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M3K8_HUMAN_65_395

Mitogen-activated protein kinase kinase kinase 8 [Protein kinase superfamily. STE Ser/Thr protein kinase family. MAP kinase kinase kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (M3K8_HUMAN):D: Protein kinase (143:150, 152, 165, 167, 207:210, 213, 214, 217, 257, 258, 260, 269, 270)
132:134
132:134, 143:150, 152, 165, 167, 207:210, 213, 214, 217, 257, 258, 260, 269, 270

Full PDB list

4y83, 4y85, 5iu2

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
1
3
2
L
1
3
4
F
1
4
3
I
1
4
4
P
1
4
5
R
1
4
6
G
1
4
7
F
1
4
9
G
1
5
0
V
1
5
2
A
1
6
5
K
1
6
7
M
2
0
7
E
2
0
8
A
2
0
9
G
2
1
0
G
2
1
3
S
2
1
4
E
2
1
7
S
2
5
7
N
2
5
8
V
2
6
0
V
2
6
9
D
2
7
0
[1]4y85.a 49924 . . . . . . . . . . . . . . . . . . . . . . . .
[2]4y83.a 49b23 . . . . . . . . . . . . . . . . . . . . . . . .
[3]5iu2.a 6da37 . . . . . . . . . . . . . . . . . . . . . . . .

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
W
1
3
2
K
1
3
3
L
1
3
4
F
1
4
3
I
1
4
4
P
1
4
5
R
1
4
6
G
1
4
7
A
1
4
8
F
1
4
9
G
1
5
0
V
1
5
2
A
1
6
5
K
1
6
7
M
2
0
7
E
2
0
8
A
2
0
9
G
2
1
0
G
2
1
3
S
2
1
4
E
2
1
7
S
2
5
7
N
2
5
8
V
2
6
0
V
2
6
9
D
2
7
0
[1]4y85.a . . . . . * * * * * . . . . . . . . . . . . . . . .
[2]4y83.a . . . . * . * * . . . . . . . . . . . . . . . . . .
[3]5iu2.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
4y85.a:499
4y83.a:49b
5iu2.a:6da
[1] 4y85.a
0
0.5 9.5
[2] 4y83.a 0.2
0
7.5
[3] 5iu2.a 1.2 2.6
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
4y85.a
4y83.a
5iu2.a
[1] 4y85.a
0
.31 .45
[2] 4y83.a .31
0
.40
[3] 5iu2.a .45 .40
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
4y85.a
4y83.a
5iu2.a
[1] 4y85.a
0
2.1 7.1
[2] 4y83.a 2.1
0
6.8
[3] 5iu2.a 7.1 6.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.1 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
4y85.a
4y83.a
5iu2.a
[1] 4y85.a
0
3.5 7.7
[2] 4y83.a 3.5
0
8.0
[3] 5iu2.a 7.7 8.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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