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CDK6_HUMAN_1_312

Cyclin-dependent kinase 6 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDK6_HUMAN):D: Protein kinase (17:24, 26, 27, 29, 41, 43, 61, 77, 96, 98:104, 106, 107, 149, 150, 152, 162:168)17:24, 26, 27, 29, 41, 43, 61, 77, 96, 98:104, 106, 107, 149, 150, 152, 162:168

Full PDB list

1bi7, 1bi8, 1blx, 1g3n, 1jow, 1xo2, 2euf, 2f2c, 3nup, 3nux, 4aua, 4ez5, 4tth, 5l2i, 5l2s, 5l2t (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
9
G
2
0
Y
2
4
V
2
7
A
4
1
K
4
3
E
6
1
V
7
7
F
9
8
E
9
9
H
1
0
0
V
1
0
1
D
1
0
2
Q
1
0
3
D
1
0
4
T
1
0
6
T
1
0
7
Q
1
4
9
N
1
5
0
L
1
5
2
A
1
6
2
D
1
6
3
L
1
6
6
A
1
6
7
R
1
6
8
[1]1blx.a RG-M23 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jow.b none - - . . . . . . . . . . . . . . . . . . . . . . .
[1]1xo2.b fse21 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2euf.b lqq33 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2f2c.b ap928 . . - . . . . . . . . . . . . . . . . . . . . . .
[1]3nup.a 3nu22 . . - . . . . . . . . . . . . . . . . . . . . - -
[1]3nux.a 3nv28 . . - . . . . . . . . . . . . . . . . . . . . . -
[1]4aua.a 4au16 . . - . . . . . . . . . . . . . . . . . . . . . -
[1]4ez5.a 0rs36 . . - . . . . . . . . . . . . . . . . . . . . . -
[1]4tth.b 24v31 . . - . . . . . . . . . . . . . . . . . . . . . .
[1]5l2s.a 6zv37 . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5l2t.a 6zz32 . . . . . . . . . . . . . . . . . . . . . . . . -
[2]1bi7.a RGR-M34 . . . . . . - . . . . . . . . . . . . . . . . . .
[2]1bi8.a RGD-M31 . . . . . . - . . . . . . . . . . . . . . . . . .
[2]1g3n.a RG-K24 . . . . . . . . . . . . . . . . . . . . . . . . .

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
A
1
7
E
1
8
I
1
9
G
2
0
E
2
1
G
2
2
A
2
3
Y
2
4
K
2
6
V
2
7
K
2
9
A
4
1
K
4
3
E
6
1
V
7
7
L
9
6
F
9
8
E
9
9
H
1
0
0
V
1
0
1
D
1
0
2
Q
1
0
3
D
1
0
4
T
1
0
6
T
1
0
7
Q
1
4
9
N
1
5
0
L
1
5
2
A
1
6
2
D
1
6
3
F
1
6
4
G
1
6
5
L
1
6
6
A
1
6
7
R
1
6
8
[1]1blx.a . . . . . . . . . . . . * . . . . . . * . . . . . . . . . * . . . . .
[1]1jow.b - - - - - - - . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]1xo2.b . * * * * . . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[1]2euf.b . * * * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2f2c.b . . * * - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3nup.a . . * . - - - - . . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]3nux.a . . . . . . . - . . . . * . . . . . . . . . . . . . . . . . . . . . -
[1]4aua.a . * * * . . . - . . . . * . . . . . . . . . . . . . . . . * . . . . -
[1]4ez5.a . . * * . . . - . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4tth.b . * * * * - - - . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5l2s.a . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5l2t.a . . * * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[2]1bi7.a . . . . . . . . . . . . . - . . . . * . . . . . . . . . . . * . . . .
[2]1bi8.a . . . . . . . . . . . . * - . . . . * * . . . . . . . . . . * . . . .
[2]1g3n.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
1blx.a:RG-M
1jow.b is apo
1xo2.b:fse
2euf.b:lqq
2f2c.b:ap9
3nup.a:3nu
3nux.a:3nv
4aua.a:4au
4ez5.a:0rs
4tth.b:24v
5l2s.a:6zv
5l2t.a:6zz
1bi7.a:RGR-M
1bi8.a:RGD-M
1g3n.a:RG-K
[1] 1blx.a
0
- 2.1 1.8 2.0 1.4 1.5 0.8 2.8 2.2 2.2 1.9 0.1 0.1 0
[1] 1jow.b 0.1
-
0.6 1.3 2.2 0.1 0.6 0 1.0 0.9 0.9 1.6 0 0 0
[1] 1xo2.b 3.1 -
0.1
0.5 3.2 1.2 1.3 0.1 0.7 0.4 1.1 2.2 5.3 5.8 3.6
[1] 2euf.b 1.4 - 0
0
1.8 0.5 1.0 0 0.1 0.1 0.8 0.5 2.9 3.0 1.9
[1] 2f2c.b 1.4 - 0.2 0.5
0.1
0 0.4 0 0.2 0.3 0.2 0.6 1.5 2.2 2.3
[1] 3nup.a 0.8 - 0.6 0.5 1.0
0
0.2 0 1.2 0.6 0.6 0.8 1.4 1.6 0.7
[1] 3nux.a 0.6 - 1.0 0.5 1.6 0.1
0
0 0.9 0.5 0.4 0.8 0.9 1.3 0.5
[1] 4aua.a 0.7 - 1.1 0.6 2.8 0.4 0.3
0
0.9 0.7 0.9 1.2 2.3 3.6 1.0
[1] 4ez5.a 1.3 - 0 0.2 1.1 0.3 0.1 0
0
0.3 0 0.3 1.9 2.5 1.6
[1] 4tth.b 1.7 - 0.1 0.3 2.1 0.7 1.1 0.2 0.2
0
0.6 1.0 3.7 4.1 1.9
[1] 5l2s.a 0.8 - 0.1 0.6 1.1 0.3 0.7 0 0.3 0.4
0
0.4 1.8 2.3 1.4
[1] 5l2t.a 1.5 - 0.7 0.4 1.8 0.2 0.1 0.1 1.1 1.0 0.6
0
2.6 4.0 1.2
[2] 1bi7.a 0 - 6.8 5.6 5.8 6.7 7.0 4.4 8.5 6.7 9.4 6.2
0
0 0
[2] 1bi8.a 0 - 7.1 6.5 4.0 5.7 6.2 2.9 7.9 5.7 8.0 7.1 0
0
0
[2] 1g3n.a 0.2 - 5.1 4.4 3.9 4.3 4.3 2.7 6.6 5.0 6.2 5.0 0.2 0.6
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
1blx.a
1jow.b
1xo2.b
2euf.b
2f2c.b
3nup.a
3nux.a
4aua.a
4ez5.a
4tth.b
5l2s.a
5l2t.a
1bi7.a
1bi8.a
1g3n.a
[1] 1blx.a
0
.19 .40 .28 .23 .14 .13 .19 .22 .32 .23 .21 .34 .23 .27
[1] 1jow.b .19
0
.28 .23 .15 .14 .14 .21 .17 .25 .16 .24 .42 .37 .36
[1] 1xo2.b .40 .28
0
.17 .20 .27 .29 .22 .19 .12 .20 .21 .61 .58 .57
[1] 2euf.b .28 .23 .17
0
.11 .16 .17 .14 .09 .07 .11 .15 .51 .47 .44
[1] 2f2c.b .23 .15 .20 .11
0
.10 .13 .15 .06 .11 .06 .15 .46 .41 .38
[1] 3nup.a .14 .14 .27 .16 .10
0
.06 .11 .11 .18 .11 .13 .39 .35 .33
[1] 3nux.a .13 .14 .29 .17 .13 .06
0
.09 .11 .21 .10 .11 .38 .35 .32
[1] 4aua.a .19 .21 .22 .14 .15 .11 .09
0
.11 .16 .11 .12 .45 .41 .40
[1] 4ez5.a .22 .17 .19 .09 .06 .11 .11 .11
0
.11 .04 .11 .45 .41 .39
[1] 4tth.b .32 .25 .12 .07 .11 .18 .21 .16 .11
0
.13 .17 .55 .50 .47
[1] 5l2s.a .23 .16 .20 .11 .06 .11 .10 .11 .04 .13
0
.14 .46 .42 .39
[1] 5l2t.a .21 .24 .21 .15 .15 .13 .11 .12 .11 .17 .14
0
.46 .45 .42
[2] 1bi7.a .34 .42 .61 .51 .46 .39 .38 .45 .45 .55 .46 .46
0
.18 .20
[2] 1bi8.a .23 .37 .58 .47 .41 .35 .35 .41 .41 .50 .42 .45 .18
0
.15
[2] 1g3n.a .27 .36 .57 .44 .38 .33 .32 .40 .39 .47 .39 .42 .20 .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.8 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
1blx.a
1jow.b
1xo2.b
2euf.b
2f2c.b
3nup.a
3nux.a
4aua.a
4ez5.a
4tth.b
5l2s.a
5l2t.a
1bi7.a
1bi8.a
1g3n.a
[1] 1blx.a
0
3.6 4.0 3.9 3.8 1.8 2.2 2.7 2.5 3.8 2.7 2.5 5.6 5.2 5.2
[1] 1jow.b 3.6
0
0.7 0.8 0.6 1.9 2.4 2.6 2.5 0.7 2.4 2.6 7.0 6.5 6.3
[1] 1xo2.b 4.0 0.7
0
1.1 1.4 2.0 2.4 2.4 2.4 0.6 2.3 2.4 7.0 6.3 6.1
[1] 2euf.b 3.9 0.8 1.1
0
1.4 1.9 2.4 2.4 2.4 0.6 2.4 2.5 6.8 6.1 5.9
[1] 2f2c.b 3.8 0.6 1.4 1.4
0
2.1 2.5 2.7 2.6 1.4 2.4 2.6 7.1 6.5 6.3
[1] 3nup.a 1.8 1.9 2.0 1.9 2.1
0
0.6 0.9 0.6 2.0 0.6 0.8 4.3 3.7 3.4
[1] 3nux.a 2.2 2.4 2.4 2.4 2.5 0.6
0
1.1 0.5 2.4 0.8 0.7 4.9 4.2 4.0
[1] 4aua.a 2.7 2.6 2.4 2.4 2.7 0.9 1.1
0
1.0 2.4 1.3 1.1 5.2 4.5 4.4
[1] 4ez5.a 2.5 2.5 2.4 2.4 2.6 0.6 0.5 1.0
0
2.4 0.7 0.7 5.1 4.3 4.1
[1] 4tth.b 3.8 0.7 0.6 0.6 1.4 2.0 2.4 2.4 2.4
0
2.3 2.5 6.9 6.4 6.2
[1] 5l2s.a 2.7 2.4 2.3 2.4 2.4 0.6 0.8 1.3 0.7 2.3
0
0.9 5.4 4.5 4.2
[1] 5l2t.a 2.5 2.6 2.4 2.5 2.6 0.8 0.7 1.1 0.7 2.5 0.9
0
5.2 4.4 4.2
[2] 1bi7.a 5.6 7.0 7.0 6.8 7.1 4.3 4.9 5.2 5.1 6.9 5.4 5.2
0
1.7 2.0
[2] 1bi8.a 5.2 6.5 6.3 6.1 6.5 3.7 4.2 4.5 4.3 6.4 4.5 4.4 1.7
0
1.0
[2] 1g3n.a 5.2 6.3 6.1 5.9 6.3 3.4 4.0 4.4 4.1 6.2 4.2 4.2 2.0 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.4 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
1blx.a
1jow.b
1xo2.b
2euf.b
2f2c.b
3nup.a
3nux.a
4aua.a
4ez5.a
4tth.b
5l2s.a
5l2t.a
1bi7.a
1bi8.a
1g3n.a
[1] 1blx.a
0
4.1 4.2 4.0 4.0 2.1 2.3 2.6 2.5 4.0 3.3 2.5 5.2 4.9 4.9
[1] 1jow.b 4.1
0
0.8 1.1 1.0 2.6 3.0 3.0 3.0 1.1 2.9 3.1 7.9 7.6 7.3
[1] 1xo2.b 4.2 0.8
0
1.2 1.4 2.6 2.8 2.8 2.8 1.1 2.7 2.9 7.7 7.3 7.0
[1] 2euf.b 4.0 1.1 1.2
0
1.4 2.5 2.7 2.7 2.7 0.7 2.7 2.9 7.5 7.1 6.9
[1] 2f2c.b 4.0 1.0 1.4 1.4
0
2.6 2.9 3.0 2.9 1.4 2.8 3.0 7.9 7.5 7.2
[1] 3nup.a 2.1 2.6 2.6 2.5 2.6
0
0.9 1.2 1.1 2.6 1.0 1.1 4.5 3.9 3.6
[1] 3nux.a 2.3 3.0 2.8 2.7 2.9 0.9
0
1.2 0.9 2.8 1.1 1.0 4.9 4.2 4.0
[1] 4aua.a 2.6 3.0 2.8 2.7 3.0 1.2 1.2
0
1.4 2.8 1.3 1.2 5.2 4.5 4.4
[1] 4ez5.a 2.5 3.0 2.8 2.7 2.9 1.1 0.9 1.4
0
2.8 1.2 1.1 5.0 4.3 4.1
[1] 4tth.b 4.0 1.1 1.1 0.7 1.4 2.6 2.8 2.8 2.8
0
2.7 2.9 7.7 7.4 7.2
[1] 5l2s.a 3.3 2.9 2.7 2.7 2.8 1.0 1.1 1.3 1.2 2.7
0
0.9 5.4 4.7 4.4
[1] 5l2t.a 2.5 3.1 2.9 2.9 3.0 1.1 1.0 1.2 1.1 2.9 0.9
0
5.2 4.4 4.2
[2] 1bi7.a 5.2 7.9 7.7 7.5 7.9 4.5 4.9 5.2 5.0 7.7 5.4 5.2
0
1.8 2.1
[2] 1bi8.a 4.9 7.6 7.3 7.1 7.5 3.9 4.2 4.5 4.3 7.4 4.7 4.4 1.8
0
1.3
[2] 1g3n.a 4.9 7.3 7.0 6.9 7.2 3.6 4.0 4.4 4.1 7.2 4.4 4.2 2.1 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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