If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

MK08_HUMAN_2_364_JIP

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (MK08_HUMAN):D: Protein kinase (30, 83, 112, 113, 117, 118, 121:123, 126, 127, 130, 131, 133, 159:163, 285:289)
323:329
30, 83, 112, 113, 117, 118, 121:123, 126, 127, 130, 131, 133, 159:163, 285:289, 323:329

Full PDB list

1ukh, 1uki, 2g01, 2gmx, 2h96, 2no3, 2xrw, 2xs0, 3elj, 3o17, 3o2m, 3pze, 3v3v, 3vud, 3vug, 3vuh, 3vui, 3vuk, 3vul, 3vum, 4awi, 4e73, 4g1w, 4hys, 4hyu, 4izy, 4l7f, 4qtd, 4ux9, 4yr8, 5len (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
1
1
2
A
1
1
3
Q
1
1
7
V
1
1
8
M
1
2
1
L
1
2
3
E
1
2
6
R
1
2
7
Y
1
3
0
Y
1
3
3
V
1
5
9
K
1
6
0
S
1
6
1
D
1
6
2
C
1
6
3
H
2
8
6
L
2
8
9
V
3
2
3
W
3
2
4
D
3
2
6
P
3
2
7
E
3
2
9
[1]2xs0.a RPSRDHLYLPLE106 . . . . . . . . . . . . . . . . . . . . . .
[1]3o2m.b PKRPTTLNLF84 . . . . . . . . . . . . . . . . . . . . . .
[1]3vui.a PKRPTTLNLF84 . . . . . . . . . . . . . . A . . . . . . .
[1]3vum.a RPKRPTTLNLF95 . . . . . . . . . . . . . . A . . . . . . .
[1]4hys.a PKRPTTLNL72 . . . . . . . . . . . . . . . - - . . . . .
[1]4ux9.a PRPTLQLPLA77 . . . . . . . . . . . . . . . . . . . . . .
[1]4ux9.b PTLQLPLA59 . . . . . . . . . . . . . . . - . . . . . .
[1]4ux9.c QRPRPTLQLPLA97 . . . . . . . . . . . . . . . - . . . . . .
[1]4ux9.d QRPRP-QLPL77 . . . . . . . . . . . . . . . - . . . . . .
[1]4yr8.c K9 . . . . . . . . . . . . . . . . . . . . . .
[1]4yr8.f KKIKN43 . . . . . . . . . . . . . . . . . . . . . .
[1]5len.b D-Y,PKRPTTLNLF103 . . . . . . . . . . . . . . . . . . . . . .
[2]4yr8.a none . . . . . . . . . . . . . . . . . . . . . .

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
K
3
0
K
8
3
D
1
1
2
A
1
1
3
Q
1
1
7
V
1
1
8
M
1
2
1
E
1
2
2
L
1
2
3
E
1
2
6
R
1
2
7
Y
1
3
0
L
1
3
1
Y
1
3
3
V
1
5
9
K
1
6
0
S
1
6
1
D
1
6
2
C
1
6
3
E
2
8
5
H
2
8
6
N
2
8
7
K
2
8
8
L
2
8
9
V
3
2
3
W
3
2
4
Y
3
2
5
D
3
2
6
P
3
2
7
S
3
2
8
E
3
2
9
[1]2xs0.a . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3o2m.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3vui.a . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . .
[1]3vum.a . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . .
[1]4hys.a . . . . . . . . . . . . . . . . . . . - - - - - . . . . . . .
[1]4ux9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ux9.b . . . . . . . . . . . . . . . . . . . - - - - . . . . . . . .
[1]4ux9.c . . . . . . . . . . . . . . . . . . . - - - - . . . . . . . .
[1]4ux9.d . . . . . . . . . * . . . . . . . . . - - . . . . . . . . . .
[1]4yr8.c . . . . . . * . . * . . . . . . . . . . . . . . . . . . . . .
[1]4yr8.f . . . . . . * . . * . . . . . . . . . - . . . . . . . . . . .
[1]5len.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4yr8.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2xs0.a:RPSRDHLYLPLE
3o2m.b:PKRPTTLNLF
3vui.a:PKRPTTLNLF
3vum.a:RPKRPTTLNLF
4hys.a:PKRPTTLNL
4ux9.a:PRPTLQLPLA
4ux9.b:PTLQLPLA
4ux9.c:QRPRPTLQLPLA
4ux9.d:QRPRP-QLPL
4yr8.c:K
4yr8.f:KKIKN
5len.b:D-Y,PKRPTTLNLF
4yr8.a is apo
[1] 2xs0.a
0
1.3 1.0 1.2 1.3 0.3 0.1 0.7 0.2 0 0.6 1.1 -
[1] 3o2m.b 0.3
0.1
0.1 0 0.3 0.1 0.2 0.4 0.3 0 0.1 0 -
[1] 3vui.a 0.8 0.4
0.1
0.3 0.1 0.5 0.4 0.6 0.6 0 0 0.1 -
[1] 3vum.a 0.5 0.3 0.1
0.5
0.6 0.4 0.3 0.6 0.6 0 0.3 0.2 -
[1] 4hys.a 0.5 0.5 0.3 0.4
0
0.2 0.1 0.6 0.4 0 0 0.2 -
[1] 4ux9.a 0.2 0.2 0.2 0.2 0.4
0
0 0.4 0.2 0 0.1 0.1 -
[1] 4ux9.b 0.3 0.9 1.1 0.9 0.8 0
0
0.7 0.3 0 0.4 0.7 -
[1] 4ux9.c 0.5 0.9 0.8 1.1 1.1 0.2 0.1
0
0.2 0 0.4 0.9 -
[1] 4ux9.d 0.3 0.4 0.5 0.4 0.5 0 0 0.6
0
0 0.4 0.4 -
[1] 4yr8.c 0.8 1.3 1.2 1.1 1.5 0.2 0.5 1.3 0.4
0
0 1.1 -
[1] 4yr8.f 0.5 0.8 1.1 0.8 1.4 0.2 0.3 1.2 0.4 0
0
0.7 -
[1] 5len.b 0.8 0.3 0.2 0.4 0.5 0.2 0.1 1.0 0.5 0 0.4
0.2
-
[2] 4yr8.a 4.3 1.0 1.4 1.1 1.8 0.4 0.4 1.7 1.6 0 0.1 6.8
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2xs0.a
3o2m.b
3vui.a
3vum.a
4hys.a
4ux9.a
4ux9.b
4ux9.c
4ux9.d
4yr8.c
4yr8.f
5len.b
4yr8.a
[1] 2xs0.a
0
.08 .08 .08 .09 .06 .02 .04 .04 .06 .08 .06 .33
[1] 3o2m.b .08
0
.02 .02 .03 .03 .08 .05 .05 .09 .10 .05 .36
[1] 3vui.a .08 .02
0
.03 .03 .04 .08 .06 .05 .08 .09 .05 .37
[1] 3vum.a .08 .02 .03
0
.04 .05 .08 .05 .05 .10 .11 .05 .38
[1] 4hys.a .09 .03 .03 .04
0
.05 .08 .07 .06 .09 .09 .05 .37
[1] 4ux9.a .06 .03 .04 .05 .05
0
.06 .06 .03 .07 .08 .04 .34
[1] 4ux9.b .02 .08 .08 .08 .08 .06
0
.04 .03 .07 .07 .06 .34
[1] 4ux9.c .04 .05 .06 .05 .07 .06 .04
0
.05 .08 .10 .06 .35
[1] 4ux9.d .04 .05 .05 .05 .06 .03 .03 .05
0
.06 .07 .03 .34
[1] 4yr8.c .06 .09 .08 .10 .09 .07 .07 .08 .06
0
.01 .10 .28
[1] 4yr8.f .08 .10 .09 .11 .09 .08 .07 .10 .07 .01
0
.10 .28
[1] 5len.b .06 .05 .05 .05 .05 .04 .06 .06 .03 .10 .10
0
.35
[2] 4yr8.a .33 .36 .37 .38 .37 .34 .34 .35 .34 .28 .28 .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.1 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
2xs0.a
3o2m.b
3vui.a
3vum.a
4hys.a
4ux9.a
4ux9.b
4ux9.c
4ux9.d
4yr8.c
4yr8.f
5len.b
4yr8.a
[1] 2xs0.a
0
2.8 3.1 2.9 1.0 3.1 1.3 1.2 2.3 2.0 1.6 0.8 2.8
[1] 3o2m.b 2.8
0
0.9 0.8 0.9 1.5 0.6 0.7 0.8 3.3 3.1 2.7 3.7
[1] 3vui.a 3.1 0.9
0
0.5 0.8 1.8 0.7 0.8 1.0 3.5 3.2 3.0 3.8
[1] 3vum.a 2.9 0.8 0.5
0
0.8 1.7 0.5 0.6 1.0 3.4 3.1 2.8 3.6
[1] 4hys.a 1.0 0.9 0.8 0.8
0
0.7 0.7 0.8 0.9 1.0 1.0 0.5 2.9
[1] 4ux9.a 3.1 1.5 1.8 1.7 0.7
0
0.3 0.4 0.8 3.4 3.3 3.0 3.8
[1] 4ux9.b 1.3 0.6 0.7 0.5 0.7 0.3
0
0.3 0.6 1.3 1.3 1.2 2.9
[1] 4ux9.c 1.2 0.7 0.8 0.6 0.8 0.4 0.3
0
0.7 1.4 1.4 1.2 2.9
[1] 4ux9.d 2.3 0.8 1.0 1.0 0.9 0.8 0.6 0.7
0
2.3 2.3 2.3 3.5
[1] 4yr8.c 2.0 3.3 3.5 3.4 1.0 3.4 1.3 1.4 2.3
0
0.3 2.0 2.8
[1] 4yr8.f 1.6 3.1 3.2 3.1 1.0 3.3 1.3 1.4 2.3 0.3
0
1.6 2.7
[1] 5len.b 0.8 2.7 3.0 2.8 0.5 3.0 1.2 1.2 2.3 2.0 1.6
0
2.8
[2] 4yr8.a 2.8 3.7 3.8 3.6 2.9 3.8 2.9 2.9 3.5 2.8 2.7 2.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
2xs0.a
3o2m.b
3vui.a
3vum.a
4hys.a
4ux9.a
4ux9.b
4ux9.c
4ux9.d
4yr8.c
4yr8.f
5len.b
4yr8.a
[1] 2xs0.a
0
3.9 4.3 4.2 1.9 3.8 2.1 2.1 3.1 2.9 2.4 1.4 3.2
[1] 3o2m.b 3.9
0
2.0 1.8 1.6 2.2 1.1 1.1 1.7 4.2 4.1 3.8 4.7
[1] 3vui.a 4.3 2.0
0
1.3 1.5 2.9 1.2 1.3 2.0 4.6 4.4 4.1 4.5
[1] 3vum.a 4.2 1.8 1.3
0
1.5 2.6 1.1 1.1 1.8 4.5 4.3 4.0 4.5
[1] 4hys.a 1.9 1.6 1.5 1.5
0
1.6 1.6 1.6 1.6 1.5 1.5 1.5 3.1
[1] 4ux9.a 3.8 2.2 2.9 2.6 1.6
0
1.0 0.9 1.1 4.1 4.0 3.7 4.4
[1] 4ux9.b 2.1 1.1 1.2 1.1 1.6 1.0
0
1.1 0.7 1.9 1.9 2.0 3.3
[1] 4ux9.c 2.1 1.1 1.3 1.1 1.6 0.9 1.1
0
1.1 2.1 2.1 1.9 3.3
[1] 4ux9.d 3.1 1.7 2.0 1.8 1.6 1.1 0.7 1.1
0
2.9 2.9 3.0 4.0
[1] 4yr8.c 2.9 4.2 4.6 4.5 1.5 4.1 1.9 2.1 2.9
0
0.5 2.8 3.3
[1] 4yr8.f 2.4 4.1 4.4 4.3 1.5 4.0 1.9 2.1 2.9 0.5
0
2.5 3.1
[1] 5len.b 1.4 3.8 4.1 4.0 1.5 3.7 2.0 1.9 3.0 2.8 2.5
0
3.2
[2] 4yr8.a 3.2 4.7 4.5 4.5 3.1 4.4 3.3 3.3 4.0 3.3 3.1 3.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...