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DAPK3_HUMAN_7_287

Death-associated protein kinase 3 [Protein kinase superfamily. CAMK Ser/Thr protein kinase family. DAP kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DAPK3_HUMAN):D: Protein kinase (19:22, 27, 40, 42, 77, 93:96, 100, 141, 143, 144, 146, 160, 161)
R: Activation segment (161)
19:22, 27, 40, 42, 77, 93:96, 100, 141, 143, 144, 146, 160, 161

Full PDB list

1yrp, 2j90, 3bhy, 3bqr, 5a6n, 5a6o (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
9
G
2
0
S
2
1
V
2
7
A
4
0
K
4
2
I
7
7
L
9
3
E
9
4
L
9
5
V
9
6
E
1
0
0
E
1
4
3
N
1
4
4
M
1
4
6
I
1
6
0
D
1
6
1
[1]1yrp.a none . . . . . . . . . . . . . . . . .
[1]2j90.a iza23 . . . . . . . . . . . . . . . . .
[1]3bhy.a cl-7cp26 . . . . . . . . . . . . . . . . .
[1]3bqr.a 4rb24 . . . . . . . . . . . . . . . . .
[1]5a6n.a u7e15 . . . . . . . . . . . . . . . . .

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
G
2
0
S
2
1
G
2
2
V
2
7
A
4
0
K
4
2
I
7
7
L
9
3
E
9
4
L
9
5
V
9
6
E
1
0
0
K
1
4
1
E
1
4
3
N
1
4
4
M
1
4
6
I
1
6
0
D
1
6
1
[1]1yrp.a . * . . . . . . . . . . . . . . . . .
[1]2j90.a . . . . . . . . . . . . . . . . . . .
[1]3bhy.a . . . . . . . . . . . . . . . . . . *
[1]3bqr.a . . . . . . . . . . . . . . . . . . .
[1]5a6n.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
1yrp.a is apo
2j90.a:iza
3bhy.a:cl-7cp
3bqr.a:4rb
5a6n.a:u7e
[1] 1yrp.a
-
0.4 0.9 1.5 0.8
[1] 2j90.a -
0
0.4 0.8 0.1
[1] 3bhy.a - 0.8
0
1.2 0.7
[1] 3bqr.a - 0 0.3
0
0
[1] 5a6n.a - 0.5 0.8 0.7
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
1yrp.a
2j90.a
3bhy.a
3bqr.a
5a6n.a
[1] 1yrp.a
0
.10 .12 .11 .13
[1] 2j90.a .10
0
.10 .05 .05
[1] 3bhy.a .12 .10
0
.08 .12
[1] 3bqr.a .11 .05 .08
0
.04
[1] 5a6n.a .13 .05 .12 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1yrp.a
2j90.a
3bhy.a
3bqr.a
5a6n.a
[1] 1yrp.a
0
0.7 0.8 0.8 0.9
[1] 2j90.a 0.7
0
0.8 0.7 0.6
[1] 3bhy.a 0.8 0.8
0
0.7 1.1
[1] 3bqr.a 0.8 0.7 0.7
0
0.8
[1] 5a6n.a 0.9 0.6 1.1 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
1yrp.a
2j90.a
3bhy.a
3bqr.a
5a6n.a
[1] 1yrp.a
0
1.0 0.8 0.9 1.2
[1] 2j90.a 1.0
0
1.1 1.1 0.8
[1] 3bhy.a 0.8 1.1
0
0.9 1.3
[1] 3bqr.a 0.9 1.1 0.9
0
1.1
[1] 5a6n.a 1.2 0.8 1.3 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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