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ADK_HUMAN_15_362

Adenosine kinase [Carbohydrate kinase PfkB family]

Composition of the binding site

Protein chains monomer
A1 (ADK_HUMAN):31, 33, 35, 54:57, 59, 80:82, 85, 140, 141, 150:153, 155, 187, 190, 218, 223, 313, 314, 31731, 33, 35, 54:57, 59, 80:82, 85, 140, 141, 150:153, 155, 187, 190, 218, 223, 313, 314, 317

Full PDB list

1bx4, 2i6a, 2i6b, 4o1l

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
N
3
1
L
3
3
D
3
5
Q
5
5
I
5
6
L
5
7
G
8
0
G
8
1
S
8
2
N
8
5
C
1
4
0
L
1
5
1
A
1
5
3
L
1
5
5
F
1
8
7
T
1
9
0
F
2
1
8
Y
2
2
3
N
3
1
3
G
3
1
4
D
3
1
7
[1]1bx4.a adn19 . . . . . . . . . . . . . . . . . . . . .
[1]2i6a.a 5i519 . . . . . . . . . . . . . . . . . . . . .
[1]2i6b.a 89i30 . . . . . . . . . . . . . . . . . . . . .
[1]4o1l.a ho421 . . . . . . . . . . . . . . . . . . . . .

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
N
3
1
L
3
3
D
3
5
D
5
4
Q
5
5
I
5
6
L
5
7
E
5
9
G
8
0
G
8
1
S
8
2
N
8
5
C
1
4
0
A
1
4
1
S
1
5
0
L
1
5
1
I
1
5
2
A
1
5
3
L
1
5
5
F
1
8
7
T
1
9
0
F
2
1
8
Y
2
2
3
N
3
1
3
G
3
1
4
D
3
1
7
[1]1bx4.a . . . . . . * . . . . . . . . . . . . . . . . . . .
[1]2i6a.a . . . . . . * . . . . . . . . * * . . . . . . . . .
[1]2i6b.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4o1l.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
1bx4.a:adn
2i6a.a:5i5
2i6b.a:89i
4o1l.a:ho4
[1] 1bx4.a
0
0 5.3 0.1
[1] 2i6a.a 0.1
0
5.6 0.1
[1] 2i6b.a 0.1 0.1
0.1
0.2
[1] 4o1l.a 0.2 0 5.2
0.2
[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
1bx4.a
2i6a.a
2i6b.a
4o1l.a
[1] 1bx4.a
0
.05 .21 .07
[1] 2i6a.a .05
0
.22 .03
[1] 2i6b.a .21 .22
0
.21
[1] 4o1l.a .07 .03 .21
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
1bx4.a
2i6a.a
2i6b.a
4o1l.a
[1] 1bx4.a
0
0.4 3.4 0.3
[1] 2i6a.a 0.4
0
3.5 0.3
[1] 2i6b.a 3.4 3.5
0
3.5
[1] 4o1l.a 0.3 0.3 3.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
1bx4.a
2i6a.a
2i6b.a
4o1l.a
[1] 1bx4.a
0
0.7 3.5 0.6
[1] 2i6a.a 0.7
0
3.6 0.7
[1] 2i6b.a 3.5 3.6
0
3.7
[1] 4o1l.a 0.6 0.7 3.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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