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EPHB2_HUMAN_604_902

Ephrin type-B receptor 2 [Protein kinase superfamily. Tyr protein kinase family. Ephrin receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPHB2_HUMAN):D: Protein kinase (627, 629:631, 635, 651, 653, 699:702, 706, 750, 753, 764)627, 629:631, 635, 651, 653, 699:702, 706, 750, 753, 764
Metals (Me):Mg

Full PDB list

1jpa, 2hen, 3zfm

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
I
6
2
7
A
6
2
9
E
6
3
1
V
6
3
5
A
6
5
1
K
6
5
3
E
7
0
0
F
7
0
1
M
7
0
2
S
7
0
6
L
7
5
3
D
7
6
4
[1]1jpa.b anp10 . . . . . . . . . . . .
[1]2hen.b adp27 . . . . . . . . . . . . Mg
[1]3zfm.a none . - - . . . . . . . . .

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 Me
I
6
2
7
A
6
2
9
G
6
3
0
E
6
3
1
V
6
3
5
A
6
5
1
K
6
5
3
T
6
9
9
E
7
0
0
F
7
0
1
M
7
0
2
S
7
0
6
R
7
5
0
L
7
5
3
D
7
6
4
[1]1jpa.b . . . . . . . . . . . . . . .
[1]2hen.b . . . . . . . . . . . . . . . Mg
[1]3zfm.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
1jpa.b:anp
2hen.b:adp
3zfm.a is apo
[1] 1jpa.b
0
0.3 -
[1] 2hen.b 0
0
-
[1] 3zfm.a 0 0.2
-
[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
1jpa.b
2hen.b
3zfm.a
[1] 1jpa.b
0
.02 .01
[1] 2hen.b .02
0
.01
[1] 3zfm.a .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
1jpa.b
2hen.b
3zfm.a
[1] 1jpa.b
0
0.9 0.5
[1] 2hen.b 0.9
0
0.7
[1] 3zfm.a 0.5 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1jpa.b
2hen.b
3zfm.a
[1] 1jpa.b
0
1.3 1.1
[1] 2hen.b 1.3
0
1.6
[1] 3zfm.a 1.1 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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