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M3K12_HUMAN_113_402

Mitogen-activated protein kinase kinase kinase 12 [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 (M3K12_HUMAN):D: Protein kinase (131:137, 139, 150, 152, 174, 190:197, 200, 243)131:137, 139, 150, 152, 174, 190:197, 200, 243

Full PDB list

5cen, 5ceo, 5cep, 5ceq, 5vo1, 5vo2

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
V
1
3
1
G
1
3
2
S
1
3
3
G
1
3
4
Q
1
3
6
V
1
3
9
A
1
5
0
I
1
7
4
M
1
9
0
E
1
9
1
F
1
9
2
C
1
9
3
A
1
9
4
Q
1
9
5
G
1
9
6
Q
1
9
7
L
2
4
3
[1]5cen.a none . . . . . . . . . . . . . . . . .
[1]5ceo.a 50d32 . . . . . . . . . . . . . . . . .
[1]5cep.a 50e25 . . . . . . . . . . . . . . . . .
[1]5ceq.a 50f29 . . . . . . . . . . . . . . . . .
[1]5vo1.a 9fs29 . . . . . . . . . . . . . . . . .
[1]5vo2.a 9fv29 . . . . . . . . . . . . . . . . .

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
1
3
1
G
1
3
2
S
1
3
3
G
1
3
4
A
1
3
5
Q
1
3
6
G
1
3
7
V
1
3
9
A
1
5
0
K
1
5
2
I
1
7
4
M
1
9
0
E
1
9
1
F
1
9
2
C
1
9
3
A
1
9
4
Q
1
9
5
G
1
9
6
Q
1
9
7
E
2
0
0
L
2
4
3
[1]5cen.a . . * . . . . . . . . . . . . . . . . . .
[1]5ceo.a . . . . . . . . . . . . . . . . . . . . .
[1]5cep.a . . . . . . . . . . . . . . . . . . . . .
[1]5ceq.a . . . . . . . . . . . . . . . . . . . . .
[1]5vo1.a . . . . . . . . . . . . . . . . . . . . .
[1]5vo2.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
5cen.a is apo
5ceo.a:50d
5cep.a:50e
5ceq.a:50f
5vo1.a:9fs
5vo2.a:9fv
[1] 5cen.a
-
2.6 0.7 1.3 1.3 1.4
[1] 5ceo.a -
0
0 0 0.1 0
[1] 5cep.a - 0.8
0
0.3 0.1 0
[1] 5ceq.a - 0.1 0
0
0.1 0
[1] 5vo1.a - 0.2 0 0
0
0
[1] 5vo2.a - 0.2 0 0 0
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
5cen.a
5ceo.a
5cep.a
5ceq.a
5vo1.a
5vo2.a
[1] 5cen.a
0
.18 .19 .17 .16 .16
[1] 5ceo.a .18
0
.04 0 .01 .01
[1] 5cep.a .19 .04
0
.03 .03 .03
[1] 5ceq.a .17 0 .03
0
.01 .01
[1] 5vo1.a .16 .01 .03 .01
0
0
[1] 5vo2.a .16 .01 .03 .01 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
5cen.a
5ceo.a
5cep.a
5ceq.a
5vo1.a
5vo2.a
[1] 5cen.a
0
1.6 1.8 1.5 1.6 1.7
[1] 5ceo.a 1.6
0
1.0 0.6 0.7 0.8
[1] 5cep.a 1.8 1.0
0
0.6 0.5 0.5
[1] 5ceq.a 1.5 0.6 0.6
0
0.3 0.4
[1] 5vo1.a 1.6 0.7 0.5 0.3
0
0.3
[1] 5vo2.a 1.7 0.8 0.5 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue 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
5cen.a
5ceo.a
5cep.a
5ceq.a
5vo1.a
5vo2.a
[1] 5cen.a
0
1.6 2.1 2.1 2.1 2.2
[1] 5ceo.a 1.6
0
1.7 1.5 1.6 1.6
[1] 5cep.a 2.1 1.7
0
0.7 0.6 0.7
[1] 5ceq.a 2.1 1.5 0.7
0
0.5 0.6
[1] 5vo1.a 2.1 1.6 0.6 0.5
0
0.5
[1] 5vo2.a 2.2 1.6 0.7 0.6 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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