Iodine in PDB 3zh8: A Novel Small Molecule Apkc Inhibitor

Enzymatic activity of A Novel Small Molecule Apkc Inhibitor

All present enzymatic activity of A Novel Small Molecule Apkc Inhibitor:
2.7.11.13;

Protein crystallography data

The structure of A Novel Small Molecule Apkc Inhibitor, PDB code: 3zh8 was solved by S.Kjaer, A.G.Purkiss, B.Kostelecky, P.P.Knowles, E.Soriano, J.Murray-Rust, N.Q.Mcdonald, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.23 / 2.74
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 113.580, 113.580, 82.410, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 25.7

Other elements in 3zh8:

The structure of A Novel Small Molecule Apkc Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Iodine atom in the A Novel Small Molecule Apkc Inhibitor (pdb code 3zh8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 12 binding sites of Iodine where determined in the A Novel Small Molecule Apkc Inhibitor, PDB code: 3zh8:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 1 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I901

b:61.4
occ:1.00
 N A:ASP558 3.7 67.2 1.0
CG2 A:VAL562 4.1 62.8 1.0
CB A:ASP558 4.3 65.8 1.0
CA A:ASP557 4.4 67.0 1.0
CG2 A:ILE561 4.4 66.5 1.0
CB A:SER317 4.5 65.4 1.0
OD1 A:ASP557 4.5 66.4 1.0
CA A:ASP558 4.6 69.7 1.0
C A:ASP557 4.6 67.7 1.0
CB A:ASP557 4.6 68.5 1.0
CB A:ILE561 4.6 68.6 1.0
O A:ASP558 4.7 75.1 1.0
CG A:ASP557 4.9 67.5 1.0
OG A:SER317 4.9 67.0 1.0
CG A:LYS277 4.9 53.6 1.0
CD A:LYS277 5.0 53.6 1.0
CD1 A:ILE561 5.0 66.4 1.0

Iodine binding site 2 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 2 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I902

b:87.2
occ:1.00
 NE A:ARG347 3.9 65.1 1.0
CA A:PHE348 4.1 50.7 1.0
CB A:PHE348 4.2 52.5 1.0
CZ A:ARG347 4.3 70.1 1.0
NH2 A:ARG347 4.3 71.8 1.0
N A:PHE348 4.3 48.7 1.0
CD1 A:PHE348 4.3 60.5 1.0
CG1 A:VAL526 4.5 58.2 1.0
CD A:ARG347 4.5 60.6 1.0
CG A:ARG347 4.6 55.4 1.0
O A:GLU344 4.8 59.5 1.0
CG2 A:VAL516 4.8 77.6 1.0
CG A:PHE348 4.8 56.2 1.0
C A:ARG347 4.9 48.8 1.0

Iodine binding site 3 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 3 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I903

b:29.9
occ:0.29
 CD2 A:TYR256 0.9 63.7 0.9
CE2 A:TYR256 1.1 63.6 0.9
CG A:TYR256 1.4 62.6 0.9
CZ A:TYR256 1.6 61.5 0.9
CD1 A:TYR256 1.9 61.4 0.9
CE1 A:TYR256 2.0 61.1 0.9
CB A:TYR256 2.9 62.8 1.0
OH A:TYR256 2.9 59.5 0.9
N A:ALA257 3.5 55.7 1.0
H9A A:C581582 3.6 48.0 1.0
CA A:TYR256 3.7 61.2 1.0
N A:TYR256 3.8 60.1 1.0
CB A:ALA257 3.8 53.2 1.0
C A:TYR256 3.9 60.8 1.0
CA A:ALA257 4.3 53.8 1.0
C9 A:C581582 4.7 40.0 1.0
O A:TYR256 4.9 64.6 1.0
H9 A:C581582 4.9 48.0 1.0
H8A A:C581582 5.0 45.9 1.0

Iodine binding site 4 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 4 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I904

b:53.3
occ:0.53
 CA A:ASP387 3.1 48.6 1.0
N A:ASP387 3.3 50.1 1.0
N A:TYR388 3.5 44.3 1.0
CD A:LYS274 3.5 51.1 1.0
CZ A:PHE297 3.5 47.0 1.0
NZ A:LYS274 3.8 50.6 1.0
C A:ASP387 3.8 47.5 1.0
S A:C581582 4.1 43.1 1.0
OG1 A:THR386 4.2 50.7 1.0
CE1 A:PHE297 4.2 60.3 1.0
CE A:LYS274 4.2 50.6 1.0
CB A:ASP387 4.3 48.4 1.0
CD2 A:TYR388 4.3 49.5 1.0
OD1 A:ASP387 4.4 50.0 1.0
CE2 A:PHE297 4.4 54.2 1.0
C A:THR386 4.5 49.1 1.0
CA A:TYR388 4.8 42.1 1.0
CG A:LYS274 4.8 51.6 1.0
CG A:ASP387 4.9 49.8 1.0
CB A:LYS274 4.9 52.5 1.0
CG A:TYR388 4.9 47.3 1.0
CE2 A:TYR388 4.9 50.8 1.0
CB A:TYR388 4.9 45.4 1.0

Iodine binding site 5 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 5 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I901

b:56.7
occ:1.00
 O B:HOH2002 3.5 27.8 1.0
N B:ASP558 3.6 59.4 1.0
CG2 B:VAL562 4.0 52.7 1.0
CB B:ASP558 4.2 58.6 1.0
CG2 B:ILE561 4.2 52.3 1.0
CA B:ASP557 4.3 61.3 1.0
CB B:SER317 4.4 51.7 1.0
OD1 B:ASP557 4.4 61.1 1.0
CB B:ILE561 4.4 55.4 1.0
CA B:ASP558 4.5 61.3 1.0
C B:ASP557 4.5 62.1 1.0
O B:ASP558 4.6 60.6 1.0
CB B:ASP557 4.6 61.6 1.0
CD B:LYS277 4.7 42.9 1.0
OG B:SER317 4.7 46.0 1.0
CD1 B:ILE561 4.8 56.5 1.0
NH2 B:ARG318 4.8 70.4 1.0
CG B:ASP557 4.9 61.3 1.0
C B:ASP558 5.0 63.0 1.0
N B:VAL562 5.0 55.0 1.0

Iodine binding site 6 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 6 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I902

b:70.9
occ:1.00
 NH1 B:ARG347 3.7 67.7 1.0
CZ B:ARG347 3.9 63.6 1.0
CA B:PHE348 4.0 49.1 1.0
NE B:ARG347 4.1 58.5 1.0
CB B:PHE348 4.1 52.3 1.0
CD B:ARG347 4.1 55.0 1.0
N B:PHE348 4.2 46.8 1.0
CD1 B:PHE348 4.3 59.8 1.0
NH2 B:ARG347 4.5 64.0 1.0
O B:GLU344 4.7 56.6 1.0
CG1 B:VAL526 4.7 49.4 1.0
CG B:PHE348 4.7 55.1 1.0
CG2 B:VAL516 4.8 55.4 1.0
C B:ARG347 4.9 45.2 1.0

Iodine binding site 7 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 7 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I903

b:29.8
occ:0.24
 CD2 B:TYR256 1.0 57.7 0.9
CE2 B:TYR256 1.2 57.5 0.9
CG B:TYR256 1.3 57.4 0.9
CZ B:TYR256 1.6 55.9 0.9
CD1 B:TYR256 1.6 56.5 0.9
CE1 B:TYR256 1.8 56.2 0.9
CB B:TYR256 2.8 58.1 1.0
OH B:TYR256 3.0 53.8 0.9
N B:TYR256 3.6 56.2 1.0
H9A B:C581581 3.6 45.8 1.0
N B:ALA257 3.6 52.3 1.0
CA B:TYR256 3.6 58.3 1.0
C B:TYR256 3.9 58.1 1.0
CB B:ALA257 4.1 48.4 1.0
CA B:ALA257 4.5 49.5 1.0
C9 B:C581581 4.6 38.2 1.0
N B:SER255 4.7 52.0 1.0
OG B:SER255 4.8 48.9 1.0
C B:SER255 4.8 53.9 1.0
H21 B:EDO1583 4.8 80.2 1.0
H9 B:C581581 4.9 45.8 1.0
H22 B:EDO1583 4.9 80.2 1.0
O B:TYR256 5.0 61.9 1.0
H8A B:C581581 5.0 44.8 1.0

Iodine binding site 8 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 8 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I904

b:58.6
occ:0.61
 CA B:ASP387 3.0 42.7 1.0
N B:ASP387 3.1 43.6 1.0
NZ B:LYS274 3.4 46.4 1.0
N B:TYR388 3.4 40.7 1.0
CD B:LYS274 3.5 46.6 1.0
C B:ASP387 3.7 41.8 1.0
CZ B:PHE297 3.7 42.0 1.0
CD1 B:ILE323 3.8 52.2 1.0
CE B:LYS274 4.0 46.3 1.0
CB B:ASP387 4.1 40.8 1.0
S B:C581581 4.1 51.5 1.0
OG1 B:THR386 4.2 40.3 1.0
CD2 B:TYR388 4.3 46.2 1.0
OD1 B:ASP387 4.3 40.7 1.0
C B:THR386 4.4 41.5 1.0
CE1 B:PHE297 4.5 42.8 1.0
CE2 B:PHE297 4.6 42.9 1.0
CA B:TYR388 4.7 40.1 1.0
CG B:ASP387 4.8 40.3 1.0
CG B:LYS274 4.8 45.6 1.0
OE2 B:GLU293 4.8 42.5 1.0
CG B:TYR388 4.8 43.4 1.0
CE2 B:TYR388 4.9 47.1 1.0
CB B:TYR388 4.9 42.3 1.0
O B:ASP387 5.0 40.4 1.0

Iodine binding site 9 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 9 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I901

b:77.8
occ:1.00
 N C:ASP558 3.8 85.0 1.0
CG2 C:ILE561 3.9 68.9 1.0
CB C:ILE561 4.1 72.3 1.0
CG2 C:VAL562 4.2 74.7 1.0
CB C:ASP558 4.2 83.4 1.0
CD1 C:ILE561 4.2 69.6 1.0
CA C:ASP557 4.5 88.9 1.0
CA C:ASP558 4.5 85.8 1.0
OD1 C:ASP557 4.6 86.7 1.0
CB C:SER317 4.6 66.7 1.0
O C:ASP558 4.6 84.8 1.0
C C:ASP557 4.6 89.0 1.0
CG1 C:ILE561 4.7 72.4 1.0
CB C:ASP557 4.8 89.5 1.0
N C:VAL562 4.9 71.9 1.0
OG C:SER317 5.0 67.0 1.0

Iodine binding site 10 out of 12 in 3zh8

Go back to Iodine Binding Sites List in 3zh8
Iodine binding site 10 out of 12 in the A Novel Small Molecule Apkc Inhibitor


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of A Novel Small Molecule Apkc Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I902

b:72.9
occ:1.00
 CE C:MET521 3.9 53.0 1.0
CA C:PHE348 4.0 54.9 1.0
NE C:ARG347 4.1 75.2 1.0
N C:PHE348 4.2 56.6 1.0
CB C:PHE348 4.2 55.0 1.0
CG2 C:VAL516 4.3 73.2 1.0
CG C:ARG347 4.4 65.5 1.0
CD C:ARG347 4.5 70.8 1.0
CD1 C:PHE348 4.5 54.8 1.0
CG1 C:VAL526 4.6 65.0 1.0
C C:ARG347 4.6 58.0 1.0
CZ C:ARG347 4.7 79.5 1.0
O C:ARG347 4.8 56.9 1.0
CG1 C:VAL516 4.9 72.2 1.0
O C:GLU344 4.9 65.5 1.0
NH2 C:ARG347 4.9 81.0 1.0
CG C:PHE348 4.9 54.0 1.0
CB C:ARG347 4.9 62.6 1.0

Reference:

S.Kjaer, M.Linch, A.Purkiss, B.Kostelecky, P.P.Knowles, C.Rosse, P.Riou, C.Soudy, S.Kaye, B.Patel, E.Soriano, J.Murray-Rust, C.Barton, C.Dillon, J.Roffey, P.J.Parker, N.Q.Mcdonald. Adenosine-Binding Motif Mimicry and Cellular Effects of A Thieno[2,3-D]Pyrimidine-Based Chemical Inhibitor of Atypical Protein Kinase C Isozymes. Biochem.J. V. 451 329 2013.
ISSN: ISSN 0264-6021
PubMed: 23418854
DOI: 10.1042/BJ20121871
Page generated: Sun Dec 13 19:31:37 2020

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