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KS6B1_HUMAN_76_373

Ribosomal protein S6 kinase beta-1 [Protein kinase superfamily. AGC Ser/Thr protein kinase family. S6 kinase subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KS6B1_HUMAN):D: Protein kinase (95, 97:105, 121, 123:125, 143, 156, 172:176, 178, 179, 222, 223, 225, 235, 236, 239:241)95, 97:105, 121, 123:125, 143, 156, 172:176, 178, 179, 222, 223, 225, 235, 236, 239:241, 382, 386
Metals (Me):Mn/Zn

Full PDB list

3a60, 3a61, 3a62, 3we4, 3wf5, 3wf6, 3wf7, 3wf8, 3wf9, 4l3j, 4l3l, 4l42, 4l43, 4l44, 4l45, 4l46, 4rlo, 4rlp (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
9
7
G
9
8
K
9
9
G
1
0
0
G
1
0
1
Y
1
0
2
G
1
0
3
K
1
0
4
V
1
0
5
A
1
2
1
K
1
2
3
L
1
2
5
E
1
4
3
V
1
5
6
L
1
7
2
E
1
7
3
Y
1
7
4
L
1
7
5
E
1
7
9
E
2
2
2
M
2
2
5
T
2
3
5
D
2
3
6
L
2
3
9
C
2
4
0
K
2
4
1
[1]3a62.a stu35 . . . . . . . . . . . . . . . . . . . . . . . . . - Mn
[1]3wf5.a fz824 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3wf6.a fz924 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3wf7.a fs928 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3wf8.a f7632 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]3wf9.a fs733 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4l42.a 5fi28 . . . . . . . . . . . . . . . . . . . . . . . . . . Zn
[1]4l45.a 5fi28 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rlo.a 3t337 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4rlp.a 72b41 . . . . . . . . . . . . - . . . . . . . . . . . . .

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 Me
R
9
5
L
9
7
G
9
8
K
9
9
G
1
0
0
G
1
0
1
Y
1
0
2
G
1
0
3
K
1
0
4
V
1
0
5
A
1
2
1
K
1
2
3
V
1
2
4
L
1
2
5
E
1
4
3
V
1
5
6
L
1
7
2
E
1
7
3
Y
1
7
4
L
1
7
5
S
1
7
6
G
1
7
8
E
1
7
9
E
2
2
2
N
2
2
3
M
2
2
5
T
2
3
5
D
2
3
6
L
2
3
9
C
2
4
0
K
2
4
1
F
3
8
2
F
3
8
6
[1]3a62.a . . . * * . . . . . . * . . . . . . . . . . . . . . . . . . - - - Mn
[1]3wf5.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . * - - Zn
[1]3wf6.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . * - - Zn
[1]3wf7.a . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . - - Zn
[1]3wf8.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Zn
[1]3wf9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - - Zn
[1]4l42.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . W - Zn
[1]4l45.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]4rlo.a . . . . * * . * . . . . . . . . . . . . . . . . . . . . . . . - -
[1]4rlp.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
3a62.a:stu
3wf5.a:fz8
3wf6.a:fz9
3wf7.a:fs9
3wf8.a:f76
3wf9.a:fs7
4l42.a:5fi
4l45.a:5fi
4rlo.a:3t3
4rlp.a:72b
[1] 3a62.a
0
2.5 1.6 4.8 4.3 4.3 3.7 3.3 1.3 0.5
[1] 3wf5.a 0.4
0
0 1.9 1.4 1.6 1.9 1.7 1.2 1.1
[1] 3wf6.a 0.6 0.4
0
2.3 1.3 1.5 1.7 1.3 1.5 2.0
[1] 3wf7.a 1.5 0.1 0.1
0.1
0.1 0.5 0.1 0.2 1.2 1.4
[1] 3wf8.a 1.0 0.5 0.4 0.6
0
0 0.6 0.5 0.9 0.9
[1] 3wf9.a 0.9 0.4 0.4 0.6 0
0
0.7 0.5 1.0 0.9
[1] 4l42.a 0.4 0.4 0.2 0.3 0.5 0.5
0
0 0.7 0.9
[1] 4l45.a 3.1 0.2 0.3 0.3 1.9 1.8 0.1
0
2.5 3.0
[1] 4rlo.a 0.1 2.5 1.7 4.1 5.4 5.6 3.9 4.0
0.1
0.4
[1] 4rlp.a 0.1 1.6 0.8 4.1 3.9 3.5 3.4 3.1 0.7
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
3a62.a
3wf5.a
3wf6.a
3wf7.a
3wf8.a
3wf9.a
4l42.a
4l45.a
4rlo.a
4rlp.a
[1] 3a62.a
0
.21 .21 .18 .20 .19 .21 .26 .14 .12
[1] 3wf5.a .21
0
.06 .13 .08 .08 .09 .16 .19 .16
[1] 3wf6.a .21 .06
0
.15 .10 .11 .12 .18 .21 .16
[1] 3wf7.a .18 .13 .15
0
.08 .08 .06 .12 .23 .19
[1] 3wf8.a .20 .08 .10 .08
0
0 .04 .09 .21 .18
[1] 3wf9.a .19 .08 .11 .08 0
0
.04 .10 .21 .17
[1] 4l42.a .21 .09 .12 .06 .04 .04
0
.11 .23 .20
[1] 4l45.a .26 .16 .18 .12 .09 .10 .11
0
.28 .24
[1] 4rlo.a .14 .19 .21 .23 .21 .21 .23 .28
0
.08
[1] 4rlp.a .12 .16 .16 .19 .18 .17 .20 .24 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
3a62.a
3wf5.a
3wf6.a
3wf7.a
3wf8.a
3wf9.a
4l42.a
4l45.a
4rlo.a
4rlp.a
[1] 3a62.a
0
1.3 1.2 1.8 1.5 1.5 1.6 1.4 2.1 1.9
[1] 3wf5.a 1.3
0
0.4 1.2 0.9 0.9 0.9 1.0 3.7 3.5
[1] 3wf6.a 1.2 0.4
0
1.2 0.9 0.9 1.0 0.9 3.6 3.4
[1] 3wf7.a 1.8 1.2 1.2
0
1.0 1.0 1.1 1.1 3.6 3.3
[1] 3wf8.a 1.5 0.9 0.9 1.0
0
0.1 0.8 0.8 3.8 3.6
[1] 3wf9.a 1.5 0.9 0.9 1.0 0.1
0
0.8 0.7 3.8 3.5
[1] 4l42.a 1.6 0.9 1.0 1.1 0.8 0.8
0
7.4 4.0 3.7
[1] 4l45.a 1.4 1.0 0.9 1.1 0.8 0.7 7.4
0
3.8 3.5
[1] 4rlo.a 2.1 3.7 3.6 3.6 3.8 3.8 4.0 3.8
0
0.9
[1] 4rlp.a 1.9 3.5 3.4 3.3 3.6 3.5 3.7 3.5 0.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
3a62.a
3wf5.a
3wf6.a
3wf7.a
3wf8.a
3wf9.a
4l42.a
4l45.a
4rlo.a
4rlp.a
[1] 3a62.a
0
1.4 1.3 2.1 1.6 1.6 1.7 1.6 2.2 2.1
[1] 3wf5.a 1.4
0
0.8 2.0 1.4 1.4 1.4 1.6 4.0 3.8
[1] 3wf6.a 1.3 0.8
0
1.8 1.2 1.2 1.2 1.4 3.9 3.8
[1] 3wf7.a 2.1 2.0 1.8
0
1.7 1.7 1.9 1.9 4.0 3.7
[1] 3wf8.a 1.6 1.4 1.2 1.7
0
0.3 1.3 1.4 4.1 3.9
[1] 3wf9.a 1.6 1.4 1.2 1.7 0.3
0
1.2 1.3 4.1 3.9
[1] 4l42.a 1.7 1.4 1.2 1.9 1.3 1.2
0
7.1 4.3 4.1
[1] 4l45.a 1.6 1.6 1.4 1.9 1.4 1.3 7.1
0
4.2 4.0
[1] 4rlo.a 2.2 4.0 3.9 4.0 4.1 4.1 4.3 4.2
0
1.2
[1] 4rlp.a 2.1 3.8 3.8 3.7 3.9 3.9 4.1 4.0 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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