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KPCD_HUMAN_229_282

Protein kinase C delta type [Protein kinase superfamily. AGC Ser/Thr protein kinase family. PKC subfamily]

Composition of the binding site

Protein chains monomer
A1 (KPCD_HUMAN):238:242, 250:254, 257238:242, 250:254, 257
Metals (Me):Zn

Full PDB list

1ptq, 1ptr, 3uej, 3uey, 3uff, 3ugd, 3ugi, 3ugl (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 Me
Y
2
3
8
M
2
3
9
S
2
4
0
P
2
4
1
T
2
4
2
L
2
5
0
L
2
5
1
W
2
5
2
G
2
5
3
L
2
5
4
Q
2
5
7
[1]1ptr.a prb29 . . . . . . . . . . . Zn
[1]3uej.a none . . . . . . . . . . . Zn

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 Me
Y
2
3
8
M
2
3
9
S
2
4
0
P
2
4
1
T
2
4
2
L
2
5
0
L
2
5
1
W
2
5
2
G
2
5
3
L
2
5
4
Q
2
5
7
[1]1ptr.a . . . . . . . . . . . Zn
[1]3uej.a . . . . . . . . . . . Zn

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
1ptr.a:prb
3uej.a is apo
[1] 1ptr.a
0
-
[1] 3uej.a 1.5
-
[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
1ptr.a
3uej.a
[1] 1ptr.a
0
.14
[1] 3uej.a .14
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
1ptr.a
3uej.a
[1] 1ptr.a
0
0.6
[1] 3uej.a 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1ptr.a
3uej.a
[1] 1ptr.a
0
0.8
[1] 3uej.a 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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