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NEK1_HUMAN_1_328

Serine/threonine-protein kinase Nek1 [Protein kinase superfamily. NEK Ser/Thr protein kinase family. NIMA subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NEK1_HUMAN):D: Protein kinase (10, 11, 18, 31, 33, 80:83, 86, 87, 135)10, 11, 18, 31, 33, 80:83, 86, 87, 135

Full PDB list

4apc, 4b9d

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
0
G
1
1
A
1
8
V
3
1
K
3
3
M
8
0
D
8
1
Y
8
2
C
8
3
G
8
6
D
8
7
F
1
3
5
[1]4apc.b none . . . . . . . . . . . .
[1]4b9d.b ck723 . . . . . . . . . . . .

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
I
1
0
G
1
1
A
1
8
V
3
1
K
3
3
M
8
0
D
8
1
Y
8
2
C
8
3
G
8
6
D
8
7
F
1
3
5
[1]4apc.b . . . . . . . . . . . .
[1]4b9d.b . . . . . . . . . . . .

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
4apc.b is apo
4b9d.b:ck7
[1] 4apc.b
-
0.5
[1] 4b9d.b -
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
4apc.b
4b9d.b
[1] 4apc.b
0
.04
[1] 4b9d.b .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
4apc.b
4b9d.b
[1] 4apc.b
0
0.5
[1] 4b9d.b 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
4apc.b
4b9d.b
[1] 4apc.b
0
0.8
[1] 4b9d.b 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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