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PTN11_HUMAN_103_220

Tyrosine-protein phosphatase non-receptor type 11 [Protein-tyrosine phosphatase family. Non-receptor class 2 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTN11_HUMAN):D: SH2 2 (112:114)
D: Tyrosine-protein phosphatase (249, 250, 253, 254, 257, 261, 493, 495, 496, 499, 500, 503)
108:111, 217:219
108:114, 217:219, 249, 250, 253, 254, 257, 261, 493, 495, 496, 499, 500, 503

Full PDB list

2shp, 4dgp, 4dgx, 4gwf, 4h1o, 4h34, 4jeg, 4nwf, 4nwg, 4ohd, 4ohe, 4ohh, 4ohi, 4ohl, 5df6, 5ehp, 5ehr, 5i6v, 5ibm, 5ibs, 5x7b, 5x94, 5xzr, 6bn5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
1
0
8
E
1
1
0
R
1
1
1
F
1
1
3
H
1
1
4
N
2
1
7
T
2
1
8
T
2
1
9
E
2
4
9
E
2
5
0
T
2
5
3
L
2
5
4
Q
2
5
7
L
2
6
1
P
4
9
5
K
4
9
6
Q
4
9
9
M
5
0
0
[1]4gwf.a pge10 . . . . . . . . . . . . . . . . . .
[1]4ohl.b none . . . . . . . . . . . . . . . . . .
[1]5ehp.a 5oa23 . . . . . . . . . . . . . . . . . .
[1]5ehr.a 5od23 . . . . . . . . . . . . . . . . . .
[1]5xzr.a 8j628 . . . . . . . . . . . . . . . . . .
[1]6bn5.a dzj23 . . . . . . . . . . . . . . . . . .
[2]4jeg.a none . . . . . . K E - - - - - - - - - -

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
T
1
0
8
S
1
0
9
E
1
1
0
R
1
1
1
W
1
1
2
F
1
1
3
H
1
1
4
N
2
1
7
T
2
1
8
T
2
1
9
E
2
4
9
E
2
5
0
T
2
5
3
L
2
5
4
Q
2
5
7
L
2
6
1
D
4
9
3
P
4
9
5
K
4
9
6
Q
4
9
9
M
5
0
0
S
5
0
3
[1]4gwf.a . . . . . . . . . . . . . . . . . . . . . .
[1]4ohl.b . . . . . . . . . . . . . . . . . . * . . .
[1]5ehp.a . . . . . . . . . . . . . . . . . . . . . .
[1]5ehr.a . . . . . . . . . . . . . . . . . . . . . .
[1]5xzr.a . . . . . . . . . . . . . . . . . . . . . .
[1]6bn5.a . . . . . . . . . . . . . . . . . . . . . .
[2]4jeg.a . . . * . . . . K E - - - - - - - - - - - -

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
4gwf.a:pge
4ohl.b is apo
5ehp.a:5oa
5ehr.a:5od
5xzr.a:8j6
6bn5.a:dzj
4jeg.a is apo
[1] 4gwf.a
0
- 0.2 0.1 0.4 0 -
[1] 4ohl.b 1.0
-
1.8 1.5 2.9 3.3 -
[1] 5ehp.a 0.4 -
0
0 0.4 0.7 -
[1] 5ehr.a 0 - 0.7
0
1.2 0.4 -
[1] 5xzr.a 0 - 0.1 0
0
0 -
[1] 6bn5.a 0 - 0.4 0.1 0.3
0
-
[2] 4jeg.a 1.9 - 6.1 7.0 7.2 2.4
-
[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
4gwf.a
4ohl.b
5ehp.a
5ehr.a
5xzr.a
6bn5.a
4jeg.a
[1] 4gwf.a
0
.18 .04 .08 .02 .02 .32
[1] 4ohl.b .18
0
.20 .23 .18 .20 .49
[1] 5ehp.a .04 .20
0
.06 .03 .05 .29
[1] 5ehr.a .08 .23 .06
0
.06 .06 .35
[1] 5xzr.a .02 .18 .03 .06
0
.02 .32
[1] 6bn5.a .02 .20 .05 .06 .02
0
.32
[2] 4jeg.a .32 .49 .29 .35 .32 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
4gwf.a
4ohl.b
5ehp.a
5ehr.a
5xzr.a
6bn5.a
4jeg.a
[1] 4gwf.a
0
1.1 0.5 0.8 0.7 0.8 2.5
[1] 4ohl.b 1.1
0
1.3 1.4 1.6 1.2 2.7
[1] 5ehp.a 0.5 1.3
0
0.4 0.7 1.0 2.6
[1] 5ehr.a 0.8 1.4 0.4
0
0.8 1.2 2.7
[1] 5xzr.a 0.7 1.6 0.7 0.8
0
1.0 2.6
[1] 6bn5.a 0.8 1.2 1.0 1.2 1.0
0
2.6
[2] 4jeg.a 2.5 2.7 2.6 2.7 2.6 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
4gwf.a
4ohl.b
5ehp.a
5ehr.a
5xzr.a
6bn5.a
4jeg.a
[1] 4gwf.a
0
1.5 1.0 1.3 1.1 1.1 2.8
[1] 4ohl.b 1.5
0
1.6 1.7 1.9 1.6 2.9
[1] 5ehp.a 1.0 1.6
0
0.6 1.0 1.2 2.8
[1] 5ehr.a 1.3 1.7 0.6
0
1.1 1.4 2.9
[1] 5xzr.a 1.1 1.9 1.0 1.1
0
1.3 2.7
[1] 6bn5.a 1.1 1.6 1.2 1.4 1.3
0
2.9
[2] 4jeg.a 2.8 2.9 2.8 2.9 2.7 2.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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