If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

CDK9_HUMAN_1_331

Cyclin-dependent kinase 9 [Protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CDK9_HUMAN):D: Protein kinase (23:33, 46, 48, 66, 70, 79, 103:109, 149, 151, 153, 154, 156, 166:169)
R: T-loop (166:169)
23:33, 46, 48, 66, 70, 79, 103:109, 149, 151, 153, 154, 156, 166:169

Full PDB list

3blh, 3blq, 3blr, 3lq5, 3mi9, 3mia, 3my1, 3tn8, 3tnh, 3tni, 4bcf, 4bcg, 4bch, 4bci, 4bcj, 4ec9, 4imy, 4ogr, 4or5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
A
2
3
I
2
5
G
2
6
Q
2
7
G
2
8
T
2
9
F
3
0
E
3
2
V
3
3
A
4
6
K
4
8
E
6
6
L
7
0
V
7
9
F
1
0
3
D
1
0
4
F
1
0
5
C
1
0
6
E
1
0
7
H
1
0
8
D
1
0
9
D
1
4
9
K
1
5
1
A
1
5
3
N
1
5
4
L
1
5
6
A
1
6
6
D
1
6
7
F
1
6
8
[1]3blq.a atp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3blr.a cpb28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3lq5.a slq32 . . . . - - . . . . . . . . . . . . . . . . . . . . . . .
[1]3mi9.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3mia.a anp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3my1.a rfz20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3tn8.a f1816 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcf.a t6q33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcg.a t3c30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bch.a t7z33 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bci.a t3e27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcj.a t9n24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4imy.a amp23 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4or5.a yt31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4ogr.a adn19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
A
2
3
K
2
4
I
2
5
G
2
6
Q
2
7
G
2
8
T
2
9
F
3
0
G
3
1
E
3
2
V
3
3
A
4
6
K
4
8
E
6
6
L
7
0
V
7
9
F
1
0
3
D
1
0
4
F
1
0
5
C
1
0
6
E
1
0
7
H
1
0
8
D
1
0
9
D
1
4
9
K
1
5
1
A
1
5
3
N
1
5
4
L
1
5
6
A
1
6
6
D
1
6
7
F
1
6
8
G
1
6
9
[1]3blq.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3blr.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]3lq5.a . . . . * - - * . . . . * . . . . . . . . . . . . . . . . . . .
[1]3mi9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3mia.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3my1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3tn8.a . . . . . . * * * . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcf.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcg.a . . . . . . * * . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bch.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bci.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bcj.a . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . .
[1]4imy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4or5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4ogr.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3blq.a:atp,mg
3blr.a:cpb
3lq5.a:slq
3mi9.a is apo
3mia.a:anp,mg
3my1.a:rfz
3tn8.a:f18
4bcf.a:t6q
4bcg.a:t3c
4bch.a:t7z
4bci.a:t3e
4bcj.a:t9n
4imy.a:amp
4or5.a:yt3
4ogr.a:adn
[1] 3blq.a
0.1
0.1 0.5 - 0.6 0.5 0.2 0.7 0.2 0.3 0.8 0.4 1.4 0 0.1
[1] 3blr.a 4.7
0
0.8 - 4.1 0.5 0.2 1.0 0.5 0.5 1.0 0.6 1.0 0 0.3
[1] 3lq5.a 2.1 0.2
0
- 2.7 0.1 0.7 0.2 0.1 0.4 0.4 0.4 1.5 0.1 0.2
[1] 3mi9.a 0.1 0.2 0.3
-
0.6 0.2 0.7 0.5 0.2 0.2 0.5 0.3 1.4 0.2 0.1
[1] 3mia.a 0.2 0 0.1 -
0.2
0.1 0.3 0.1 0 0 0.2 0.1 1.2 0.1 0.1
[1] 3my1.a 0.6 0.1 0.4 - 0.8
0.1
0.3 0.4 0.2 1.0 0.1 0.1 1.4 0.1 0
[1] 3tn8.a 6.7 1.3 1.8 - 6.0 1.7
0.1
1.9 0.7 1.1 0.9 0.7 0.5 0.3 1.3
[1] 4bcf.a 3.4 0 0.3 - 3.6 0.2 0.2
0.2
0 0.1 0.2 0.1 0.7 0.1 0
[1] 4bcg.a 6.7 0.1 0.7 - 5.1 0.1 0.1 1.0
0
0.7 0.2 0.1 0.9 1.8 0.1
[1] 4bch.a 3.8 0 0.5 - 3.5 0.3 0.1 0.4 0
0.2
0.7 0.3 0.8 0.1 0.3
[1] 4bci.a 1.0 0.1 0.6 - 1.4 0.2 0 0.6 0 0.5
0.1
0 1.0 0 0
[1] 4bcj.a 1.4 0.1 0.7 - 3.0 0.2 0 1.2 0.1 0.5 0.3
0.1
0.8 0.1 0.2
[1] 4imy.a 0.1 0.2 0.5 - 0.5 0.1 0.3 0.8 0.2 0.4 0.2 0.2
0.7
0 0.1
[1] 4or5.a 0.3 0.3 0.3 - 0.3 0.2 0.5 0.5 0.3 0.4 0.4 0.4 1.1
0.2
0.1
[2] 4ogr.a 3.5 0.2 0.4 - 4.2 0.4 0.9 0.6 0.2 0.8 0.3 0.5 2.3 0.1
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
3blq.a
3blr.a
3lq5.a
3mi9.a
3mia.a
3my1.a
3tn8.a
4bcf.a
4bcg.a
4bch.a
4bci.a
4bcj.a
4imy.a
4or5.a
4ogr.a
[1] 3blq.a
0
.17 .13 .06 .05 .10 .29 .16 .27 .17 .08 .14 .05 .06 .21
[1] 3blr.a .17
0
.18 .19 .18 .22 .20 .09 .14 .07 .15 .11 .18 .19 .33
[1] 3lq5.a .13 .18
0
.11 .10 .13 .28 .16 .27 .17 .07 .13 .10 .12 .20
[1] 3mi9.a .06 .19 .11
0
.03 .10 .29 .15 .28 .17 .08 .14 .05 .04 .20
[1] 3mia.a .05 .18 .10 .03
0
.09 .28 .13 .25 .14 .06 .12 .03 .04 .19
[1] 3my1.a .10 .22 .13 .10 .09
0
.26 .17 .27 .18 .07 .12 .06 .08 .18
[1] 3tn8.a .29 .20 .28 .29 .28 .26
0
.16 .11 .16 .23 .17 .25 .27 .36
[1] 4bcf.a .16 .09 .16 .15 .13 .17 .16
0
.14 .03 .11 .05 .12 .13 .29
[1] 4bcg.a .27 .14 .27 .28 .25 .27 .11 .14
0
.15 .22 .17 .25 .26 .37
[1] 4bch.a .17 .07 .17 .17 .14 .18 .16 .03 .15
0
.12 .05 .13 .15 .31
[1] 4bci.a .08 .15 .07 .08 .06 .07 .23 .11 .22 .12
0
.07 .05 .08 .22
[1] 4bcj.a .14 .11 .13 .14 .12 .12 .17 .05 .17 .05 .07
0
.10 .13 .28
[1] 4imy.a .05 .18 .10 .05 .03 .06 .25 .12 .25 .13 .05 .10
0
.03 .20
[1] 4or5.a .06 .19 .12 .04 .04 .08 .27 .13 .26 .15 .08 .13 .03
0
.19
[2] 4ogr.a .21 .33 .20 .20 .19 .18 .36 .29 .37 .31 .22 .28 .20 .19
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

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
3blq.a
3blr.a
3lq5.a
3mi9.a
3mia.a
3my1.a
3tn8.a
4bcf.a
4bcg.a
4bch.a
4bci.a
4bcj.a
4imy.a
4or5.a
4ogr.a
[1] 3blq.a
0
2.3 1.8 3.0 3.1 2.9 3.3 2.6 2.6 2.5 3.0 2.9 3.1 3.1 1.8
[1] 3blr.a 2.3
0
1.0 2.8 2.9 1.4 1.7 0.8 1.1 1.1 1.7 1.4 2.6 2.9 1.9
[1] 3lq5.a 1.8 1.0
0
2.8 2.8 1.0 1.0 0.9 1.0 1.3 1.6 1.2 2.6 2.8 1.1
[1] 3mi9.a 3.0 2.8 2.8
0
0.3 2.5 3.5 2.9 2.9 2.4 2.0 2.2 0.8 0.3 3.7
[1] 3mia.a 3.1 2.9 2.8 0.3
0
2.6 3.6 3.0 3.0 2.5 2.1 2.3 0.8 0.3 3.8
[1] 3my1.a 2.9 1.4 1.0 2.5 2.6
0
1.6 1.4 1.3 1.2 1.1 0.8 2.2 2.6 2.5
[1] 3tn8.a 3.3 1.7 1.0 3.5 3.6 1.6
0
1.5 1.1 1.8 2.1 1.8 3.2 3.5 2.4
[1] 4bcf.a 2.6 0.8 0.9 2.9 3.0 1.4 1.5
0
0.9 1.0 1.7 1.2 2.7 2.9 2.2
[1] 4bcg.a 2.6 1.1 1.0 2.9 3.0 1.3 1.1 0.9
0
1.1 1.6 1.3 2.7 2.9 2.1
[1] 4bch.a 2.5 1.1 1.3 2.4 2.5 1.2 1.8 1.0 1.1
0
1.1 1.0 2.1 2.4 2.4
[1] 4bci.a 3.0 1.7 1.6 2.0 2.1 1.1 2.1 1.7 1.6 1.1
0
0.7 1.7 2.0 2.9
[1] 4bcj.a 2.9 1.4 1.2 2.2 2.3 0.8 1.8 1.2 1.3 1.0 0.7
0
2.0 2.3 2.8
[1] 4imy.a 3.1 2.6 2.6 0.8 0.8 2.2 3.2 2.7 2.7 2.1 1.7 2.0
0
0.8 3.5
[1] 4or5.a 3.1 2.9 2.8 0.3 0.3 2.6 3.5 2.9 2.9 2.4 2.0 2.3 0.8
0
3.7
[2] 4ogr.a 1.8 1.9 1.1 3.7 3.8 2.5 2.4 2.2 2.1 2.4 2.9 2.8 3.5 3.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.0 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
3blq.a
3blr.a
3lq5.a
3mi9.a
3mia.a
3my1.a
3tn8.a
4bcf.a
4bcg.a
4bch.a
4bci.a
4bcj.a
4imy.a
4or5.a
4ogr.a
[1] 3blq.a
0
2.9 2.1 4.0 4.1 3.4 3.3 3.4 3.1 3.4 3.8 3.8 3.8 4.2 2.0
[1] 3blr.a 2.9
0
1.8 3.5 3.5 2.0 2.2 1.3 1.8 1.3 2.0 1.8 3.1 3.6 2.5
[1] 3lq5.a 2.1 1.8
0
3.7 3.8 1.8 1.7 2.1 1.7 2.1 2.4 2.2 3.4 3.7 1.6
[1] 3mi9.a 4.0 3.5 3.7
0
0.4 3.3 4.4 3.6 4.0 3.4 3.1 3.3 1.1 0.8 4.4
[1] 3mia.a 4.1 3.5 3.8 0.4
0
3.4 4.5 3.7 4.1 3.4 3.2 3.4 1.2 0.8 4.5
[1] 3my1.a 3.4 2.0 1.8 3.3 3.4
0
2.3 2.0 2.0 1.8 1.6 1.5 2.8 3.4 3.3
[1] 3tn8.a 3.3 2.2 1.7 4.4 4.5 2.3
0
2.2 1.5 2.4 2.8 2.6 3.9 4.5 2.7
[1] 4bcf.a 3.4 1.3 2.1 3.6 3.7 2.0 2.2
0
1.6 1.1 1.8 1.6 3.2 3.7 3.0
[1] 4bcg.a 3.1 1.8 1.7 4.0 4.1 2.0 1.5 1.6
0
1.6 2.1 2.0 3.6 4.1 2.6
[1] 4bch.a 3.4 1.3 2.1 3.4 3.4 1.8 2.4 1.1 1.6
0
1.3 1.4 2.9 3.4 3.0
[1] 4bci.a 3.8 2.0 2.4 3.1 3.2 1.6 2.8 1.8 2.1 1.3
0
0.9 2.7 3.2 3.7
[1] 4bcj.a 3.8 1.8 2.2 3.3 3.4 1.5 2.6 1.6 2.0 1.4 0.9
0
2.9 3.4 3.5
[1] 4imy.a 3.8 3.1 3.4 1.1 1.2 2.8 3.9 3.2 3.6 2.9 2.7 2.9
0
1.3 4.1
[1] 4or5.a 4.2 3.6 3.7 0.8 0.8 3.4 4.5 3.7 4.1 3.4 3.2 3.4 1.3
0
4.5
[2] 4ogr.a 2.0 2.5 1.6 4.4 4.5 3.3 2.7 3.0 2.6 3.0 3.7 3.5 4.1 4.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...