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NAHK_BIFL2_2_359

N-acetylhexosamine 1-kinase [Protein kinase superfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NAHK_BIFL2):D: Protein kinase (30:32, 54, 55, 146, 149, 208, 210, 213, 228, 231, 246, 254, 303, 306, 307, 317, 318)30:32, 54, 55, 146, 149, 208, 210, 213, 228, 231, 246, 254, 303, 306, 307, 317, 318

Full PDB list

4ocj, 4ock, 4oco, 4ocp, 4ocq, 4ocu, 4ocv, 4wh1, 4wh2, 4wh3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
G
3
0
H
3
1
I
3
2
F
5
5
I
1
4
6
F
1
4
9
D
2
0
8
K
2
1
0
N
2
1
3
D
2
2
8
T
2
3
1
R
2
4
6
E
2
5
4
C
3
0
3
R
3
0
6
F
3
0
7
Y
3
1
7
[1]4ocj.a ndg15 . . . . . . . . . . . . . . . . .
[1]4oco.a gn119 . . . . . . . . . . . . . . . . .
[1]4ocp.a gn1,mg20 . . . . . . . . . . . . . . . . .
[1]4ocq.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

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PDB.ch
A1
G
3
0
H
3
1
I
3
2
I
5
4
F
5
5
I
1
4
6
F
1
4
9
D
2
0
8
K
2
1
0
N
2
1
3
D
2
2
8
T
2
3
1
R
2
4
6
E
2
5
4
C
3
0
3
R
3
0
6
F
3
0
7
Y
3
1
7
F
3
1
8
[1]4ocj.a . . . . . . . . . . . . . . . . . . .
[1]4oco.a . . . . . . . . . . . . . . . . . . .
[1]4ocp.a . . . . . . . . . . . . . . . . . . .
[1]4ocq.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
4ocj.a:ndg
4oco.a:gn1
4ocp.a:gn1,mg
4ocq.a is apo
[1] 4ocj.a
0
0.2 0.3 -
[1] 4oco.a 0
0.1
0.1 -
[1] 4ocp.a 0.1 0.2
0.2
-
[1] 4ocq.a 0.1 0.3 0.4
-
[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
4ocj.a
4oco.a
4ocp.a
4ocq.a
[1] 4ocj.a
0
.03 .02 .01
[1] 4oco.a .03
0
.02 .02
[1] 4ocp.a .02 .02
0
.02
[1] 4ocq.a .01 .02 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.2 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
4ocj.a
4oco.a
4ocp.a
4ocq.a
[1] 4ocj.a
0
0.2 0.2 0.1
[1] 4oco.a 0.2
0
0.3 0.2
[1] 4ocp.a 0.2 0.3
0
0.2
[1] 4ocq.a 0.1 0.2 0.2
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

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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
4ocj.a
4oco.a
4ocp.a
4ocq.a
[1] 4ocj.a
0
0.3 0.2 0.1
[1] 4oco.a 0.3
0
0.3 0.3
[1] 4ocp.a 0.2 0.3
0
0.2
[1] 4ocq.a 0.1 0.3 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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