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PKN1_HUMAN_604_942

Serine/threonine-protein kinase N1 [Protein kinase superfamily. AGC Ser/Thr protein kinase family. PKC subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PKN1_HUMAN):D: Protein kinase (621:624, 626:629, 642, 644, 679, 695:698, 701, 702, 744, 745, 747, 757, 758)621:624, 626:629, 642, 644, 679, 695:698, 701, 702, 744, 745, 747, 757, 758, 904, 908

Full PDB list

4otd, 4otg, 4oth, 4oti

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
6
2
1
G
6
2
2
R
6
2
3
G
6
2
4
F
6
2
6
G
6
2
7
K
6
2
8
V
6
2
9
A
6
4
2
K
6
4
4
V
6
7
9
M
6
9
5
E
6
9
6
Y
6
9
7
S
6
9
8
G
7
0
1
D
7
0
2
D
7
4
4
N
7
4
5
L
7
4
7
A
7
5
7
D
7
5
8
F
9
0
4
[1]4otg.a 2v933 . . . . . . . . . . . . . . . . . . . . . . -
[1]4oth.a drn33 . . . . . . . . . . . . . . . . . . . . . . .
[2]4otd.a none . . . . . . . . . . . . . . . . . . . . . . .
[2]4oti.a mi123 . . . . . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

[download in TSV format]
   
PDB.ch
A1
L
6
2
1
G
6
2
2
R
6
2
3
G
6
2
4
F
6
2
6
G
6
2
7
K
6
2
8
V
6
2
9
A
6
4
2
K
6
4
4
V
6
7
9
M
6
9
5
E
6
9
6
Y
6
9
7
S
6
9
8
G
7
0
1
D
7
0
2
D
7
4
4
N
7
4
5
L
7
4
7
A
7
5
7
D
7
5
8
F
9
0
4
F
9
0
8
[1]4otg.a . . . . * . . . . . . . . . . . . . . . . . - .
[1]4oth.a . . . . * . . . . . . . . . . . . . . . . . * .
[2]4otd.a . . . . . . . . . . . . . . . . . . . . . . * .
[2]4oti.a . . . . . . . . . . . . . . . . . . . . . . * .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4otg.a:2v9
4oth.a:drn
4otd.a is apo
4oti.a:mi1
[1] 4otg.a
0
1.3 - 3.2
[1] 4oth.a 3.6
0.1
- 3.4
[2] 4otd.a 3.3 1.9
-
0.3
[2] 4oti.a 3.3 1.2 -
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
4otg.a
4oth.a
4otd.a
4oti.a
[1] 4otg.a
0
.20 .28 .33
[1] 4oth.a .20
0
.22 .19
[2] 4otd.a .28 .22
0
.09
[2] 4oti.a .33 .19 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4otg.a
4oth.a
4otd.a
4oti.a
[1] 4otg.a
0
1.6 1.2 1.3
[1] 4oth.a 1.6
0
1.1 1.1
[2] 4otd.a 1.2 1.1
0
1.1
[2] 4oti.a 1.3 1.1 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4otg.a
4oth.a
4otd.a
4oti.a
[1] 4otg.a
0
2.1 1.7 2.4
[1] 4oth.a 2.1
0
1.0 2.2
[2] 4otd.a 1.7 1.0
0
1.1
[2] 4oti.a 2.4 2.2 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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