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BMP2K_HUMAN_40_344

BMP-2-inducible protein kinase [Protein kinase superfamily. Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BMP2K_HUMAN):D: Protein kinase (57:61, 63:65, 77, 79, 109, 130:137, 140, 182, 184, 185, 187, 197, 198)57:61, 63:65, 77, 79, 109, 130:137, 140, 182, 184, 185, 187, 197, 198

Full PDB list

4w9w, 4w9x, 5i3o, 5i3r, 5ikw

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
5
7
A
5
8
E
5
9
G
6
0
S
6
3
T
6
4
V
6
5
A
7
7
K
7
9
V
1
0
9
M
1
3
0
E
1
3
1
Y
1
3
2
C
1
3
3
R
1
3
4
A
1
3
5
G
1
3
6
Q
1
3
7
N
1
4
0
E
1
8
4
N
1
8
5
L
1
8
7
C
1
9
7
D
1
9
8
[1]4w9w.a ydj25 . . . . . . . . . . . . . . . . . . . . . . . .
[1]4w9x.a 3jw26 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i3o.a idv28 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i3r.a idk29 . . . . . . . . . . . . . . . . . . . . . . . .
[1]5ikw.a 6bu28 . . . . . . . . . . . . . . . . . . . . . . . .

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
5
7
A
5
8
E
5
9
G
6
0
G
6
1
S
6
3
T
6
4
V
6
5
A
7
7
K
7
9
V
1
0
9
M
1
3
0
E
1
3
1
Y
1
3
2
C
1
3
3
R
1
3
4
A
1
3
5
G
1
3
6
Q
1
3
7
N
1
4
0
K
1
8
2
E
1
8
4
N
1
8
5
L
1
8
7
C
1
9
7
D
1
9
8
[1]4w9w.a . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]4w9x.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i3o.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5i3r.a . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]5ikw.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
4w9w.a:ydj
4w9x.a:3jw
5i3o.a:idv
5i3r.a:idk
5ikw.a:6bu
[1] 4w9w.a
0
0.6 1.3 0.6 0.5
[1] 4w9x.a 0
0
0.8 0.5 0.5
[1] 5i3o.a 0.6 2.8
0.1
0.3 0.6
[1] 5i3r.a 0.5 2.2 0.1
0.1
0
[1] 5ikw.a 0.5 2.1 0.4 0.1
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
4w9w.a
4w9x.a
5i3o.a
5i3r.a
5ikw.a
[1] 4w9w.a
0
.07 .14 .10 .08
[1] 4w9x.a .07
0
.14 .12 .11
[1] 5i3o.a .14 .14
0
.06 .06
[1] 5i3r.a .10 .12 .06
0
.05
[1] 5ikw.a .08 .11 .06 .05
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
4w9w.a
4w9x.a
5i3o.a
5i3r.a
5ikw.a
[1] 4w9w.a
0
0.6 1.4 1.3 1.0
[1] 4w9x.a 0.6
0
1.3 1.2 0.9
[1] 5i3o.a 1.4 1.3
0
0.3 0.8
[1] 5i3r.a 1.3 1.2 0.3
0
0.7
[1] 5ikw.a 1.0 0.9 0.8 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4w9w.a
4w9x.a
5i3o.a
5i3r.a
5ikw.a
[1] 4w9w.a
0
0.8 1.4 1.3 1.1
[1] 4w9x.a 0.8
0
1.3 1.2 1.1
[1] 5i3o.a 1.4 1.3
0
0.7 1.1
[1] 5i3r.a 1.3 1.2 0.7
0
1.1
[1] 5ikw.a 1.1 1.1 1.1 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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