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M3K7_HUMAN_27_330

Mitogen-activated protein kinase kinase kinase 7 [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 (M3K7_HUMAN):R: Interaction with MAPK8IP1 (42:47, 50, 61:63, 73, 76:78, 80, 81, 89, 90, 102, 104:111, 114, 144, 152:155, 160, 161, 163, 173:179)
D: Protein kinase (42:47, 50, 61:63, 73, 76:78, 80, 81, 89, 90, 102, 104:111, 114, 144, 152:155, 160, 161, 163, 173:179)
42:47, 50, 61:63, 73, 76:78, 80, 81, 89, 90, 102, 104:111, 114, 144, 152:155, 160, 161, 163, 173:179

Full PDB list

2eva, 2yiy, 4gs6, 4l3p, 4l52, 4l53, 4o91, 5e7r, 5gjd, 5gjf, 5gjg, 5jgd, 5v5n (Pocketome entry); 5j7s, 5j8i, 5j9l, 5jga, 5jgb, 5jh6, 5jk3 (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
4
2
G
4
3
R
4
4
G
4
5
F
4
7
V
5
0
A
6
1
I
6
2
K
6
3
V
7
6
E
7
7
Q
8
0
L
8
1
I
8
9
V
9
0
L
1
0
2
M
1
0
4
E
1
0
5
Y
1
0
6
A
1
0
7
E
1
0
8
G
1
0
9
G
1
1
0
S
1
1
1
N
1
1
4
L
1
4
4
L
1
5
2
I
1
5
3
H
1
5
4
P
1
6
0
N
1
6
1
L
1
6
3
I
1
7
3
C
1
7
4
D
1
7
5
F
1
7
6
[1]2eva.a adn19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2yiy.a yiy33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gs6.a 1fm26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . .
[1]4l3p.a 1uh30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4l52.a 1ul33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4l53.a 1uo26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4o91.a ng239 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5e7r.a 5kw32 . . . - - . . . . - - - . . . . . . . . . . . . . . . . . . . . . * . .
[1]5gjd.a 6v337 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5gjf.a 6v443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5gjg.a 6v542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5jgd.a 6kd32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]5v5n.a edh24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
V
4
2
G
4
3
R
4
4
G
4
5
A
4
6
F
4
7
V
5
0
A
6
1
I
6
2
K
6
3
A
7
3
V
7
6
E
7
7
L
7
8
Q
8
0
L
8
1
I
8
9
V
9
0
L
1
0
2
M
1
0
4
E
1
0
5
Y
1
0
6
A
1
0
7
E
1
0
8
G
1
0
9
G
1
1
0
S
1
1
1
N
1
1
4
L
1
4
4
L
1
5
2
I
1
5
3
H
1
5
4
R
1
5
5
P
1
6
0
N
1
6
1
L
1
6
3
I
1
7
3
C
1
7
4
D
1
7
5
F
1
7
6
G
1
7
7
T
1
7
8
A
1
7
9
[1]2eva.a . . . . . . . . . . . . * . . * . . . * . . . . . . . . . . . . * . . . . . * * . * -
[1]2yiy.a . . . . . . . . . . . . * . . * . . . . . . . . . . . . . . . . . . . . . . . * . - -
[1]4gs6.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . * . . . . * * * . - -
[1]4l3p.a . . . . . . . . . . . . * . . . . . . * . . . . . . . . . . . . * . . . . . . * * - -
[1]4l52.a . . . . . . . . . . . . * . . * . . . * . . . . . . . . . . . . . . . . . . . * * * -
[1]4l53.a . . . . . . . . . * . . * . . . . . . * . . . . . . . . . . . . . . . . . . . * * . -
[1]4o91.a . . . . . . . . . . . . * . . * . . . . . . . . . . . . . . . . . . . . . . . * . - -
[1]5e7r.a . . . - - - . . . . - - - - - . . . . * . . . . . . . . . . . . * . . . . * * * . - -
[1]5gjd.a . . . . . . . . . . . . * . . * . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]5gjf.a . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . * . . .
[1]5gjg.a . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . * * * - - -
[2]5jgd.a . . . . . . . . . * . * * . . . . . . * . . . . . . . . . . . . . . . . . . * * . . *
[2]5v5n.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
2eva.a:adn
2yiy.a:yiy
4gs6.a:1fm
4l3p.a:1uh
4l52.a:1ul
4l53.a:1uo
4o91.a:ng2
5e7r.a:5kw
5gjd.a:6v3
5gjf.a:6v4
5gjg.a:6v5
5jgd.a:6kd
5v5n.a:edh
[1] 2eva.a
0.1
6.7 1.0 1.5 1.3 1.4 11 2.0 7.0 4.6 4.8 0.3 0.6
[1] 2yiy.a 1.7
0
4.4 4.7 4.3 4.1 0.7 4.1 1.6 1.8 5.2 2.3 1.9
[1] 4gs6.a 0.1 6.0
0.3
0.5 0.5 0.4 10 0.8 7.4 4.3 3.7 0.3 0.3
[1] 4l3p.a 0.5 6.6 0.7
0
0 0.2 9.9 1.2 5.7 4.5 2.7 0.8 0.9
[1] 4l52.a 0.6 7.2 0.6 0.1
0
0 11 1.4 8.1 4.5 3.8 1.0 0.7
[1] 4l53.a 0.3 6.5 0.5 0 0
0
9.5 0.9 7.3 4.6 2.5 0.6 0.6
[1] 4o91.a 1.4 0.5 3.9 4.0 4.0 4.4
0.1
4.0 0.5 2.0 4.3 1.8 1.1
[1] 5e7r.a 0.1 4.1 0.9 1.8 1.5 1.6 6.0
0.4
4.4 4.3 4.2 0.6 0.9
[1] 5gjd.a 2.1 1.0 4.0 4.4 4.5 4.4 0.7 3.6
0
2.6 4.4 1.4 1.1
[1] 5gjf.a 0.6 1.1 1.7 0.8 0.7 0.9 1.3 1.0 0.3
0
2.9 0.3 0.2
[1] 5gjg.a 1.0 5.8 0.9 0 0 0 6.1 0.5 5.3 4.6
0
0 0.1
[2] 5jgd.a 1.2 11 1.5 1.6 1.3 1.3 13 2.4 11 7.4 6.4
0
0.2
[2] 5v5n.a 1.1 10 1.2 1.2 1.2 1.2 11 1.4 10 6.2 6.4 0
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
2eva.a
2yiy.a
4gs6.a
4l3p.a
4l52.a
4l53.a
4o91.a
5e7r.a
5gjd.a
5gjf.a
5gjg.a
5jgd.a
5v5n.a
[1] 2eva.a
0
.25 .16 .19 .16 .23 .22 .22 .22 .27 .22 .29 .26
[1] 2yiy.a .25
0
.24 .23 .24 .25 .07 .22 .08 .17 .19 .42 .35
[1] 4gs6.a .16 .24
0
.12 .13 .16 .20 .21 .20 .24 .22 .34 .23
[1] 4l3p.a .19 .23 .12
0
.12 .12 .20 .21 .20 .24 .20 .34 .25
[1] 4l52.a .16 .24 .13 .12
0
.12 .20 .27 .20 .24 .24 .33 .27
[1] 4l53.a .23 .25 .16 .12 .12
0
.21 .24 .22 .25 .18 .37 .30
[1] 4o91.a .22 .07 .20 .20 .20 .21
0
.21 .05 .13 .16 .40 .34
[1] 5e7r.a .22 .22 .21 .21 .27 .24 .21
0
.21 .23 .11 .41 .36
[1] 5gjd.a .22 .08 .20 .20 .20 .22 .05 .21
0
.12 .17 .39 .33
[1] 5gjf.a .27 .17 .24 .24 .24 .25 .13 .23 .12
0
.19 .45 .39
[1] 5gjg.a .22 .19 .22 .20 .24 .18 .16 .11 .17 .19
0
.41 .37
[2] 5jgd.a .29 .42 .34 .34 .33 .37 .40 .41 .39 .45 .41
0
.16
[2] 5v5n.a .26 .35 .23 .25 .27 .30 .34 .36 .33 .39 .37 .16
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.3 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
2eva.a
2yiy.a
4gs6.a
4l3p.a
4l52.a
4l53.a
4o91.a
5e7r.a
5gjd.a
5gjf.a
5gjg.a
5jgd.a
5v5n.a
[1] 2eva.a
0
1.9 0.4 0.7 1.1 1.0 1.8 1.4 2.2 2.8 2.2 1.4 1.3
[1] 2yiy.a 1.9
0
2.0 2.2 2.4 2.2 0.8 1.7 1.1 1.1 2.9 2.3 2.3
[1] 4gs6.a 0.4 2.0
0
0.8 0.9 0.8 1.9 1.4 1.6 2.1 2.1 1.2 1.1
[1] 4l3p.a 0.7 2.2 0.8
0
0.8 0.8 2.1 1.6 1.9 2.3 2.1 1.5 1.4
[1] 4l52.a 1.1 2.4 0.9 0.8
0
0.5 2.3 1.9 2.4 3.0 2.4 1.7 1.6
[1] 4l53.a 1.0 2.2 0.8 0.8 0.5
0
2.2 1.7 2.3 2.9 2.2 1.6 1.4
[1] 4o91.a 1.8 0.8 1.9 2.1 2.3 2.2
0
1.7 0.8 1.1 2.7 2.2 2.2
[1] 5e7r.a 1.4 1.7 1.4 1.6 1.9 1.7 1.7
0
1.6 1.5 1.2 1.3 1.2
[1] 5gjd.a 2.2 1.1 1.6 1.9 2.4 2.3 0.8 1.6
0
1.4 2.6 2.9 2.2
[1] 5gjf.a 2.8 1.1 2.1 2.3 3.0 2.9 1.1 1.5 1.4
0
2.4 3.5 2.9
[1] 5gjg.a 2.2 2.9 2.1 2.1 2.4 2.2 2.7 1.2 2.6 2.4
0
2.5 2.3
[2] 5jgd.a 1.4 2.3 1.2 1.5 1.7 1.6 2.2 1.3 2.9 3.5 2.5
0
0.5
[2] 5v5n.a 1.3 2.3 1.1 1.4 1.6 1.4 2.2 1.2 2.2 2.9 2.3 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
2eva.a
2yiy.a
4gs6.a
4l3p.a
4l52.a
4l53.a
4o91.a
5e7r.a
5gjd.a
5gjf.a
5gjg.a
5jgd.a
5v5n.a
[1] 2eva.a
0
2.6 1.0 0.8 1.2 1.2 2.5 2.4 2.8 3.5 2.9 1.5 1.5
[1] 2yiy.a 2.6
0
2.6 2.7 2.6 2.7 1.4 2.1 1.5 1.9 3.8 2.8 2.8
[1] 4gs6.a 1.0 2.6
0
1.0 1.0 0.9 2.6 2.2 2.4 2.9 2.8 1.4 1.3
[1] 4l3p.a 0.8 2.7 1.0
0
1.0 0.9 2.6 2.3 2.5 2.9 2.8 1.6 1.5
[1] 4l52.a 1.2 2.6 1.0 1.0
0
0.7 2.7 2.5 2.8 3.4 2.9 1.7 1.6
[1] 4l53.a 1.2 2.7 0.9 0.9 0.7
0
2.6 2.5 2.7 3.3 2.6 1.6 1.5
[1] 4o91.a 2.5 1.4 2.6 2.6 2.7 2.6
0
2.2 1.0 1.5 3.6 2.8 2.7
[1] 5e7r.a 2.4 2.1 2.2 2.3 2.5 2.5 2.2
0
2.1 1.9 2.0 2.3 2.3
[1] 5gjd.a 2.8 1.5 2.4 2.5 2.8 2.7 1.0 2.1
0
1.7 3.6 3.2 2.7
[1] 5gjf.a 3.5 1.9 2.9 2.9 3.4 3.3 1.5 1.9 1.7
0
3.6 3.8 3.4
[1] 5gjg.a 2.9 3.8 2.8 2.8 2.9 2.6 3.6 2.0 3.6 3.6
0
3.1 2.9
[2] 5jgd.a 1.5 2.8 1.4 1.6 1.7 1.6 2.8 2.3 3.2 3.8 3.1
0
0.9
[2] 5v5n.a 1.5 2.8 1.3 1.5 1.6 1.5 2.7 2.3 2.7 3.4 2.9 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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