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PDPK1_HUMAN_408_556

3-phosphoinositide-dependent protein kinase 1 [Protein kinase superfamily. AGC Ser/Thr protein kinase family. PDPK1 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PDPK1_HUMAN):D: PH (465:468, 472, 474, 486, 495, 521)465:468, 472, 474, 486, 495, 521

Full PDB list

1w1d, 1w1g, 1w1h, 2vki

Pocket contact map

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PDB.ch
   
ligand
A1
K
4
6
5
K
4
6
7
R
4
7
2
R
4
7
4
Y
4
8
6
K
4
9
5
R
5
2
1
[1]1w1d.a 4ip28 . . . . . . .
[1]1w1g.a 4pt33 . . . . . . .
[2]1w1h.b none . . . . . . .
[3]2vki.a none E . . . . . .

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
K
4
6
5
R
4
6
6
K
4
6
7
G
4
6
8
R
4
7
2
R
4
7
4
Y
4
8
6
K
4
9
5
R
5
2
1
[1]1w1d.a . . . . . . . . .
[1]1w1g.a . . . . . . . . .
[2]1w1h.b . . * . . . . . .
[3]2vki.a E . * . * * . . .

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
1w1d.a:4ip
1w1g.a:4pt
1w1h.b is apo
2vki.a is apo
[1] 1w1d.a
0
0 - -
[1] 1w1g.a 0
0.1
- -
[2] 1w1h.b 4.1 3.9
-
-
[3] 2vki.a 4.6 4.6 -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 clusters)

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
1w1d.a
1w1g.a
1w1h.b
2vki.a
[1] 1w1d.a
0
.01 .46 .52
[1] 1w1g.a .01
0
.44 .51
[2] 1w1h.b .46 .44
0
.53
[3] 2vki.a .52 .51 .53
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
1w1d.a
1w1g.a
1w1h.b
2vki.a
[1] 1w1d.a
0
0.1 1.3 0.9
[1] 1w1g.a 0.1
0
1.3 1.0
[2] 1w1h.b 1.3 1.3
0
1.2
[3] 2vki.a 0.9 1.0 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1w1d.a
1w1g.a
1w1h.b
2vki.a
[1] 1w1d.a
0
0.2 1.9 2.1
[1] 1w1g.a 0.2
0
1.9 2.1
[2] 1w1h.b 1.9 1.9
0
2.0
[3] 2vki.a 2.1 2.1 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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