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.

RET_HUMAN_702_1013

Proto-oncogene tyrosine-protein kinase receptor Ret [Protein kinase superfamily. Tyr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RET_HUMAN):D: Protein kinase (730:735, 738, 756, 758, 775, 779, 788, 802, 804:811, 878, 879, 881, 891, 892)
R: Inhibitors binding (805:807)
730:735, 738, 756, 758, 775, 779, 788, 802, 804:811, 878, 879, 881, 891, 892

Full PDB list

2ivs, 2ivt, 2ivu, 2ivv, 2x2k, 2x2l, 2x2m, 4cki, 4ckj, 5amn, 5fm2, 5fm3 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
7
3
0
G
7
3
1
E
7
3
2
G
7
3
3
F
7
3
5
V
7
3
8
A
7
5
6
K
7
5
8
E
7
7
5
L
7
7
9
I
7
8
8
L
8
0
2
V
8
0
4
E
8
0
5
Y
8
0
6
A
8
0
7
K
8
0
8
Y
8
0
9
G
8
1
0
S
8
1
1
R
8
7
8
N
8
7
9
L
8
8
1
S
8
9
1
D
8
9
2
[1]2ivs.a ack22 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ivt.a amp23 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ivu.a zd630 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ivv.a pp121 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2k.a x2k19 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2l.a x2l20 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2m.a x2m18 . . . - . . . . . . . . . . . . . . . . . . . . .
[1]4cki.a adn19 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5amn.a dtq22 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5fm3.a pp121 . . . . . . . . . . . . . . . . . * . . . . . . .

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
L
7
3
0
G
7
3
1
E
7
3
2
G
7
3
3
E
7
3
4
F
7
3
5
V
7
3
8
A
7
5
6
K
7
5
8
E
7
7
5
L
7
7
9
I
7
8
8
L
8
0
2
V
8
0
4
E
8
0
5
Y
8
0
6
A
8
0
7
K
8
0
8
Y
8
0
9
G
8
1
0
S
8
1
1
R
8
7
8
N
8
7
9
L
8
8
1
S
8
9
1
D
8
9
2
[1]2ivs.a . . . . . . . . * . . . . . . . . . . . . . . . . *
[1]2ivt.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ivu.a . . . . . . . . . . . . . . . . . . . . . . . . . *
[1]2ivv.a . . . . . . . . . . . . . . . . . . . . . . . . . *
[1]2x2k.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2l.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2x2m.a . . . - - . . . . . . . . . . . . . . . . . . . . .
[1]4cki.a . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]5amn.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5fm3.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
2ivs.a:ack
2ivt.a:amp
2ivu.a:zd6
2ivv.a:pp1
2x2k.a:x2k
2x2l.a:x2l
2x2m.a:x2m
4cki.a:adn
5amn.a:dtq
5fm3.a:pp1
[1] 2ivs.a
0
0.8 1.7 1.5 0.2 0.2 0.1 0 1.3 2.0
[1] 2ivt.a 0.2
0
0.6 0.2 0 0.1 0 0 0.4 0.2
[1] 2ivu.a 0.1 0.7
0
0 0.1 0 0 0 0.1 0
[1] 2ivv.a 0 1.0 0.3
0
0.1 0 0 0 0.3 0
[1] 2x2k.a 0.3 0.8 0.6 0.4
0
0 0 0.2 0.4 0.3
[1] 2x2l.a 0.4 0.5 0.6 0.3 0
0
0 0.2 0.6 0.3
[1] 2x2m.a 0.2 0.1 1.0 0.8 0 0.1
0
0.2 1.2 0.7
[1] 4cki.a 0 0.6 1.5 1.1 0.2 0.1 0.1
0
1.5 1.3
[1] 5amn.a 0.1 0.5 0.1 0 0.1 0 0.1 0.1
0
0
[1] 5fm3.a 0.4 1.1 0.8 0.3 0.4 1.1 0 0.3 0.6
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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
2ivs.a
2ivt.a
2ivu.a
2ivv.a
2x2k.a
2x2l.a
2x2m.a
4cki.a
5amn.a
5fm3.a
[1] 2ivs.a
0
.11 .11 .10 .09 .11 .09 .04 .11 .17
[1] 2ivt.a .11
0
.06 .05 .04 .05 .03 .07 .04 .09
[1] 2ivu.a .11 .06
0
.03 .04 .05 .08 .08 .02 .13
[1] 2ivv.a .10 .05 .03
0
.05 .05 .07 .07 .03 .12
[1] 2x2k.a .09 .04 .04 .05
0
.03 .07 .07 .03 .12
[1] 2x2l.a .11 .05 .05 .05 .03
0
.06 .08 .04 .12
[1] 2x2m.a .09 .03 .08 .07 .07 .06
0
.05 .06 .11
[1] 4cki.a .04 .07 .08 .07 .07 .08 .05
0
.07 .13
[1] 5amn.a .11 .04 .02 .03 .03 .04 .06 .07
0
.11
[1] 5fm3.a .17 .09 .13 .12 .12 .12 .11 .13 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
2ivs.a
2ivt.a
2ivu.a
2ivv.a
2x2k.a
2x2l.a
2x2m.a
4cki.a
5amn.a
5fm3.a
[1] 2ivs.a
0
0.5 0.9 0.8 0.5 0.9 0.5 0.3 2.0 1.4
[1] 2ivt.a 0.5
0
0.6 0.5 0.6 0.7 0.4 0.5 1.7 1.3
[1] 2ivu.a 0.9 0.6
0
0.3 1.0 0.7 0.5 0.9 1.4 1.1
[1] 2ivv.a 0.8 0.5 0.3
0
0.9 0.6 0.4 0.8 1.5 1.1
[1] 2x2k.a 0.5 0.6 1.0 0.9
0
0.9 0.4 0.4 2.1 1.5
[1] 2x2l.a 0.9 0.7 0.7 0.6 0.9
0
0.4 0.9 1.7 1.1
[1] 2x2m.a 0.5 0.4 0.5 0.4 0.4 0.4
0
0.5 1.2 1.0
[1] 4cki.a 0.3 0.5 0.9 0.8 0.4 0.9 0.5
0
2.0 1.5
[1] 5amn.a 2.0 1.7 1.4 1.5 2.1 1.7 1.2 2.0
0
1.9
[1] 5fm3.a 1.4 1.3 1.1 1.1 1.5 1.1 1.0 1.5 1.9
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
2ivs.a
2ivt.a
2ivu.a
2ivv.a
2x2k.a
2x2l.a
2x2m.a
4cki.a
5amn.a
5fm3.a
[1] 2ivs.a
0
0.9 1.1 0.9 0.7 1.1 0.8 0.7 3.1 2.0
[1] 2ivt.a 0.9
0
0.8 0.7 0.8 1.0 0.6 1.0 2.4 1.9
[1] 2ivu.a 1.1 0.8
0
0.7 1.1 0.9 0.9 1.1 1.4 1.3
[1] 2ivv.a 0.9 0.7 0.7
0
0.8 0.6 0.6 1.0 1.5 1.3
[1] 2x2k.a 0.7 0.8 1.1 0.8
0
0.9 0.5 0.8 2.6 2.1
[1] 2x2l.a 1.1 1.0 0.9 0.6 0.9
0
0.5 1.1 2.4 2.0
[1] 2x2m.a 0.8 0.6 0.9 0.6 0.5 0.5
0
0.9 1.2 1.3
[1] 4cki.a 0.7 1.0 1.1 1.0 0.8 1.1 0.9
0
3.1 2.1
[1] 5amn.a 3.1 2.4 1.4 1.5 2.6 2.4 1.2 3.1
0
2.7
[1] 5fm3.a 2.0 1.9 1.3 1.3 2.1 2.0 1.3 2.1 2.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...