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CDK12_HUMAN_714_1051

Cyclin-dependent kinase 12 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDK12_HUMAN):D: Protein kinase (732:737, 741, 743, 754, 756, 787, 813:819, 821, 825, 859, 861, 863, 864, 866, 877)
1037:1046
732:737, 741, 743, 754, 756, 787, 813:819, 821, 825, 859, 861, 863, 864, 866, 877, 1037:1046

Full PDB list

4cxa, 4nst, 4un0, 5acb

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
7
3
3
E
7
3
5
G
7
3
6
T
7
3
7
V
7
4
1
K
7
4
3
A
7
5
4
K
7
5
6
F
8
1
3
E
8
1
4
Y
8
1
5
M
8
1
6
D
8
1
7
H
8
1
8
D
8
1
9
K
8
6
1
S
8
6
3
N
8
6
4
L
8
6
6
D
8
7
7
Q
1
0
3
7
C
1
0
3
9
H
1
0
4
0
[1]4cxa.a anp31 . . . . . . . . . . . . . . . . . . . . . . .
[1]4nst.a adp,al,mg,mg30 . . . . . . . . . . . . . . . . . . . . . . .
[1]4un0.c none . . . . . . . . . . . . . . . . . . . . - - -
[1]5acb.c 5i140 . . . . . . . . . . . . . . . . . . . . . * .

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
7
3
2
I
7
3
3
G
7
3
4
E
7
3
5
G
7
3
6
T
7
3
7
V
7
4
1
K
7
4
3
A
7
5
4
K
7
5
6
V
7
8
7
F
8
1
3
E
8
1
4
Y
8
1
5
M
8
1
6
D
8
1
7
H
8
1
8
D
8
1
9
M
8
2
1
E
8
2
5
D
8
5
9
K
8
6
1
S
8
6
3
N
8
6
4
L
8
6
6
D
8
7
7
Q
1
0
3
7
D
1
0
3
8
C
1
0
3
9
H
1
0
4
0
E
1
0
4
1
L
1
0
4
2
W
1
0
4
3
S
1
0
4
4
K
1
0
4
5
K
1
0
4
6
[1]4cxa.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4nst.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . .
[1]4un0.c . . . . . . . . . . . . . . . . . . . . . . . . . . - - - - - - - - - -
[1]5acb.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . - - - - - -

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
4cxa.a:anp
4nst.a:adp,al,mg
4un0.c is apo
5acb.c:5i1
[1] 4cxa.a
0.1
0.6 - 4.8
[1] 4nst.a 0.3
0.3
- 4.8
[1] 4un0.c 0.7 1.1
-
0.1
[1] 5acb.c 0.4 0.7 -
0.5
[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
4cxa.a
4nst.a
4un0.c
5acb.c
[1] 4cxa.a
0
.03 .17 .18
[1] 4nst.a .03
0
.16 .16
[1] 4un0.c .17 .16
0
.03
[1] 5acb.c .18 .16 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
4cxa.a
4nst.a
4un0.c
5acb.c
[1] 4cxa.a
0
0.6 1.0 2.7
[1] 4nst.a 0.6
0
1.1 2.8
[1] 4un0.c 1.0 1.1
0
0.6
[1] 5acb.c 2.7 2.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
4cxa.a
4nst.a
4un0.c
5acb.c
[1] 4cxa.a
0
0.9 1.2 3.2
[1] 4nst.a 0.9
0
1.1 3.2
[1] 4un0.c 1.2 1.1
0
0.8
[1] 5acb.c 3.2 3.2 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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