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PTN22_HUMAN_1_298

Tyrosine-protein phosphatase non-receptor type 22 [Protein-tyrosine phosphatase family. Non-receptor class 4 subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (PTN22_HUMAN):D: Tyrosine-protein phosphatase (28, 32, 55, 56, 58:63, 133, 134, 136:138, 194:196, 227:233, 271, 274, 275, 277, 278)
R: Substrate binding (227:233)
28, 32, 55, 56, 58:63, 133, 134, 136:138, 194:196, 227:233, 271, 274, 275, 277, 278

Full PDB list

2p6x, 2qcj, 2qct, 3brh, 3h2x, 3olr, 3omh, 4j51 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
3
2
I
5
5
N
5
8
R
5
9
Y
6
0
K
6
1
D
6
2
I
6
3
E
1
3
3
M
1
3
4
K
1
3
6
K
1
3
7
K
1
3
8
D
1
9
5
H
1
9
6
C
2
2
7
S
2
2
8
A
2
2
9
G
2
3
0
C
2
3
1
G
2
3
2
R
2
3
3
S
2
7
1
Q
2
7
4
T
2
7
5
Q
2
7
8
[1]2p6x.a none . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qct.a 56134 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3brh.a DNEYTAR59 . . . . . . . . . . . . . A . S . . . . . . . . . .
[1]3brh.b DNEY36 . . . . . . . . . . . . . A . S . . . . . . . . . .
[1]3olr.a YGEEptrDDLY87 . . . . . . . . . . . . . . . S . . . . . . . . . .
[1]3olr.b YGEEptrDDL74 . . . . . . . . . . . . . . . S . . . . . . . . . .
[1]3omh.a DGEEptrDDPF81 . . . . . . . . . . . . . . . S . . . . . . . . . .
[1]3omh.d DGEEptrDDP69 . . . . . . . . . . . . . . . S . . . . . . . . . .
[1]4j51.b n7536 . . . . . . . . . . . . . . . . . . . . . . . . . .

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
F
2
8
K
3
2
I
5
5
K
5
6
N
5
8
R
5
9
Y
6
0
K
6
1
D
6
2
I
6
3
E
1
3
3
M
1
3
4
K
1
3
6
K
1
3
7
K
1
3
8
P
1
9
4
D
1
9
5
H
1
9
6
C
2
2
7
S
2
2
8
A
2
2
9
G
2
3
0
C
2
3
1
G
2
3
2
R
2
3
3
S
2
7
1
Q
2
7
4
T
2
7
5
E
2
7
7
Q
2
7
8
[1]2p6x.a . * . . . . . . . . . . . . . . . . . . . . * . . . . . . .
[1]2qct.a . . . . . . . . . . . . . . . . . . . . . . . . . . * . . .
[1]3brh.a . * . . . . . . . . . . . . . . A * S . . . . . . . * . . .
[1]3brh.b . * . . . . . * . . . . . . . . A * S . . . . . . . * . . .
[1]3olr.a . * . . . . . * . . . . . . . . . . S . . . . . . . * . . .
[1]3olr.b . * . . . . . * . . . . . . . . . . S . . . . . . . * . . .
[1]3omh.a . * . . . . . * . . . . . . . . . . S . . . . . . . . . . .
[1]3omh.d . * . . . . . . . . . . . . . . . . S . . . . . . . * . . .
[1]4j51.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
2p6x.a is apo
2qct.a:561
3brh.a:DNEYTAR
3brh.b:DNEY
3olr.a:YGEEptrDDLY
3olr.b:YGEEptrDDL
3omh.a:DGEEptrDDPF
3omh.d:DGEEptrDDP
4j51.b:n75
[1] 2p6x.a
-
1.1 1.1 0.1 1.2 1.2 0.9 1.0 0
[1] 2qct.a -
0
0.9 0.2 1.7 1.9 1.8 0.9 0.6
[1] 3brh.a - 5.2
1.2
0.4 4.6 1.6 1.1 3.1 2.3
[1] 3brh.b - 4.3 3.9
0.4
4.7 1.9 2.5 3.6 2.9
[1] 3olr.a - 2.1 3.1 0.2
0.4
0.4 0.1 0.3 0.9
[1] 3olr.b - 2.3 2.7 0 0.3
0.3
0.1 0 0.3
[1] 3omh.a - 2.3 3.0 0.1 0.3 0.3
0
0.5 0.7
[1] 3omh.d - 2.2 1.7 0 0.7 0.6 0.6
0.4
0.2
[1] 4j51.b - 0.9 0.9 0 1.2 1.4 1.2 1.1
0.1
[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
2p6x.a
2qct.a
3brh.a
3brh.b
3olr.a
3olr.b
3omh.a
3omh.d
4j51.b
[1] 2p6x.a
0
.10 .24 .24 .13 .13 .14 .10 .02
[1] 2qct.a .10
0
.27 .28 .17 .18 .18 .11 .10
[1] 3brh.a .24 .27
0
.08 .22 .23 .23 .19 .24
[1] 3brh.b .24 .28 .08
0
.20 .21 .21 .24 .25
[1] 3olr.a .13 .17 .22 .20
0
.02 .05 .10 .13
[1] 3olr.b .13 .18 .23 .21 .02
0
.05 .11 .13
[1] 3omh.a .14 .18 .23 .21 .05 .05
0
.11 .15
[1] 3omh.d .10 .11 .19 .24 .10 .11 .11
0
.10
[1] 4j51.b .02 .10 .24 .25 .13 .13 .15 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
2p6x.a
2qct.a
3brh.a
3brh.b
3olr.a
3olr.b
3omh.a
3omh.d
4j51.b
[1] 2p6x.a
0
1.1 3.7 4.0 0.9 0.8 1.0 1.2 0.2
[1] 2qct.a 1.1
0
3.5 3.7 0.9 1.0 0.9 1.0 1.1
[1] 3brh.a 3.7 3.5
0
0.5 3.7 3.8 3.7 3.4 3.7
[1] 3brh.b 4.0 3.7 0.5
0
3.9 4.0 3.9 3.6 3.9
[1] 3olr.a 0.9 0.9 3.7 3.9
0
0.3 0.5 0.7 0.8
[1] 3olr.b 0.8 1.0 3.8 4.0 0.3
0
0.6 0.8 0.8
[1] 3omh.a 1.0 0.9 3.7 3.9 0.5 0.6
0
0.7 1.0
[1] 3omh.d 1.2 1.0 3.4 3.6 0.7 0.8 0.7
0
1.1
[1] 4j51.b 0.2 1.1 3.7 3.9 0.8 0.8 1.0 1.1
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
2p6x.a
2qct.a
3brh.a
3brh.b
3olr.a
3olr.b
3omh.a
3omh.d
4j51.b
[1] 2p6x.a
0
1.6 3.9 4.0 1.1 1.1 1.2 1.6 0.3
[1] 2qct.a 1.6
0
3.4 3.5 1.6 1.7 1.6 1.6 1.9
[1] 3brh.a 3.9 3.4
0
1.3 4.1 4.2 4.0 3.6 4.0
[1] 3brh.b 4.0 3.5 1.3
0
4.1 4.2 4.1 3.6 4.1
[1] 3olr.a 1.1 1.6 4.1 4.1
0
0.5 0.8 1.4 1.6
[1] 3olr.b 1.1 1.7 4.2 4.2 0.5
0
0.9 1.5 1.6
[1] 3omh.a 1.2 1.6 4.0 4.1 0.8 0.9
0
1.3 1.6
[1] 3omh.d 1.6 1.6 3.6 3.6 1.4 1.5 1.3
0
2.0
[1] 4j51.b 0.3 1.9 4.0 4.1 1.6 1.6 1.6 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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