLY132 4.9 28.6 1.0
H5 A:W3C501 4.9 36.2 1.0
CA A:VAL139 5.0 26.0 1.0
C10 A:W3C501 5.0 28.7 1.0
C9 A:W3C501 5.0 28.8 1.0

Fluorine binding site 3 out of 7 in 8out

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Fluorine binding site 3 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.1
occ:1.00
 F4 A:W3C501 0.0 29.1 1.0
C8 A:W3C501 1.3 29.1 1.0
F5 A:W3C501 2.1 28.9 1.0
F3 A:W3C501 2.1 29.4 1.0
C7 A:W3C501 2.4 29.0 1.0
H A:W3C501 2.7 34.3 1.0
C6 A:W3C501 2.8 28.5 1.0
H5 A:W3C501 2.9 36.2 1.0
H6 A:W3C501 2.9 35.6 1.0
CA A:GLY132 3.1 28.7 1.0
C A:GLY132 3.1 28.3 1.0
C10 A:W3C501 3.1 28.7 1.0
N3 A:W3C501 3.3 28.5 1.0
O A:GLY132 3.3 28.0 1.0
N A:GLY132 3.4 28.6 1.0
O A:VAL131 3.6 29.3 1.0
O1 A:W3C501 3.6 29.2 1.0
C9 A:W3C501 3.6 28.8 1.0
C A:VAL131 3.7 29.2 1.0
N2 A:W3C501 3.7 28.2 1.0
N A:SER133 3.7 28.0 1.0
H4 A:W3C501 3.7 33.2 1.0
CG2 A:VAL131 3.9 29.7 1.0
C14 A:W3C501 4.3 28.2 1.0
CB A:VAL139 4.3 26.6 1.0
C5 A:W3C501 4.5 28.1 1.0
CG2 A:VAL139 4.5 26.9 1.0
CA A:SER133 4.5 28.3 0.6
CA A:SER133 4.5 28.3 0.4
C11 A:W3C501 4.6 28.9 1.0
C A:SER133 4.6 28.4 1.0
C13 A:W3C501 4.7 28.8 1.0
H10 A:W3C501 4.7 34.6 1.0
CB A:VAL131 4.7 29.5 1.0
C12 A:W3C501 4.7 28.7 1.0
H7 A:W3C501 4.7 35.9 1.0
CA A:VAL131 4.7 29.3 1.0
O A:HOH672 4.8 33.2 1.0
O A:SER133 4.8 28.8 1.0

Fluorine binding site 4 out of 7 in 8out

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Fluorine binding site 4 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.4
occ:1.00
 F3 A:W3C501 0.0 29.4 1.0
C8 A:W3C501 1.3 29.1 1.0
F5 A:W3C501 2.1 28.9 1.0
F4 A:W3C501 2.1 29.1 1.0
C7 A:W3C501 2.4 29.0 1.0
H A:W3C501 2.6 34.3 1.0
O1 A:W3C501 2.8 29.2 1.0
O A:SER133 3.1 28.8 1.0
H4 A:W3C501 3.1 33.2 1.0
N A:SER133 3.2 28.0 1.0
C A:SER133 3.3 28.4 1.0
C A:GLY132 3.4 28.3 1.0
H6 A:W3C501 3.6 35.6 1.0
O A:HOH672 3.7 33.2 1.0
C6 A:W3C501 3.7 28.5 1.0
CA A:GLY132 3.7 28.7 1.0
CA A:SER133 3.8 28.3 0.6
CA A:SER133 3.8 28.3 0.4
N A:GLY134 3.9 27.6 1.0
O A:GLY132 4.0 28.0 1.0
CA A:GLY134 4.3 27.6 1.0
C10 A:W3C501 4.3 28.7 1.0
H5 A:W3C501 4.4 36.2 1.0
N2 A:W3C501 4.5 28.2 1.0
N3 A:W3C501 4.6 28.5 1.0
O A:HOH669 4.7 38.5 1.0
N A:GLY132 4.7 28.6 1.0
C9 A:W3C501 4.9 28.8 1.0
O A:VAL131 4.9 29.3 1.0
O A:HOH639 5.0 22.1 1.0

Fluorine binding site 5 out of 7 in 8out

Go back to Fluorine Binding Sites List in 8out
Fluorine binding site 5 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.0
occ:1.00
 F A:W3C501 0.0 29.0 1.0
C A:W3C501 1.3 28.8 1.0
F1 A:W3C501 2.1 28.9 1.0
F2 A:W3C501 2.1 28.9 1.0
O A:W3C501 2.2 28.3 1.0
CE A:MET190 3.0 32.4 1.0
OE1 A:GLN136 3.1 29.2 1.0
CD A:GLN136 3.2 28.8 1.0
NE2 A:GLN136 3.2 28.4 1.0
C1 A:W3C501 3.5 28.1 1.0
SD A:MET190 3.5 35.1 1.0
H2 A:W3C501 3.5 30.7 1.0
CD A:LYS152 3.8 41.1 1.0
O A:HOH629 3.9 27.7 1.0
CB A:GLN136 4.0 25.8 1.0
CB A:LYS152 4.1 33.0 1.0
CG A:GLN136 4.2 27.1 1.0
H12 A:W3C501 4.2 31.2 1.0
N A:W3C501 4.3 27.9 1.0
C15 A:W3C501 4.3 28.0 1.0
CG A:LYS152 4.3 36.9 1.0
C2 A:W3C501 4.3 27.9 1.0
CE A:LYS152 4.8 45.5 1.0
NZ A:LYS152 5.0 48.1 1.0

Fluorine binding site 6 out of 7 in 8out

Go back to Fluorine Binding Sites List in 8out
Fluorine binding site 6 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.9
occ:1.00
 F1 A:W3C501 0.0 28.9 1.0
C A:W3C501 1.3 28.8 1.0
F A:W3C501 2.1 29.0 1.0
F2 A:W3C501 2.1 28.9 1.0
O A:W3C501 2.2 28.3 1.0
H12 A:W3C501 2.5 31.2 1.0
C1 A:W3C501 2.9 28.1 1.0
C15 A:W3C501 3.0 28.0 1.0
CG2 A:VAL139 3.5 26.9 1.0
O A:HOH652 3.5 18.2 1.0
O A:HOH639 3.6 22.1 1.0
NE2 A:GLN136 3.8 28.4 1.0
CB A:GLN136 3.8 25.8 1.0
CD A:GLN136 4.0 28.8 1.0
C2 A:W3C501 4.2 27.9 1.0
CG A:GLN136 4.3 27.1 1.0
C4 A:W3C501 4.4 27.9 1.0
H2 A:W3C501 4.4 30.7 1.0
OE1 A:GLN136 4.4 29.2 1.0
O A:HOH624 4.5 30.8 1.0
CB A:VAL139 4.7 26.6 1.0
CG1 A:VAL139 4.7 27.0 1.0
CE A:MET190 4.7 32.4 1.0
N A:W3C501 4.8 27.9 1.0
CA A:GLN136 4.8 25.2 1.0
CB A:LYS152 4.9 33.0 1.0
N2 A:W3C501 4.9 28.2 1.0
O A:GLN136 5.0 25.2 1.0

Fluorine binding site 7 out of 7 in 8out

Go back to Fluorine Binding Sites List in 8out
Fluorine binding site 7 out of 7 in the Crystal Structure of Dlk in Complex with Compound 22


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 Dlk in Complex with Compound 22 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.9
occ:1.00
 F2 A:W3C501 0.0 28.9 1.0
C A:W3C501 1.3 28.8 1.0
F A:W3C501 2.1 29.0 1.0
F1 A:W3C501 2.1 28.9 1.0
O A:W3C501 2.2 28.3 1.0
C1 A:W3C501 2.7 28.1 1.0
CE A:MET190 3.1 32.4 1.0
H2 A:W3C501 3.3 30.7 1.0
C15 A:W3C501 3.4 28.0 1.0
C2 A:W3C501 3.4 27.9 1.0
H12 A:W3C501 3.5 31.2 1.0
N A:W3C501 3.7 27.9 1.0
CB A:LYS152 3.9 33.0 1.0
CB A:ALA150 4.0 27.9 1.0
CG2 A:VAL139 4.1 26.9 1.0
SD A:MET190 4.2 35.1 1.0
CG1 A:VAL139 4.2 27.0 1.0
C4 A:W3C501 4.5 27.9 1.0
N1 A:W3C501 4.5 27.6 1.0
H1 A:W3C501 4.6 30.9 1.0
CA A:LYS152 4.6 31.2 1.0
N A:LYS152 4.6 30.0 1.0
CB A:VAL139 4.7 26.6 1.0
CG A:LYS152 4.8 36.9 1.0
C A:VAL151 4.8 29.3 1.0
C A:ALA150 4.9 27.9 1.0
C3 A:W3C501 4.9 27.7 1.0
CD A:LYS152 4.9 41.1 1.0
N A:VAL151 5.0 27.9 1.0

Reference:

K.Le, M.J.Soth, J.B.Cross, G.Liu, W.J.Ray, J.Ma, S.G.Goodwani, P.J.Acton, V.Buggia-Prevot, O.Akkermans, J.Barker, M.L.Conner, Y.Jiang, Z.Liu, P.Mcewan, J.Warner-Schmidt, A.Xu, M.Zebisch, C.J.Heijnen, B.Abrahams, P.Jones. Discovery of Iacs-52825, A Potent and Selective Dlk Inhibitor For Treatment of Chemotherapy-Induced Peripheral Neuropathy. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37436942
DOI: 10.1021/ACS.JMEDCHEM.3C00788
Page generated: Fri Aug 2 21:15:38 2024

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