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EPHB2_HUMAN_16_199_pep

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: Eph LBD (41, 42, 44, 48, 49, 58, 60:63, 65, 66, 93:96, 99:102, 146:152, 155:159, 184:186, 188)41, 42, 44, 48, 49, 58, 60:63, 65, 66, 93:96, 99:102, 146:152, 155:159, 184:186, 188

Full PDB list

1kgy, 1nuk, 1shw, 2qbx, 3etp

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
4
1
G
4
2
E
4
4
T
5
8
Q
6
0
V
6
1
C
6
2
N
6
3
F
6
5
S
9
3
V
9
4
R
9
5
D
9
6
S
9
9
I
1
0
0
P
1
0
1
F
1
4
7
Q
1
4
9
V
1
5
0
D
1
5
1
R
1
5
5
V
1
5
6
M
1
5
7
K
1
5
8
I
1
5
9
C
1
8
4
M
1
8
5
S
1
8
6
I
1
8
8
[1]1nuk.a none . . . . . . . . . . . . . . . . . . . . - . . . . . . . .
[1]2qbx.a SNEWIQPRL80 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qbx.b SNEWIQPRLPQ96 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3etp.a none . . . . . . . . . . . . . . . . I . . . . . . . . . . . .
[2]1kgy.a QEFSPNL58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1kgy.c FSPNL40 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[3]1shw.b QLFTPFS59 . . . . . . . . . . . . . . . . . . - - - - - . . . . . .

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
S
4
1
G
4
2
E
4
4
G
4
8
Y
4
9
T
5
8
Q
6
0
V
6
1
C
6
2
N
6
3
F
6
5
E
6
6
S
9
3
V
9
4
R
9
5
D
9
6
S
9
9
I
1
0
0
P
1
0
1
S
1
0
2
S
1
4
6
F
1
4
7
S
1
4
8
Q
1
4
9
V
1
5
0
D
1
5
1
L
1
5
2
R
1
5
5
V
1
5
6
M
1
5
7
K
1
5
8
I
1
5
9
C
1
8
4
M
1
8
5
S
1
8
6
I
1
8
8
[1]1nuk.a . . * . . . . . . . . . . . . . . . . . . . . . . . - - . * * . . . . .
[1]2qbx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . . . . .
[1]2qbx.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . . . . .
[1]3etp.a . . . . . . . . . . . . . . . . . . . . . I . . . . . . . * * . . . . .
[2]1kgy.a . . * . . . . . . . * . . . * . . * * . * * * * * . . . . . . . . . . .
[2]1kgy.c . . . . . . . . . . * * . . * . . * * . * * * * . . . . . . . . . . . .
[3]1shw.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
1nuk.a is apo
2qbx.a:SNEWIQPRL
2qbx.b:SNEWIQPRLPQ
3etp.a is apo
1kgy.a:QEFSPNL
1kgy.c:FSPNL
1shw.b:QLFTPFS
[1] 1nuk.a
-
1.9 2.5 - 5.3 3.8 1.9
[1] 2qbx.a -
0.2
0.1 - 5.4 4.2 4.1
[1] 2qbx.b - 0.2
0.1
- 5.6 4.1 3.6
[1] 3etp.a - 0.7 1.5
-
5.3 4.2 2.4
[2] 1kgy.a - 16 18 -
0.4
0 4.8
[2] 1kgy.c - 16 18 - 0.7
0
5.0
[3] 1shw.b - 9.9 10 - 0.9 0
0
[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
1nuk.a
2qbx.a
2qbx.b
3etp.a
1kgy.a
1kgy.c
1shw.b
[1] 1nuk.a
0
.12 .11 .02 .72 .74 .44
[1] 2qbx.a .12
0
.03 .12 .76 .77 .47
[1] 2qbx.b .11 .03
0
.10 .76 .76 .45
[1] 3etp.a .02 .12 .10
0
.73 .73 .43
[2] 1kgy.a .72 .76 .76 .73
0
.13 .33
[2] 1kgy.c .74 .77 .76 .73 .13
0
.32
[3] 1shw.b .44 .47 .45 .43 .33 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 4.1 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
1nuk.a
2qbx.a
2qbx.b
3etp.a
1kgy.a
1kgy.c
1shw.b
[1] 1nuk.a
0
3.0 3.0 0.7 5.4 5.5 4.7
[1] 2qbx.a 3.0
0
0.2 3.7 5.0 5.0 4.2
[1] 2qbx.b 3.0 0.2
0
3.7 5.0 5.0 4.2
[1] 3etp.a 0.7 3.7 3.7
0
5.7 5.8 4.8
[2] 1kgy.a 5.4 5.0 5.0 5.7
0
0.5 1.6
[2] 1kgy.c 5.5 5.0 5.0 5.8 0.5
0
1.8
[3] 1shw.b 4.7 4.2 4.2 4.8 1.6 1.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.7 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
1nuk.a
2qbx.a
2qbx.b
3etp.a
1kgy.a
1kgy.c
1shw.b
[1] 1nuk.a
0
3.4 3.3 1.2 5.9 5.9 5.0
[1] 2qbx.a 3.4
0
0.6 4.1 5.4 5.5 4.3
[1] 2qbx.b 3.3 0.6
0
4.1 5.5 5.6 4.4
[1] 3etp.a 1.2 4.1 4.1
0
6.1 6.2 4.9
[2] 1kgy.a 5.9 5.4 5.5 6.1
0
1.0 2.0
[2] 1kgy.c 5.9 5.5 5.6 6.2 1.0
0
2.0
[3] 1shw.b 5.0 4.3 4.4 4.9 2.0 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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