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EPHB4_HUMAN_598_896

Ephrin type-B receptor 4 [Protein kinase superfamily. Tyr protein kinase family. Ephrin receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPHB4_HUMAN):D: Protein kinase (619:625, 629, 645:647, 664, 668, 677, 691, 693:700, 744, 745, 747, 757, 758)619:625, 629, 645:647, 664, 668, 677, 691, 693:700, 744, 745, 747, 757, 758
Metals (Me):Mg

Full PDB list

2vwu, 2vwv, 2vww, 2vwx, 2vwy, 2vwz, 2vx0, 2vx1, 2x9f, 2xvd, 2yn8, 3zew, 4aw5, 4bb4 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
6
2
0
I
6
2
1
G
6
2
2
A
6
2
3
V
6
2
9
A
6
4
5
I
6
4
6
K
6
4
7
E
6
6
4
M
6
6
8
I
6
7
7
I
6
9
1
T
6
9
3
E
6
9
4
F
6
9
5
M
6
9
6
E
6
9
7
N
6
9
8
G
6
9
9
A
7
0
0
R
7
4
4
N
7
4
5
L
7
4
7
S
7
5
7
D
7
5
8
[1]2vwu.a 7x133 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vwv.a 7x329 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vww.a 7x230 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vwx.a 7x428 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vwy.a 7x528 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vwz.a 7x629 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vx0.a 7x730 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vx1.a 7x827 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2x9f.a x9f27 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2xvd.a as636 . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3zew.a stu35 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4aw5.a 30k37 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bb4.a 32w30 . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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 Me
E
6
1
9
V
6
2
0
I
6
2
1
G
6
2
2
A
6
2
3
G
6
2
4
E
6
2
5
V
6
2
9
A
6
4
5
I
6
4
6
K
6
4
7
E
6
6
4
M
6
6
8
I
6
7
7
I
6
9
1
T
6
9
3
E
6
9
4
F
6
9
5
M
6
9
6
E
6
9
7
N
6
9
8
G
6
9
9
A
7
0
0
R
7
4
4
N
7
4
5
L
7
4
7
S
7
5
7
D
7
5
8
[1]2vwu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vwv.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vww.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vwx.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vwy.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vwz.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vx0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2vx1.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2x9f.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2xvd.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]3zew.a * . * . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4aw5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bb4.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg

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
2vwu.a:7x1
2vwv.a:7x3
2vww.a:7x2
2vwx.a:7x4
2vwy.a:7x5
2vwz.a:7x6
2vx0.a:7x7
2vx1.a:7x8
2x9f.a:x9f
2xvd.a:as6
3zew.a:stu
4aw5.a:30k
4bb4.a:32w
[1] 2vwu.a
0
0.6 0 0 0 0 0.1 0 0.1 0.5 0.3 0 0.1
[1] 2vwv.a 0.1
0
0.2 0.2 0.2 0.2 0.2 0.2 0.1 0.2 0.2 0 0.1
[1] 2vww.a 0 0.5
0
0 0 0 0 0 0.2 0.2 0 0 0.2
[1] 2vwx.a 0 1.0 0.1
0
0 0 0.1 0 0 0.3 0.2 0.1 0.2
[1] 2vwy.a 0 1.1 0.1 0
0
0 0.1 0 0 0.3 0.2 0.1 0.2
[1] 2vwz.a 0 1.1 0.2 0.1 0
0
0.1 0 0.1 0.3 0.2 0.1 0.2
[1] 2vx0.a 0 1.3 0.1 0 0 0
0
0 0.2 0.2 0.1 0 0.1
[1] 2vx1.a 0 1.1 0.2 0.1 0 0 0.1
0
0.1 0.3 0.2 0.1 0.2
[1] 2x9f.a 0.2 2.0 0.2 0 0.1 0 0.1 0
0
0.4 0.2 0 0.1
[1] 2xvd.a 0.1 0.8 0.1 0 0 0 0 0 0
0
0 0 0.1
[1] 3zew.a 0.8 2.8 0.7 0.7 0.8 1.0 0.5 0.7 0.4 1.6
0
0.1 1.4
[1] 4aw5.a 0.5 1.3 0.7 0.6 0.7 0.7 0.6 0.7 0.6 0.4 0
0
0.6
[1] 4bb4.a 0.2 1.3 0.2 0.1 0.1 0.1 0.1 0.1 0.2 0.3 0 0
0
[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
2vwu.a
2vwv.a
2vww.a
2vwx.a
2vwy.a
2vwz.a
2vx0.a
2vx1.a
2x9f.a
2xvd.a
3zew.a
4aw5.a
4bb4.a
[1] 2vwu.a
0
.04 .04 .03 .03 .03 .05 .03 .08 .04 .15 .08 .06
[1] 2vwv.a .04
0
.04 .06 .06 .06 .06 .06 .09 .04 .16 .08 .07
[1] 2vww.a .04 .04
0
.03 .03 .03 .03 .03 .06 .02 .15 .06 .04
[1] 2vwx.a .03 .06 .03
0
0 0 .02 0 .05 .03 .15 .07 .05
[1] 2vwy.a .03 .06 .03 0
0
0 .02 0 .04 .03 .15 .07 .04
[1] 2vwz.a .03 .06 .03 0 0
0
.02 0 .04 .03 .15 .07 .04
[1] 2vx0.a .05 .06 .03 .02 .02 .02
0
.02 .03 .03 .16 .06 .05
[1] 2vx1.a .03 .06 .03 0 0 0 .02
0
.04 .03 .15 .07 .04
[1] 2x9f.a .08 .09 .06 .05 .04 .04 .03 .04
0
.06 .14 .09 .06
[1] 2xvd.a .04 .04 .02 .03 .03 .03 .03 .03 .06
0
.13 .06 .03
[1] 3zew.a .15 .16 .15 .15 .15 .15 .16 .15 .14 .13
0
.18 .13
[1] 4aw5.a .08 .08 .06 .07 .07 .07 .06 .07 .09 .06 .18
0
.06
[1] 4bb4.a .06 .07 .04 .05 .04 .04 .05 .04 .06 .03 .13 .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2vwu.a
2vwv.a
2vww.a
2vwx.a
2vwy.a
2vwz.a
2vx0.a
2vx1.a
2x9f.a
2xvd.a
3zew.a
4aw5.a
4bb4.a
[1] 2vwu.a
0
0.6 0.3 0.3 0.4 0.4 0.3 0.3 0.6 0.5 1.3 0.5 0.4
[1] 2vwv.a 0.6
0
0.5 0.6 0.7 0.7 0.7 0.7 0.9 0.8 1.4 0.8 0.8
[1] 2vww.a 0.3 0.5
0
0.3 0.3 0.3 0.3 0.3 0.6 0.6 1.3 0.5 0.5
[1] 2vwx.a 0.3 0.6 0.3
0
0.1 0.1 0.2 0.1 0.5 0.6 1.1 0.5 0.5
[1] 2vwy.a 0.4 0.7 0.3 0.1
0
0.1 0.2 0.1 0.4 0.5 1.1 0.4 0.4
[1] 2vwz.a 0.4 0.7 0.3 0.1 0.1
0
0.2 0.1 0.4 0.5 1.1 0.5 0.4
[1] 2vx0.a 0.3 0.7 0.3 0.2 0.2 0.2
0
0.2 0.4 0.5 1.1 0.5 0.4
[1] 2vx1.a 0.3 0.7 0.3 0.1 0.1 0.1 0.2
0
0.4 0.5 1.1 0.4 0.4
[1] 2x9f.a 0.6 0.9 0.6 0.5 0.4 0.4 0.4 0.4
0
0.6 1.0 0.5 0.5
[1] 2xvd.a 0.5 0.8 0.6 0.6 0.5 0.5 0.5 0.5 0.6
0
1.4 0.5 0.3
[1] 3zew.a 1.3 1.4 1.3 1.1 1.1 1.1 1.1 1.1 1.0 1.4
0
1.2 1.2
[1] 4aw5.a 0.5 0.8 0.5 0.5 0.4 0.5 0.5 0.4 0.5 0.5 1.2
0
0.4
[1] 4bb4.a 0.4 0.8 0.5 0.5 0.4 0.4 0.4 0.4 0.5 0.3 1.2 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
2vwu.a
2vwv.a
2vww.a
2vwx.a
2vwy.a
2vwz.a
2vx0.a
2vx1.a
2x9f.a
2xvd.a
3zew.a
4aw5.a
4bb4.a
[1] 2vwu.a
0
0.7 0.4 0.6 0.6 0.6 0.6 0.6 1.0 0.8 1.5 0.9 0.8
[1] 2vwv.a 0.7
0
0.7 0.8 0.9 0.9 0.8 0.8 1.2 0.9 1.6 1.1 0.9
[1] 2vww.a 0.4 0.7
0
0.5 0.5 0.5 0.5 0.5 0.9 0.8 1.5 1.0 0.8
[1] 2vwx.a 0.6 0.8 0.5
0
0.3 0.3 0.3 0.3 0.9 0.7 1.4 1.0 0.7
[1] 2vwy.a 0.6 0.9 0.5 0.3
0
0.1 0.2 0.1 0.8 0.7 1.4 1.0 0.8
[1] 2vwz.a 0.6 0.9 0.5 0.3 0.1
0
0.2 0.1 0.8 0.7 1.4 1.0 0.8
[1] 2vx0.a 0.6 0.8 0.5 0.3 0.2 0.2
0
0.2 0.8 0.7 1.4 1.0 0.8
[1] 2vx1.a 0.6 0.8 0.5 0.3 0.1 0.1 0.2
0
0.8 0.7 1.4 1.0 0.8
[1] 2x9f.a 1.0 1.2 0.9 0.9 0.8 0.8 0.8 0.8
0
0.7 1.4 1.1 0.7
[1] 2xvd.a 0.8 0.9 0.8 0.7 0.7 0.7 0.7 0.7 0.7
0
1.4 0.9 0.3
[1] 3zew.a 1.5 1.6 1.5 1.4 1.4 1.4 1.4 1.4 1.4 1.4
0
1.5 1.4
[1] 4aw5.a 0.9 1.1 1.0 1.0 1.0 1.0 1.0 1.0 1.1 0.9 1.5
0
0.9
[1] 4bb4.a 0.8 0.9 0.8 0.7 0.8 0.8 0.8 0.8 0.7 0.3 1.4 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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