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CDK5_HUMAN_1_292

Cyclin-dependent-like kinase 5 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDK5_HUMAN):D: Protein kinase (10:15, 18, 31, 33, 51, 64, 80:86, 89, 130, 131, 133, 143, 144)10:15, 18, 31, 33, 51, 64, 80:86, 89, 130, 131, 133, 143, 144

Full PDB list

1h4l, 1ung, 1unh, 1unl, 3o0g, 4au8

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
0
G
1
1
E
1
2
V
1
8
A
3
1
K
3
3
V
6
4
F
8
0
E
8
1
F
8
2
C
8
3
D
8
4
Q
8
5
D
8
6
K
8
9
Q
1
3
0
L
1
3
3
A
1
4
3
D
1
4
4
[1]1h4l.a none . - - . . . . . . . . . . . . . . . .
[1]1ung.a alh20 . - - . . . . . . . . . . . . . . . N
[1]1unh.a ixm21 . - - . . . . . . . . . . . . . . . N
[1]1unl.a rrc26 . . . . . . . . . . . . . . . . . . N
[1]1unl.b none . . . . . . . . . . . . . . . . . . N
[1]3o0g.b 3o025 . - - . . . . . . . . . . . . . . . N
[1]4au8.a z3r18 . . . . . . . . . . . . . . . . . . .

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
I
1
0
G
1
1
E
1
2
G
1
3
T
1
4
Y
1
5
V
1
8
A
3
1
K
3
3
E
5
1
V
6
4
F
8
0
E
8
1
F
8
2
C
8
3
D
8
4
Q
8
5
D
8
6
K
8
9
Q
1
3
0
N
1
3
1
L
1
3
3
A
1
4
3
D
1
4
4
[1]1h4l.a . - - - - . . . * . . . . . . . . . . . . . . *
[1]1ung.a . - - - - . . . . . . . . . . . . . . . . . . N
[1]1unh.a . - - - - . . . * . . . . . . . . . . . . . . N
[1]1unl.a . . . . . . . . * . . . . . . . . . . . . . . N
[1]1unl.b . . . . . . . . * . . . . . . . . . . . . . . N
[1]3o0g.b . - - - - - . . . . . . . . . . . . . . . . . N
[1]4au8.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
1h4l.a is apo
1ung.a:alh
1unh.a:ixm
1unl.a:rrc
1unl.b is apo
3o0g.b:3o0
4au8.a:z3r
[1] 1h4l.a
-
0.3 0 0.1 - 2.1 0.4
[1] 1ung.a -
0.1
0 0.3 - 1.4 0.5
[1] 1unh.a - 0.1
0
0.1 - 2.5 0.1
[1] 1unl.a - 0.1 0
0
- 2.1 0.4
[1] 1unl.b - 0.2 0.1 0.9
-
3.2 0.3
[1] 3o0g.b - 0.4 0.2 0.8 -
0
0
[1] 4au8.a - 0.4 0.2 1.9 - 2.6
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
1h4l.a
1ung.a
1unh.a
1unl.a
1unl.b
3o0g.b
4au8.a
[1] 1h4l.a
0
.05 .04 .03 .10 .12 .14
[1] 1ung.a .05
0
.07 .06 .12 .08 .16
[1] 1unh.a .04 .07
0
.03 .08 .14 .11
[1] 1unl.a .03 .06 .03
0
.08 .12 .12
[1] 1unl.b .10 .12 .08 .08
0
.16 .13
[1] 3o0g.b .12 .08 .14 .12 .16
0
.18
[1] 4au8.a .14 .16 .11 .12 .13 .18
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1h4l.a
1ung.a
1unh.a
1unl.a
1unl.b
3o0g.b
4au8.a
[1] 1h4l.a
0
1.1 0.8 0.8 0.9 0.9 1.2
[1] 1ung.a 1.1
0
1.0 0.6 1.2 1.4 1.4
[1] 1unh.a 0.8 1.0
0
0.6 0.5 0.9 0.9
[1] 1unl.a 0.8 0.6 0.6
0
1.3 1.0 1.5
[1] 1unl.b 0.9 1.2 0.5 1.3
0
0.6 1.8
[1] 3o0g.b 0.9 1.4 0.9 1.0 0.6
0
0.6
[1] 4au8.a 1.2 1.4 0.9 1.5 1.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1h4l.a
1ung.a
1unh.a
1unl.a
1unl.b
3o0g.b
4au8.a
[1] 1h4l.a
0
1.2 0.8 0.9 1.1 1.1 1.6
[1] 1ung.a 1.2
0
1.0 0.7 1.3 1.5 1.8
[1] 1unh.a 0.8 1.0
0
0.7 0.8 1.1 1.4
[1] 1unl.a 0.9 0.7 0.7
0
1.3 1.2 1.8
[1] 1unl.b 1.1 1.3 0.8 1.3
0
1.0 2.2
[1] 3o0g.b 1.1 1.5 1.1 1.2 1.0
0
1.4
[1] 4au8.a 1.6 1.8 1.4 1.8 2.2 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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