Fluorine in PDB 8v2l: Crystal Structure of IRAK4 Kinase Domain with Compound 8

Enzymatic activity of Crystal Structure of IRAK4 Kinase Domain with Compound 8

All present enzymatic activity of Crystal Structure of IRAK4 Kinase Domain with Compound 8:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of IRAK4 Kinase Domain with Compound 8, PDB code: 8v2l was solved by M.M.Weiss, X.Zheng, C.M.Browne, V.Campbell, D.Chen, B.Enerson, X.Fei, X.Huang, C.R.Klaus, H.Li, M.Mayo, A.A.Mcdonald, A.Paul, K.Sharma, Y.Shi, A.Slavin, D.M.Walter, K.Yuan, Y.Zhang, X.Zhu, J.Kelleher, N.Ji, D.Walker, N.Mainolfi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.85 / 2.43
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 84.735, 113.477, 134.828, 90, 90, 90
R / Rfree (%) 25.3 / 30.2

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 IRAK4 Kinase Domain with Compound 8 (pdb code 8v2l). 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 IRAK4 Kinase Domain with Compound 8, PDB code: 8v2l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 8v2l

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Fluorine binding site 1 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:39.7
occ:1.00
 F1 A:YK0501 0.0 39.7 1.0
C17 A:YK0501 1.4 41.1 1.0
F2 A:YK0501 2.3 46.0 1.0
F3 A:YK0501 2.3 44.1 1.0
C16 A:YK0501 2.4 41.4 1.0
N4 A:YK0501 2.9 38.3 1.0
CG2 A:VAL200 3.0 39.7 1.0
CG1 A:VAL200 3.2 39.5 1.0
CB A:LYS213 3.4 45.1 1.0
CD A:LYS213 3.4 50.9 1.0
C15 A:YK0501 3.4 39.6 1.0
CE1 A:TYR262 3.7 34.4 1.0
CB A:VAL200 3.7 39.1 1.0
CE A:LYS213 3.7 56.4 1.0
NZ A:LYS213 3.8 58.2 1.0
CD1 A:TYR262 3.9 33.0 1.0
CG A:LYS213 3.9 45.5 1.0
C12 A:YK0501 4.1 37.5 1.0
CA A:LYS213 4.2 40.8 1.0
N A:LYS213 4.4 38.0 1.0
CZ A:TYR262 4.5 34.6 1.0
CB A:ALA211 4.5 36.5 1.0
C14 A:YK0501 4.5 37.5 1.0
C1 A:YK0501 4.6 40.0 1.0
CA A:VAL200 4.8 39.9 1.0
CG A:TYR262 4.8 31.6 1.0
C13 A:YK0501 4.8 38.9 1.0
O A:HOH603 4.9 34.1 1.0
OH A:TYR262 4.9 40.2 1.0

Fluorine binding site 2 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 2 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:46.0
occ:1.00
 F2 A:YK0501 0.0 46.0 1.0
C17 A:YK0501 1.4 41.1 1.0
F1 A:YK0501 2.3 39.7 1.0
F3 A:YK0501 2.3 44.1 1.0
C16 A:YK0501 2.4 41.4 1.0
NZ A:LYS213 2.7 58.2 1.0
C15 A:YK0501 2.7 39.6 1.0
CE A:LYS213 3.3 56.4 1.0
CE1 A:TYR262 3.4 34.4 1.0
CZ A:TYR262 3.4 34.6 1.0
N4 A:YK0501 3.6 38.3 1.0
OH A:TYR262 3.7 40.2 1.0
O A:HOH603 3.8 34.1 1.0
CD A:LYS213 3.9 50.9 1.0
CD1 A:TYR262 3.9 33.0 1.0
CE2 A:TYR262 4.0 34.0 1.0
CB A:SER328 4.1 30.9 1.0
C14 A:YK0501 4.1 37.5 1.0
N A:ASP329 4.4 29.3 1.0
CG A:TYR262 4.4 31.6 1.0
OG A:SER328 4.4 35.8 1.0
CD2 A:TYR262 4.5 31.9 1.0
CB A:LYS213 4.6 45.1 1.0
C12 A:YK0501 4.6 37.5 1.0
CD1 A:LEU318 4.7 36.2 1.0
CG A:LYS213 4.8 45.5 1.0
CA A:ASP329 4.9 32.5 1.0
CG2 A:VAL200 4.9 39.7 1.0
C13 A:YK0501 4.9 38.9 1.0
CG2 A:VAL246 4.9 33.5 1.0

Fluorine binding site 3 out of 12 in 8v2l

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Fluorine binding site 3 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:44.1
occ:1.00
 F3 A:YK0501 0.0 44.1 1.0
C17 A:YK0501 1.4 41.1 1.0
F2 A:YK0501 2.3 46.0 1.0
F1 A:YK0501 2.3 39.7 1.0
C16 A:YK0501 2.3 41.4 1.0
N4 A:YK0501 2.7 38.3 1.0
O A:HOH603 2.8 34.1 1.0
C15 A:YK0501 3.5 39.6 1.0
CD1 A:LEU318 3.6 36.2 1.0
CG2 A:VAL200 3.7 39.7 1.0
C3 A:YK0501 3.7 40.8 1.0
NZ A:LYS213 3.8 58.2 1.0
C12 A:YK0501 3.9 37.5 1.0
C1 A:YK0501 4.0 40.0 1.0
OG A:SER328 4.0 35.8 1.0
CB A:SER328 4.3 30.9 1.0
CD A:LYS213 4.4 50.9 1.0
CG1 A:VAL200 4.4 39.5 1.0
N3 A:YK0501 4.5 38.4 1.0
C2 A:YK0501 4.5 40.5 1.0
CE A:LYS213 4.5 56.4 1.0
C14 A:YK0501 4.5 37.5 1.0
CB A:VAL200 4.6 39.1 1.0
CG A:LEU318 4.7 36.2 1.0
C13 A:YK0501 4.7 38.9 1.0
CD2 A:LEU318 4.8 35.7 1.0
C11 A:YK0501 4.8 39.1 1.0

Fluorine binding site 4 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 4 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:35.5
occ:1.00
 F1 B:YK0501 0.0 35.5 1.0
C17 B:YK0501 1.4 35.4 1.0
F3 B:YK0501 2.2 38.1 1.0
F2 B:YK0501 2.2 39.9 1.0
C16 B:YK0501 2.3 34.9 1.0
N4 B:YK0501 2.9 32.9 1.0
CG2 B:VAL200 3.0 35.3 1.0
CG1 B:VAL200 3.1 32.3 1.0
C15 B:YK0501 3.3 35.6 1.0
CD B:LYS213 3.4 46.9 1.0
CB B:LYS213 3.4 39.8 1.0
CE1 B:TYR262 3.6 33.9 1.0
CB B:VAL200 3.7 33.5 1.0
CD1 B:TYR262 3.7 32.9 1.0
CE B:LYS213 3.8 52.3 1.0
CG B:LYS213 4.0 42.0 1.0
NZ B:LYS213 4.0 55.5 1.0
C12 B:YK0501 4.1 33.3 1.0
CA B:LYS213 4.2 38.3 1.0
CZ B:TYR262 4.4 34.7 1.0
N B:LYS213 4.4 35.0 1.0
C14 B:YK0501 4.5 35.7 1.0
C1 B:YK0501 4.5 37.3 1.0
CB B:ALA211 4.5 34.5 1.0
CG B:TYR262 4.7 32.5 1.0
O B:HOH617 4.7 43.7 1.0
CA B:VAL200 4.8 34.0 1.0
C13 B:YK0501 4.8 34.5 1.0
OH B:TYR262 4.9 37.2 1.0
O B:HOH606 4.9 38.0 1.0

Fluorine binding site 5 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 5 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:39.9
occ:1.00
 F2 B:YK0501 0.0 39.9 1.0
C17 B:YK0501 1.4 35.4 1.0
F1 B:YK0501 2.2 35.5 1.0
F3 B:YK0501 2.3 38.1 1.0
C16 B:YK0501 2.4 34.9 1.0
C15 B:YK0501 2.7 35.6 1.0
NZ B:LYS213 2.8 55.5 1.0
O B:HOH606 2.8 38.0 1.0
CE1 B:TYR262 3.3 33.9 1.0
CE B:LYS213 3.3 52.3 1.0
CZ B:TYR262 3.4 34.7 1.0
O B:HOH617 3.6 43.7 1.0
N4 B:YK0501 3.6 32.9 1.0
OH B:TYR262 3.7 37.2 1.0
CD B:LYS213 3.8 46.9 1.0
CD1 B:TYR262 3.8 32.9 1.0
CE2 B:TYR262 3.9 35.0 1.0
CB B:SER328 4.0 31.7 1.0
C14 B:YK0501 4.1 35.7 1.0
N B:ASP329 4.3 31.2 1.0
CG B:TYR262 4.4 32.5 1.0
OG B:SER328 4.4 36.5 1.0
CD2 B:TYR262 4.4 34.0 1.0
CD1 B:LEU318 4.6 27.5 1.0
CB B:LYS213 4.6 39.8 1.0
C12 B:YK0501 4.7 33.3 1.0
CG2 B:VAL246 4.8 34.0 1.0
CG2 B:VAL200 4.8 35.3 1.0
CG B:LYS213 4.8 42.0 1.0
CA B:ASP329 4.9 33.2 1.0
C13 B:YK0501 4.9 34.5 1.0
CA B:SER328 5.0 31.9 1.0
OE2 B:GLU233 5.0 46.9 1.0

Fluorine binding site 6 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 6 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:38.1
occ:1.00
 F3 B:YK0501 0.0 38.1 1.0
C17 B:YK0501 1.4 35.4 1.0
F1 B:YK0501 2.2 35.5 1.0
F2 B:YK0501 2.3 39.9 1.0
C16 B:YK0501 2.3 34.9 1.0
N4 B:YK0501 2.8 32.9 1.0
O B:HOH617 2.8 43.7 1.0
C15 B:YK0501 3.5 35.6 1.0
CG2 B:VAL200 3.5 35.3 1.0
CD1 B:LEU318 3.6 27.5 1.0
C1 B:YK0501 3.9 37.3 1.0
C3 B:YK0501 3.9 37.8 1.0
C12 B:YK0501 4.0 33.3 1.0
NZ B:LYS213 4.0 55.5 1.0
OG B:SER328 4.0 36.5 1.0
CG1 B:VAL200 4.3 32.3 1.0
CB B:SER328 4.3 31.7 1.0
CD B:LYS213 4.3 46.9 1.0
CB B:VAL200 4.5 33.5 1.0
C2 B:YK0501 4.5 37.6 1.0
N3 B:YK0501 4.6 35.0 1.0
CE B:LYS213 4.6 52.3 1.0
C14 B:YK0501 4.6 35.7 1.0
CA B:GLY195 4.6 99.3 1.0
CG B:LEU318 4.7 27.2 1.0
CD2 B:LEU318 4.8 26.4 1.0
C13 B:YK0501 4.8 34.5 1.0
O B:HOH606 4.9 38.0 1.0
C11 B:YK0501 4.9 33.4 1.0

Fluorine binding site 7 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 7 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:37.5
occ:1.00
 F1 C:YK0501 0.0 37.5 1.0
C17 C:YK0501 1.4 37.4 1.0
F3 C:YK0501 2.3 39.0 1.0
F2 C:YK0501 2.3 39.4 1.0
C16 C:YK0501 2.3 38.0 1.0
N4 C:YK0501 3.0 35.6 1.0
CG2 C:VAL200 3.1 49.8 1.0
C15 C:YK0501 3.3 36.3 1.0
CG1 C:VAL200 3.4 50.2 1.0
CD C:LYS213 3.5 54.6 1.0
CE1 C:TYR262 3.5 42.0 1.0
CB C:LYS213 3.6 50.8 1.0
CE C:LYS213 3.7 58.5 1.0
CD1 C:TYR262 3.7 42.2 1.0
CB C:VAL200 3.9 49.8 1.0
NZ C:LYS213 3.9 64.7 1.0
CG C:LYS213 4.1 51.8 1.0
C12 C:YK0501 4.2 35.8 1.0
CZ C:TYR262 4.3 41.9 1.0
C14 C:YK0501 4.4 38.2 1.0
CA C:LYS213 4.5 49.0 1.0
C1 C:YK0501 4.5 43.3 1.0
CG C:TYR262 4.6 42.3 1.0
CB C:ALA211 4.6 50.5 1.0
N C:LYS213 4.7 47.8 1.0
OH C:TYR262 4.7 47.6 1.0
C13 C:YK0501 4.8 37.5 1.0
O C:HOH648 5.0 32.4 1.0
CA C:VAL200 5.0 53.4 1.0

Fluorine binding site 8 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 8 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:39.4
occ:1.00
 F2 C:YK0501 0.0 39.4 1.0
C17 C:YK0501 1.4 37.4 1.0
F3 C:YK0501 2.3 39.0 1.0
F1 C:YK0501 2.3 37.5 1.0
C16 C:YK0501 2.3 38.0 1.0
C15 C:YK0501 2.6 36.3 1.0
NZ C:LYS213 3.2 64.7 1.0
N4 C:YK0501 3.5 35.6 1.0
CB C:SER328 3.7 38.5 1.0
CZ C:TYR262 3.7 41.9 1.0
CE1 C:TYR262 3.8 42.0 1.0
CE C:LYS213 3.8 58.5 1.0
OH C:TYR262 4.0 47.6 1.0
C14 C:YK0501 4.0 38.2 1.0
OG C:SER328 4.0 43.5 1.0
CE2 C:TYR262 4.1 43.1 1.0
N C:ASP329 4.1 41.2 1.0
CD1 C:TYR262 4.2 42.2 1.0
CD C:LYS213 4.3 54.6 1.0
CD1 C:LEU318 4.3 33.2 1.0
CD2 C:TYR262 4.5 42.5 1.0
CG C:TYR262 4.6 42.3 1.0
C12 C:YK0501 4.6 35.8 1.0
CG2 C:VAL246 4.7 42.5 1.0
CA C:SER328 4.7 37.8 1.0
CA C:ASP329 4.7 43.7 1.0
O C:HOH648 4.8 32.4 1.0
C13 C:YK0501 4.8 37.5 1.0
C C:SER328 4.8 37.6 1.0
CB C:ASP329 5.0 49.3 1.0

Fluorine binding site 9 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 9 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:39.0
occ:1.00
 F3 C:YK0501 0.0 39.0 1.0
C17 C:YK0501 1.4 37.4 1.0
F1 C:YK0501 2.3 37.5 1.0
F2 C:YK0501 2.3 39.4 1.0
C16 C:YK0501 2.4 38.0 1.0
N4 C:YK0501 2.7 35.6 1.0
O C:HOH648 2.8 32.4 1.0
C15 C:YK0501 3.5 36.3 1.0
CD1 C:LEU318 3.6 33.2 1.0
CG2 C:VAL200 3.6 49.8 1.0
C1 C:YK0501 3.7 43.3 1.0
C3 C:YK0501 3.9 42.6 1.0
C12 C:YK0501 4.0 35.8 1.0
OG C:SER328 4.2 43.5 1.0
NZ C:LYS213 4.3 64.7 1.0
CG1 C:VAL200 4.4 50.2 1.0
C2 C:YK0501 4.4 43.0 1.0
CB C:SER328 4.4 38.5 1.0
CB C:VAL200 4.6 49.8 1.0
N3 C:YK0501 4.6 40.0 1.0
CD C:LYS213 4.6 54.6 1.0
C14 C:YK0501 4.6 38.2 1.0
CG C:LEU318 4.7 32.9 1.0
CE C:LYS213 4.8 58.5 1.0
CD2 C:LEU318 4.8 32.4 1.0
C13 C:YK0501 4.8 37.5 1.0
C11 C:YK0501 4.9 37.0 1.0
O C:HOH649 4.9 56.8 1.0

Fluorine binding site 10 out of 12 in 8v2l

Go back to Fluorine Binding Sites List in 8v2l
Fluorine binding site 10 out of 12 in the Crystal Structure of IRAK4 Kinase Domain with Compound 8


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 IRAK4 Kinase Domain with Compound 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F501

b:45.5
occ:1.00
 F1 D:YK0501 0.0 45.5 1.0
C17 D:YK0501 1.4 42.4 1.0
F3 D:YK0501 2.3 48.1 1.0
F2 D:YK0501 2.3 45.3 1.0
C16 D:YK0501 2.3 38.9 1.0
N4 D:YK0501 2.9 38.0 1.0
CG2 D:VAL200 2.9 59.0 1.0
CG1 D:VAL200 3.3 58.5 1.0
C15 D:YK0501 3.3 36.5 1.0
CD D:LYS213 3.6 61.8 1.0
CB D:VAL200 3.7 58.6 1.0
CB D:LYS213 3.8 59.1 1.0
CE1 D:TYR262 3.9 42.3 1.0
O D:HOH650 4.0 45.6 1.0
NZ D:LYS213 4.0 68.3 1.0
CE D:LYS213 4.0 65.4 1.0
CD1 D:TYR262 4.1 41.3 1.0
C12 D:YK0501 4.1 37.0 1.0
CG D:LYS213 4.3 59.2 1.0
C1 D:YK0501 4.4 42.4 1.0
C14 D:YK0501 4.5 37.8 1.0
CZ D:TYR262 4.6 42.2 1.0
CA D:LYS213 4.7 57.8 1.0
CB D:ALA211 4.7 48.7 1.0
C13 D:YK0501 4.8 38.2 1.0
CA D:VAL200 4.9 61.4 1.0
N D:LYS213 4.9 52.2 1.0
CG D:TYR262 4.9 40.3 1.0
OH D:TYR262 5.0 45.5 1.0

Reference:

M.M.Weiss, X.Zheng, N.Ji, C.M.Browne, V.Campbell, D.Chen, B.Enerson, X.Fei, X.Huang, C.R.Klaus, H.Li, M.Mayo, A.A.Mcdonald, A.Paul, H.Rong, K.Sharma, Y.Shi, A.Slavin, D.M.Walther, K.Yuan, Y.Zhang, X.Zhu, J.Kelleher, D.Walker, N.Mainolfi. Discovery of Kt-413, A Targeted Protein Degrader of IRAK4 and Imid Substrates Targeting MYD88 Mutant Diffuse Large B-Cell Lymphoma J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
DOI: 10.1021/ACS.JMEDCHEM.3C01823
Page generated: Sat Aug 3 01:16:14 2024

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