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NTRK2_HUMAN_526_822

BDNF/NT-3 growth factors receptor [Protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (NTRK2_HUMAN):D: Protein kinase (544, 545, 549, 552, 570, 572, 588, 592, 595, 600, 601, 617:621, 623, 667, 672, 674, 681, 683, 692:695, 697)544, 545, 549, 552, 570, 572, 588, 592, 595, 600, 601, 617:621, 623, 667, 672, 674, 681, 683, 692:695, 697

Full PDB list

4asz, 4at3, 4at4, 4at5

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
5
4
4
F
5
4
9
V
5
5
2
A
5
7
0
K
5
7
2
E
5
8
8
L
5
9
2
L
5
9
5
I
6
0
0
V
6
0
1
F
6
1
7
E
6
1
8
Y
6
1
9
M
6
2
0
K
6
2
1
G
6
2
3
F
6
7
2
H
6
7
4
N
6
8
1
L
6
8
3
I
6
9
2
G
6
9
3
D
6
9
4
F
6
9
5
M
6
9
7
[1]4at4.a t6e31 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4at5.a muj27 . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4asz.a none . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4at3.a lti24 . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
5
4
4
G
5
4
5
F
5
4
9
V
5
5
2
A
5
7
0
K
5
7
2
E
5
8
8
L
5
9
2
L
5
9
5
I
6
0
0
V
6
0
1
F
6
1
7
E
6
1
8
Y
6
1
9
M
6
2
0
K
6
2
1
G
6
2
3
L
6
6
7
F
6
7
2
H
6
7
4
N
6
8
1
L
6
8
3
I
6
9
2
G
6
9
3
D
6
9
4
F
6
9
5
M
6
9
7
[1]4at4.a . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]4at5.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4asz.a . . . . . . . . . . . . . . . . . . . . . . . * . * .
[2]4at3.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4at4.a:t6e
4at5.a:muj
4asz.a is apo
4at3.a:lti
[1] 4at4.a
0
1.5 - 3.3
[1] 4at5.a 1.2
0
- 1.7
[2] 4asz.a 3.9 5.9
-
7.2
[2] 4at3.a 5.9 2.8 -
0
[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
4at4.a
4at5.a
4asz.a
4at3.a
[1] 4at4.a
0
.12 .24 .29
[1] 4at5.a .12
0
.24 .27
[2] 4asz.a .24 .24
0
.12
[2] 4at3.a .29 .27 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
4at4.a
4at5.a
4asz.a
4at3.a
[1] 4at4.a
0
0.9 1.0 3.3
[1] 4at5.a 0.9
0
1.1 3.2
[2] 4asz.a 1.0 1.1
0
3.6
[2] 4at3.a 3.3 3.2 3.6
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
4at4.a
4at5.a
4asz.a
4at3.a
[1] 4at4.a
0
1.5 1.9 4.2
[1] 4at5.a 1.5
0
2.1 4.3
[2] 4asz.a 1.9 2.1
0
4.3
[2] 4at3.a 4.2 4.3 4.3
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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