Fluorine in PDB 7yaw: Crystal Structure of Zak in Complex with Compound Yh-180

Enzymatic activity of Crystal Structure of Zak in Complex with Compound Yh-180

All present enzymatic activity of Crystal Structure of Zak in Complex with Compound Yh-180:
2.7.11.25;

Protein crystallography data

The structure of Crystal Structure of Zak in Complex with Compound Yh-180, PDB code: 7yaw was solved by L.L.Kong, C.H.Yun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.69 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.675, 142.772, 179.132, 90, 90, 90
R / Rfree (%) 20.7 / 24.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Zak in Complex with Compound Yh-180 (pdb code 7yaw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Zak in Complex with Compound Yh-180, PDB code: 7yaw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7yaw

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Fluorine binding site 1 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:28.8
occ:1.00
 F08 D:IGS401 0.0 28.8 1.0
C07 D:IGS401 1.4 27.3 1.0
C06 D:IGS401 2.4 27.2 1.0
C09 D:IGS401 2.4 33.7 1.0
N10 D:IGS401 2.8 32.4 1.0
C13 D:IGS401 3.0 24.1 1.0
CB D:ALA43 3.3 28.1 1.0
C D:ALA43 3.3 27.4 1.0
O D:ALA43 3.3 26.8 1.0
OG1 D:THR82 3.4 22.9 1.0
N D:VAL44 3.5 27.3 1.0
N D:LYS45 3.6 26.3 1.0
C05 D:IGS401 3.6 32.3 1.0
C39 D:IGS401 3.7 36.4 1.0
O D:ILE80 3.7 22.8 1.0
N11 D:IGS401 3.8 29.2 1.0
C D:VAL44 3.8 29.0 1.0
CA D:VAL44 3.9 30.5 1.0
CG2 D:THR82 3.9 20.6 1.0
CA D:ALA43 3.9 28.4 1.0
C04 D:IGS401 4.1 37.3 1.0
CB D:LYS45 4.2 31.3 1.0
C14 D:IGS401 4.2 29.9 1.0
CB D:THR82 4.2 24.9 1.0
N D:THR82 4.2 18.1 1.0
CG1 D:VAL30 4.2 30.2 1.0
CA D:LYS45 4.4 26.3 1.0
N12 D:IGS401 4.5 30.5 1.0
O D:VAL44 4.5 27.2 1.0
C D:ILE80 4.7 23.3 1.0
CA D:THR82 4.8 25.5 1.0
F40 D:IGS401 4.8 39.2 1.0
C D:VAL81 4.8 25.0 1.0
CG2 D:VAL30 4.9 30.4 1.0
CA D:VAL81 4.9 21.3 1.0
N D:ALA43 4.9 27.2 1.0

Fluorine binding site 2 out of 8 in 7yaw

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Fluorine binding site 2 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:39.2
occ:1.00
 F40 D:IGS401 0.0 39.2 1.0
C39 D:IGS401 1.4 36.4 1.0
C09 D:IGS401 2.4 33.7 1.0
C04 D:IGS401 2.4 37.3 1.0
N10 D:IGS401 2.8 32.4 1.0
N03 D:IGS401 2.9 39.1 1.0
N11 D:IGS401 2.9 29.2 1.0
N D:ASP151 3.0 31.9 1.0
O01 D:IGS401 3.0 46.6 1.0
CA D:ASP151 3.5 33.6 1.0
S02 D:IGS401 3.6 40.7 1.0
C07 D:IGS401 3.7 27.3 1.0
C05 D:IGS401 3.7 32.3 1.0
CB D:CYS150 3.7 23.9 1.0
C13 D:IGS401 3.8 24.1 1.0
C D:CYS150 3.9 29.5 1.0
N12 D:IGS401 4.0 30.5 1.0
OD1 D:ASP151 4.0 48.7 1.0
CB D:ASP151 4.1 36.3 1.0
CA D:CYS150 4.1 29.1 1.0
CE D:LYS45 4.1 47.3 1.0
C06 D:IGS401 4.2 27.2 1.0
NZ D:LYS45 4.3 56.6 1.0
O53 D:IGS401 4.4 36.6 1.0
CG D:ASP151 4.4 50.4 1.0
C14 D:IGS401 4.4 29.9 1.0
CG2 D:ILE66 4.5 21.6 1.0
SG D:CYS150 4.6 26.1 1.0
F08 D:IGS401 4.8 28.8 1.0
C D:ASP151 4.9 34.3 1.0
C41 D:IGS401 4.9 35.2 1.0

Fluorine binding site 3 out of 8 in 7yaw

Go back to Fluorine Binding Sites List in 7yaw
Fluorine binding site 3 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:19.9
occ:1.00
 F08 A:IGS401 0.0 19.9 1.0
C07 A:IGS401 1.4 24.2 1.0
C09 A:IGS401 2.3 23.0 1.0
C06 A:IGS401 2.4 24.5 1.0
N10 A:IGS401 2.8 23.6 1.0
C13 A:IGS401 3.3 20.3 1.0
N A:LYS45 3.4 22.6 1.0
C A:ALA43 3.5 21.2 1.0
O A:ALA43 3.6 20.3 1.0
C39 A:IGS401 3.6 26.4 1.0
N11 A:IGS401 3.6 24.9 1.0
CB A:ALA43 3.6 23.9 1.0
N A:VAL44 3.6 20.8 1.0
C A:VAL44 3.6 26.9 1.0
C05 A:IGS401 3.7 25.5 1.0
OG1 A:THR82 3.7 23.1 1.0
O A:ILE80 3.7 22.1 1.0
CB A:LYS45 3.8 20.3 1.0
CA A:VAL44 3.8 23.0 1.0
CG1 A:VAL30 3.9 33.5 1.0
CG2 A:THR82 4.1 17.9 1.0
C04 A:IGS401 4.1 26.9 1.0
CA A:LYS45 4.1 23.5 1.0
CA A:ALA43 4.2 22.1 1.0
C14 A:IGS401 4.3 27.0 1.0
O A:VAL44 4.4 29.2 1.0
N12 A:IGS401 4.4 25.7 1.0
N A:THR82 4.4 17.1 1.0
CB A:THR82 4.4 22.2 1.0
F40 A:IGS401 4.7 29.8 1.0
C A:ILE80 4.7 21.1 1.0
CG2 A:VAL30 4.9 32.4 1.0
CB A:VAL30 4.9 31.6 1.0
CE A:LYS45 5.0 36.1 1.0

Fluorine binding site 4 out of 8 in 7yaw

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Fluorine binding site 4 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.8
occ:1.00
 F40 A:IGS401 0.0 29.8 1.0
C39 A:IGS401 1.4 26.4 1.0
C04 A:IGS401 2.3 26.9 1.0
N03 A:IGS401 2.4 35.5 1.0
C09 A:IGS401 2.4 23.0 1.0
N10 A:IGS401 2.7 23.6 1.0
N A:ASP151 2.9 22.4 1.0
CB A:CYS150 3.1 24.3 1.0
N11 A:IGS401 3.1 24.9 1.0
C13 A:IGS401 3.5 20.3 1.0
CA A:CYS150 3.6 23.1 1.0
C05 A:IGS401 3.6 25.5 1.0
C07 A:IGS401 3.6 24.2 1.0
CA A:ASP151 3.7 22.8 1.0
C A:CYS150 3.7 23.1 1.0
CG2 A:ILE66 3.9 16.2 1.0
SG A:CYS150 4.0 25.5 1.0
S02 A:IGS401 4.0 30.3 1.0
N12 A:IGS401 4.0 25.7 1.0
C06 A:IGS401 4.1 24.5 1.0
C14 A:IGS401 4.2 27.0 1.0
CB A:ASP151 4.3 27.2 1.0
NZ A:LYS45 4.5 37.9 1.0
CE A:LYS45 4.6 36.1 1.0
OD1 A:ASP151 4.6 41.6 1.0
O01 A:IGS401 4.7 31.9 1.0
O53 A:IGS401 4.7 42.0 1.0
F08 A:IGS401 4.7 19.9 1.0
O A:CYS150 4.9 19.1 1.0
CB A:ILE66 4.9 21.8 1.0
N A:CYS150 5.0 21.5 1.0

Fluorine binding site 5 out of 8 in 7yaw

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Fluorine binding site 5 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:28.6
occ:1.00
 F08 B:IGS401 0.0 28.6 1.0
C07 B:IGS401 1.4 24.8 1.0
C09 B:IGS401 2.3 26.3 1.0
C06 B:IGS401 2.4 28.1 1.0
N10 B:IGS401 2.8 21.9 1.0
C13 B:IGS401 3.4 25.5 1.0
N11 B:IGS401 3.5 24.6 1.0
N B:LYS45 3.5 27.9 1.0
C39 B:IGS401 3.6 26.5 1.0
CB B:ALA43 3.6 24.2 1.0
CB B:LYS45 3.6 32.2 1.0
O B:ALA43 3.6 24.3 1.0
C05 B:IGS401 3.7 25.6 1.0
C B:ALA43 3.7 23.5 1.0
O B:ILE80 3.8 19.8 1.0
OG1 B:THR82 3.8 20.6 1.0
C B:VAL44 3.9 24.9 1.0
N B:VAL44 4.0 22.7 1.0
CG2 B:THR82 4.1 23.4 1.0
C04 B:IGS401 4.1 28.8 1.0
CA B:LYS45 4.1 31.0 1.0
CG1 B:VAL30 4.1 29.4 1.0
CA B:VAL44 4.2 24.8 1.0
CA B:ALA43 4.3 25.7 1.0
C14 B:IGS401 4.3 24.5 1.0
N12 B:IGS401 4.4 26.5 1.0
CG2 B:VAL30 4.4 31.1 1.0
O B:VAL44 4.5 29.5 1.0
CB B:THR82 4.6 24.1 1.0
N B:THR82 4.6 20.4 1.0
F40 B:IGS401 4.7 29.3 1.0
CE B:LYS45 4.8 37.5 1.0
C B:ILE80 4.8 23.5 1.0
CG B:LYS45 4.8 36.8 1.0
CB B:VAL30 4.9 33.0 1.0

Fluorine binding site 6 out of 8 in 7yaw

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Fluorine binding site 6 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:29.3
occ:1.00
 F40 B:IGS401 0.0 29.3 1.0
C39 B:IGS401 1.4 26.5 1.0
C04 B:IGS401 2.3 28.8 1.0
C09 B:IGS401 2.4 26.3 1.0
N03 B:IGS401 2.5 33.5 1.0
N10 B:IGS401 2.7 21.9 1.0
N B:ASP151 3.0 19.5 1.0
CB B:CYS150 3.1 21.7 1.0
N11 B:IGS401 3.1 24.6 1.0
C13 B:IGS401 3.4 25.5 1.0
CA B:CYS150 3.5 23.9 1.0
C05 B:IGS401 3.6 25.6 1.0
C07 B:IGS401 3.6 24.8 1.0
C B:CYS150 3.7 24.2 1.0
CA B:ASP151 3.8 26.4 1.0
CG2 B:ILE66 3.8 21.0 1.0
SG B:CYS150 3.9 24.0 1.0
N12 B:IGS401 4.0 26.5 1.0
C06 B:IGS401 4.1 28.1 1.0
S02 B:IGS401 4.2 35.4 1.0
C14 B:IGS401 4.2 24.5 1.0
CB B:ASP151 4.3 24.8 1.0
F08 B:IGS401 4.7 28.6 1.0
OD1 B:ASP151 4.8 42.0 1.0
O53 B:IGS401 4.8 41.9 1.0
O01 B:IGS401 4.8 36.3 1.0
CB B:ILE66 4.8 23.1 1.0
O B:CYS150 4.9 19.0 1.0
N B:CYS150 5.0 20.2 1.0

Fluorine binding site 7 out of 8 in 7yaw

Go back to Fluorine Binding Sites List in 7yaw
Fluorine binding site 7 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:28.9
occ:1.00
 F08 C:IGS401 0.0 28.9 1.0
C07 C:IGS401 1.4 27.5 1.0
C09 C:IGS401 2.3 29.4 1.0
C06 C:IGS401 2.5 33.1 1.0
N10 C:IGS401 2.8 30.6 1.0
C13 C:IGS401 3.4 31.5 1.0
N C:LYS45 3.5 27.7 1.0
CB C:ALA43 3.6 22.4 1.0
C39 C:IGS401 3.6 32.2 1.0
N11 C:IGS401 3.6 30.8 1.0
O C:ALA43 3.6 24.0 1.0
C C:ALA43 3.7 23.3 1.0
C05 C:IGS401 3.7 32.5 1.0
OG1 C:THR82 3.7 21.5 1.0
CB C:LYS45 3.8 34.0 1.0
C C:VAL44 3.9 28.2 1.0
O C:ILE80 3.9 25.0 1.0
N C:VAL44 3.9 24.5 1.0
CG1 C:VAL30 4.0 34.9 1.0
CG2 C:THR82 4.0 23.5 1.0
CA C:VAL44 4.1 25.6 1.0
C04 C:IGS401 4.1 29.6 1.0
CA C:LYS45 4.2 32.1 1.0
CA C:ALA43 4.3 26.6 1.0
CE C:LYS45 4.4 49.2 1.0
C14 C:IGS401 4.4 28.6 1.0
N12 C:IGS401 4.4 34.4 1.0
CB C:THR82 4.5 24.7 1.0
CG2 C:VAL30 4.5 42.5 1.0
O C:VAL44 4.5 30.5 1.0
N C:THR82 4.6 21.5 1.0
F40 C:IGS401 4.7 30.5 1.0
C C:ILE80 4.8 24.5 1.0
CB C:VAL30 4.8 42.6 1.0

Fluorine binding site 8 out of 8 in 7yaw

Go back to Fluorine Binding Sites List in 7yaw
Fluorine binding site 8 out of 8 in the Crystal Structure of Zak in Complex with Compound Yh-180


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 Zak in Complex with Compound Yh-180 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:30.5
occ:1.00
 F40 C:IGS401 0.0 30.5 1.0
C39 C:IGS401 1.4 32.2 1.0
C04 C:IGS401 2.3 29.6 1.0
C09 C:IGS401 2.3 29.4 1.0
N03 C:IGS401 2.5 35.6 1.0
N10 C:IGS401 2.6 30.6 1.0
N11 C:IGS401 3.0 30.8 1.0
N C:ASP151 3.1 24.8 1.0
C13 C:IGS401 3.4 31.5 1.0
CB C:CYS150 3.5 23.4 1.0
C07 C:IGS401 3.6 27.5 1.0
C05 C:IGS401 3.6 32.5 1.0
CA C:ASP151 3.8 29.9 1.0
N12 C:IGS401 3.9 34.4 1.0
CA C:CYS150 3.9 25.9 1.0
C C:CYS150 4.0 26.0 1.0
CG2 C:ILE66 4.0 22.8 1.0
C14 C:IGS401 4.1 28.6 1.0
C06 C:IGS401 4.1 33.1 1.0
S02 C:IGS401 4.2 46.2 1.0
SG C:CYS150 4.3 27.1 1.0
CB C:ASP151 4.3 34.4 1.0
NZ C:LYS45 4.5 50.4 1.0
F08 C:IGS401 4.7 28.9 1.0
O01 C:IGS401 4.7 39.5 1.0
CE C:LYS45 4.8 49.2 1.0
OD1 C:ASP151 4.9 47.8 1.0
O53 C:IGS401 5.0 47.7 1.0

Reference:

Y.Zhou, H.Yu, A.C.Vind, L.Kong, Y.Liu, X.Song, Z.Tu, C.Yun, J.B.Smaill, Q.W.Zhang, K.Ding, S.Bekker-Jensen, X.Lu. Rational Design of Covalent Kinase Inhibitors By An Integrated Computational Workflow (Kin-Cov). J.Med.Chem. V. 66 7405 2023.
ISSN: ISSN 0022-2623
PubMed: 37220641
DOI: 10.1021/ACS.JMEDCHEM.3C00088
Page generated: Fri Aug 2 15:43:05 2024

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