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PTN11_HUMAN_249_534

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: Tyrosine-protein phosphatase (278:280, 282, 334, 335, 357, 362:368, 427, 430, 463:465, 467:469, 510, 511, 514)
R: Substrate binding (463:465, 467:469)
40, 57:64, 70, 278:280, 282, 334, 335, 357, 362:368, 427, 430, 463:465, 467:469, 510, 511, 514

Full PDB list

2shp, 3b7o, 3mow, 3o5x, 3zm0, 3zm1, 3zm2, 3zm3, 4dgp, 4dgx, 4gwf, 4h1o, 4h34, 4nwf, 4nwg, 4ohd, 4ohe, 4ohh, 4ohi, 4ohl, 4pvg, 4rdd, 5ehp, 5ehr, 5i6v, 5ibm, 5ibs, 5xzr, 6bn5 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
R
2
7
8
Y
2
7
9
I
2
8
2
L
3
3
4
Q
3
3
5
T
3
5
7
R
3
6
2
K
3
6
4
K
3
6
6
V
3
6
8
W
4
2
7
C
4
6
3
S
4
6
4
A
4
6
5
I
4
6
7
G
4
6
8
R
4
6
9
Q
5
1
0
T
5
1
1
Q
5
1
4
[1]4gwf.b none . C . . . . . . . . . . . . . . . . . .
[1]4h1o.a none . . . . . . . . . . . . . . . . . . . .
[1]4nwf.b none . . . . . . . . . . . . . . . . . . . .
[1]4ohe.a none . . . . . . . . . . . . . . . A . . . .
[1]4ohh.a none . . . . . . . . . . . . . . . . . P . .
[1]4ohi.a none . . . . . . . . . . . . . . . . . . . E
[2]3b7o.a mlt9 . . . . . . . . . . . . . . . . . . . .
[2]3mow.a b2b46 . . . . . . . . . . . . . . . . . . . .
[2]3o5x.a jzg42 . . . . . . . . . . . . . . . . . . . .
[2]4pvg.a 2wt39 . . . . . . . . . . . . . . . . . . . .
[2]4rdd.a 3lu28 . . . . . . . . . . . . . . . . . . . .
[3]4ohd.a none . . . . . . . . . . . . . T . . . . . .

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
D
4
0
Q
5
7
N
5
8
T
5
9
G
6
0
D
6
1
Y
6
2
Y
6
3
D
6
4
K
7
0
R
2
7
8
Y
2
7
9
K
2
8
0
I
2
8
2
L
3
3
4
Q
3
3
5
T
3
5
7
R
3
6
2
G
3
6
3
K
3
6
4
S
3
6
5
K
3
6
6
C
3
6
7
V
3
6
8
W
4
2
7
H
4
3
0
C
4
6
3
S
4
6
4
A
4
6
5
I
4
6
7
G
4
6
8
R
4
6
9
Q
5
1
0
T
5
1
1
Q
5
1
4
[1]4gwf.b . . * * * * * . . * . C . . . * . . . * . . . . . . . . . . . . . . .
[1]4h1o.a . * * * * G * . . * . . . . . . . . . . . . . . . . . * . . . . . . .
[1]4nwf.b . * * * * * * . . * . . . . . . . . . * . . . . . . . . . . . . . . .
[1]4ohe.a . . . * * * * . . * . . . . . . . . . . . . . . . . . * . . A . . . .
[1]4ohh.a . * * * * * * . . * . . . . . . . * . . . . . . . . . * . . . . P . .
[1]4ohi.a . * . * * * * . . * . . . . . . . . . * . . . . . . . * . . . . . . E
[2]3b7o.a - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3mow.a - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3o5x.a - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4pvg.a - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4rdd.a - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . .
[3]4ohd.a . . . * * * * . . * . . . . . . . . . . * * . . . . . . T . . . . . .

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.b is apo
4h1o.a is apo
4nwf.b is apo
4ohe.a is apo
4ohh.a is apo
4ohi.a is apo
3b7o.a:mlt
3mow.a:b2b
3o5x.a:jzg
4pvg.a:2wt
4rdd.a:3lu
4ohd.a is apo
[1] 4gwf.b
-
- - - - - 2.8 9.7 9.5 10 13 -
[1] 4h1o.a -
-
- - - - 1.5 7.0 9.2 11 14 -
[1] 4nwf.b - -
-
- - - 3.0 8.8 11 10 13 -
[1] 4ohe.a - - -
-
- - 2.5 7.9 8.8 11 13 -
[1] 4ohh.a - - - -
-
- 2.8 9.8 13 11 14 -
[1] 4ohi.a - - - - -
-
2.8 8.5 11 9.9 13 -
[2] 3b7o.a - - - - - -
0
0.3 0.2 0 0 -
[2] 3mow.a - - - - - - 0.4
0
0.3 0.2 0.2 -
[2] 3o5x.a - - - - - - 0.1 0.4
0.2
0 0.5 -
[2] 4pvg.a - - - - - - 0.4 0.5 0.6
0
0.8 -
[2] 4rdd.a - - - - - - 0.1 0 0.1 0
0
-
[3] 4ohd.a - - - - - - 2.3 15 9.4 9.0 13
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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.b
4h1o.a
4nwf.b
4ohe.a
4ohh.a
4ohi.a
3b7o.a
3mow.a
3o5x.a
4pvg.a
4rdd.a
4ohd.a
[1] 4gwf.b
0
.19 .06 .22 .19 .12 .51 .50 .53 .53 .51 .26
[1] 4h1o.a .19
0
.18 .17 .19 .15 .54 .53 .54 .54 .53 .33
[1] 4nwf.b .06 .18
0
.23 .17 .09 .52 .51 .54 .54 .53 .27
[1] 4ohe.a .22 .17 .23
0
.29 .20 .44 .41 .43 .45 .42 .29
[1] 4ohh.a .19 .19 .17 .29
0
.15 .60 .60 .62 .60 .61 .34
[1] 4ohi.a .12 .15 .09 .20 .15
0
.51 .51 .53 .52 .52 .25
[2] 3b7o.a .51 .54 .52 .44 .60 .51
0
.03 .03 .05 .01 .61
[2] 3mow.a .50 .53 .51 .41 .60 .51 .03
0
.03 .03 .02 .61
[2] 3o5x.a .53 .54 .54 .43 .62 .53 .03 .03
0
.03 .02 .62
[2] 4pvg.a .53 .54 .54 .45 .60 .52 .05 .03 .03
0
.05 .64
[2] 4rdd.a .51 .53 .53 .42 .61 .52 .01 .02 .02 .05
0
.61
[3] 4ohd.a .26 .33 .27 .29 .34 .25 .61 .61 .62 .64 .61
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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.b
4h1o.a
4nwf.b
4ohe.a
4ohh.a
4ohi.a
3b7o.a
3mow.a
3o5x.a
4pvg.a
4rdd.a
4ohd.a
[1] 4gwf.b
0
0.8 0.3 1.1 0.7 0.7 0.7 0.7 0.7 0.7 0.5 2.6
[1] 4h1o.a 0.8
0
0.7 1.1 0.6 0.5 0.5 0.5 0.5 0.7 0.7 2.5
[1] 4nwf.b 0.3 0.7
0
1.3 0.6 0.7 0.7 0.7 0.7 0.7 0.6 2.5
[1] 4ohe.a 1.1 1.1 1.3
0
1.3 1.1 0.9 0.8 0.8 0.8 0.6 2.6
[1] 4ohh.a 0.7 0.6 0.6 1.3
0
0.5 0.7 0.7 0.7 0.8 0.8 2.5
[1] 4ohi.a 0.7 0.5 0.7 1.1 0.5
0
0.7 0.6 0.6 0.7 0.8 2.5
[2] 3b7o.a 0.7 0.5 0.7 0.9 0.7 0.7
0
0.3 0.3 0.5 0.6 2.9
[2] 3mow.a 0.7 0.5 0.7 0.8 0.7 0.6 0.3
0
0.2 0.4 0.5 3.0
[2] 3o5x.a 0.7 0.5 0.7 0.8 0.7 0.6 0.3 0.2
0
0.4 0.5 2.9
[2] 4pvg.a 0.7 0.7 0.7 0.8 0.8 0.7 0.5 0.4 0.4
0
0.4 3.1
[2] 4rdd.a 0.5 0.7 0.6 0.6 0.8 0.8 0.6 0.5 0.5 0.4
0
3.2
[3] 4ohd.a 2.6 2.5 2.5 2.6 2.5 2.5 2.9 3.0 2.9 3.1 3.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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.b
4h1o.a
4nwf.b
4ohe.a
4ohh.a
4ohi.a
3b7o.a
3mow.a
3o5x.a
4pvg.a
4rdd.a
4ohd.a
[1] 4gwf.b
0
1.7 1.0 1.8 1.6 1.4 1.1 1.6 1.6 1.7 1.5 3.3
[1] 4h1o.a 1.7
0
1.4 2.0 1.0 1.2 1.0 1.5 1.4 1.3 1.2 3.3
[1] 4nwf.b 1.0 1.4
0
1.9 1.3 1.2 1.0 1.3 1.3 1.4 1.3 3.2
[1] 4ohe.a 1.8 2.0 1.9
0
2.1 1.9 1.9 1.8 1.8 2.2 1.8 3.2
[1] 4ohh.a 1.6 1.0 1.3 2.1
0
1.2 1.0 1.6 1.4 1.3 1.3 3.2
[1] 4ohi.a 1.4 1.2 1.2 1.9 1.2
0
0.9 1.4 1.3 1.3 1.2 3.3
[2] 3b7o.a 1.1 1.0 1.0 1.9 1.0 0.9
0
0.8 0.8 0.9 0.8 3.7
[2] 3mow.a 1.6 1.5 1.3 1.8 1.6 1.4 0.8
0
0.7 1.2 1.2 3.8
[2] 3o5x.a 1.6 1.4 1.3 1.8 1.4 1.3 0.8 0.7
0
1.1 1.0 3.8
[2] 4pvg.a 1.7 1.3 1.4 2.2 1.3 1.3 0.9 1.2 1.1
0
1.4 3.9
[2] 4rdd.a 1.5 1.2 1.3 1.8 1.3 1.2 0.8 1.2 1.0 1.4
0
3.9
[3] 4ohd.a 3.3 3.3 3.2 3.2 3.2 3.3 3.7 3.8 3.8 3.9 3.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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