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GRK6_HUMAN_2_576

G protein-coupled receptor kinase 6 [Protein kinase superfamily. AGC Ser/Thr protein kinase family. GPRK subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (GRK6_HUMAN):D: Protein kinase (192:196, 200, 213, 215, 263:266, 270, 315, 316, 318, 328, 329)192:196, 200, 213, 215, 263:266, 270, 315, 316, 318, 328, 329

Full PDB list

2acx, 3nyn, 3nyo

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
9
2
G
1
9
3
K
1
9
4
G
1
9
5
G
1
9
6
V
2
0
0
A
2
1
3
K
2
1
5
L
2
6
3
T
2
6
4
L
2
6
5
M
2
6
6
D
2
7
0
E
3
1
5
N
3
1
6
L
3
1
8
S
3
2
8
D
3
2
9
[1]2acx.a anp,mg32 . . . . . . . . . . . . . . . . . .
[1]3nyn.a sgv22 . . . . . . . . . . . . . . . . . .
[1]3nyo.a amp23 . . . . . . . . . . . . . . . . . .

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

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PDB.ch
A1
L
1
9
2
G
1
9
3
K
1
9
4
G
1
9
5
G
1
9
6
V
2
0
0
A
2
1
3
K
2
1
5
L
2
6
3
T
2
6
4
L
2
6
5
M
2
6
6
D
2
7
0
E
3
1
5
N
3
1
6
L
3
1
8
S
3
2
8
D
3
2
9
[1]2acx.a . . . . . . . . . . . . . . . . . .
[1]3nyn.a . . . . . . . . . . . . . . . . . *
[1]3nyo.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
2acx.a:anp,mg
3nyn.a:sgv
3nyo.a:amp
[1] 2acx.a
0.1
0.2 0.2
[1] 3nyn.a 1.3
0
0.7
[1] 3nyo.a 0.9 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
2acx.a
3nyn.a
3nyo.a
[1] 2acx.a
0
.08 .06
[1] 3nyn.a .08
0
.05
[1] 3nyo.a .06 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
2acx.a
3nyn.a
3nyo.a
[1] 2acx.a
0
1.0 1.0
[1] 3nyn.a 1.0
0
0.3
[1] 3nyo.a 1.0 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2acx.a
3nyn.a
3nyo.a
[1] 2acx.a
0
1.6 1.5
[1] 3nyn.a 1.6
0
0.5
[1] 3nyo.a 1.5 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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