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EPHB3_HUMAN_614_910

Ephrin type-B receptor 3 [Protein kinase superfamily. Tyr protein kinase family. Ephrin receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPHB3_HUMAN):D: Protein kinase (639, 647, 663, 665, 686, 695, 709, 711:715, 717, 765, 775:779)639, 647, 663, 665, 686, 695, 709, 711:715, 717, 765, 775:779
Cofactors (cF):dio

Full PDB list

3zfy, 5l6o, 5l6p

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
6
3
9
V
6
4
7
A
6
6
3
K
6
6
5
M
6
8
6
I
7
0
9
T
7
1
1
E
7
1
2
F
7
1
3
M
7
1
4
C
7
1
7
L
7
6
5
S
7
7
5
D
7
7
6
F
7
7
7
G
7
7
8
L
7
7
9
[1]3zfy.a none - . . . . . . . . . . . . . . . -
[1]5l6o.a 6p620 . . . . . . . . . . * . . . . . . dio
[1]5l6p.a 6p821 . . . . . . . . . . * . . . . . . dio

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 cF
I
6
3
9
V
6
4
7
A
6
6
3
K
6
6
5
M
6
8
6
I
6
9
5
I
7
0
9
T
7
1
1
E
7
1
2
F
7
1
3
M
7
1
4
E
7
1
5
C
7
1
7
L
7
6
5
S
7
7
5
D
7
7
6
F
7
7
7
G
7
7
8
L
7
7
9
[1]3zfy.a - . . . . . . . . . . . * . . . . . -
[1]5l6o.a . . . . . . . . . . . . * . . . . . . dio
[1]5l6p.a . . . . . . . . . . . . * . . . . . . dio

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
3zfy.a is apo
5l6o.a:6p6
5l6p.a:6p8
[1] 3zfy.a
-
0.6 0.8
[1] 5l6o.a -
0.4
0.4
[1] 5l6p.a - 0.3
0.4
[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
3zfy.a
5l6o.a
5l6p.a
[1] 3zfy.a
0
.03 .03
[1] 5l6o.a .03
0
0
[1] 5l6p.a .03 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
3zfy.a
5l6o.a
5l6p.a
[1] 3zfy.a
0
0.7 0.6
[1] 5l6o.a 0.7
0
0.8
[1] 5l6p.a 0.6 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
3zfy.a
5l6o.a
5l6p.a
[1] 3zfy.a
0
1.0 1.1
[1] 5l6o.a 1.0
0
1.2
[1] 5l6p.a 1.1 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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