If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

EPHA3_HUMAN_604_947

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EPHA3_HUMAN):D: Protein kinase (625, 627:633, 635, 651:653, 666, 669, 670, 673, 674, 677, 682, 683, 697:706, 737, 742, 744, 750, 751, 753, 762:769)625, 627:633, 635, 651:653, 666, 669, 670, 673, 674, 677, 682, 683, 697:706, 737, 742, 744, 750, 751, 753, 762:769

Full PDB list

2gsf, 2qo2, 2qo7, 2qo9, 2qob, 2qoc, 2qod, 2qof, 2qoi, 2qok, 2qol, 2qon, 2qoo, 2qoq, 3dzq, 3fxx, 3fy2, 4g2f, 4gk2, 4gk3, 4gk4, 4p4c, 4p5q, 4p5z, 4twn, 4two (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
6
2
5
V
6
2
7
G
6
2
8
A
6
2
9
G
6
3
0
E
6
3
1
F
6
3
2
V
6
3
5
A
6
5
1
I
6
5
2
K
6
5
3
E
6
7
0
I
6
7
3
M
6
7
4
F
6
7
7
I
6
8
2
I
6
8
3
I
6
9
7
T
6
9
9
E
7
0
0
Y
7
0
1
M
7
0
2
E
7
0
3
N
7
0
4
G
7
0
5
S
7
0
6
L
7
3
7
Y
7
4
2
H
7
4
4
R
7
5
0
L
7
5
3
V
7
6
2
S
7
6
3
D
7
6
4
F
7
6
5
L
7
6
7
S
7
6
8
[1]2qo7.a anp,mg32 . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . - -
[1]2qo9.a anp,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2qob.a none . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . .
[1]2qok.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A
[1]2qon.a none . . . . . . . . . . . . . . . . . . . . * . . . . . . A . . . . . . . . .
[1]2qoo.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . F . . . . . . . - -
[1]3fy2.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4g2f.a c0724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gk2.a l6631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]4gk3.a l8726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4gk4.a l9028 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4p4c.a 25q25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]4p5q.a q0b30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4p5z.a q7m37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]4twn.a b9639 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4two.a 37w26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3dzq.a ifc34 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -

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
K
6
2
5
V
6
2
7
G
6
2
8
A
6
2
9
G
6
3
0
E
6
3
1
F
6
3
2
G
6
3
3
V
6
3
5
A
6
5
1
I
6
5
2
K
6
5
3
D
6
6
6
G
6
6
9
E
6
7
0
I
6
7
3
M
6
7
4
F
6
7
7
I
6
8
2
I
6
8
3
I
6
9
7
V
6
9
8
T
6
9
9
E
7
0
0
Y
7
0
1
M
7
0
2
E
7
0
3
N
7
0
4
G
7
0
5
S
7
0
6
L
7
3
7
Y
7
4
2
H
7
4
4
R
7
5
0
N
7
5
1
L
7
5
3
V
7
6
2
S
7
6
3
D
7
6
4
F
7
6
5
G
7
6
6
L
7
6
7
S
7
6
8
R
7
6
9
[1]2qo7.a . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . . * * - - -
[1]2qo9.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]2qob.a . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . . * . . . .
[1]2qok.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . A .
[1]2qon.a . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . A . . . . . . . * . . . .
[1]2qoo.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . F . . . . . . . * - - - -
[1]3fy2.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4g2f.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * * . . .
[1]4gk2.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * * . - -
[1]4gk3.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4gk4.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4p4c.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * - - - -
[1]4p5q.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4p5z.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * - - - -
[1]4twn.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . *
[1]4two.a . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[2]3dzq.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

zoom: [−] [+]; [view as image]; [download as text]

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2qo7.a:anp,mg
2qo9.a:anp,mg
2qob.a is apo
2qok.a is apo
2qon.a is apo
2qoo.a is apo
3fy2.a is apo
4g2f.a:c07
4gk2.a:l66
4gk3.a:l87
4gk4.a:l90
4p4c.a:25q
4p5q.a:q0b
4p5z.a:q7m
4twn.a:b96
4two.a:37w
3dzq.a:ifc
[1] 2qo7.a
0
0 - - - - - 0.2 0.7 0.3 0.4 0 0 7.0 8.5 0.2 8.4
[1] 2qo9.a 0
0
- - - - - 0 0.1 0.1 0.2 0 0 7.2 8.4 0 8.4
[1] 2qob.a 0 0
-
- - - - 0.2 0.6 0.6 0.3 0.2 0.2 6.1 8.4 0.3 7.6
[1] 2qok.a 0.1 0.1 -
-
- - - 0.2 0.3 0.4 0.4 0.2 0.1 6.9 8.5 0.2 8.2
[1] 2qon.a 0.1 0.1 - -
-
- - 0.2 0.3 0.2 0.4 0.1 0.1 7.3 8.8 0.2 8.3
[1] 2qoo.a 0.1 0.1 - - -
-
- 0.3 0.8 1.0 0.9 0.4 0.2 6.9 7.9 0.2 8.2
[1] 3fy2.a 0 0 - - - -
-
0.1 0.1 0.1 0.2 0 0 7.2 8.0 0 7.9
[1] 4g2f.a 0 0 - - - - -
0.1
0.2 0 0.3 0.1 0 7.0 9.1 0 8.8
[1] 4gk2.a 0 0.1 - - - - - 0
0
0.1 0.3 0.1 0.1 7.6 9.2 0.2 9.0
[1] 4gk3.a 0 0 - - - - - 0 0.1
0
0.4 0.1 0.2 7.4 8.5 0 8.0
[1] 4gk4.a 0 0 - - - - - 0 0 0
0.1
0.1 0.1 7.0 8.5 0 8.0
[1] 4p4c.a 0 0 - - - - - 0 0.1 0 0.2
0
0.2 6.8 7.3 0 7.4
[1] 4p5q.a 0 0 - - - - - 0.1 0.3 0.1 0.3 0.2
0
7.1 8.6 0 8.0
[1] 4p5z.a 1.7 1.7 - - - - - 0 2.6 1.9 2.1 0 0.1
0.2
1.1 0.1 0.2
[1] 4twn.a 6.0 5.6 - - - - - 1.5 3.1 2.7 2.1 1.9 1.9 1.3
0
1.5 0.4
[1] 4two.a 0 0 - - - - - 0.1 0.4 0.2 0.3 0.2 0 7.0 8.6
0
7.3
[2] 3dzq.a 9.7 9.9 - - - - - 4.6 6.6 5.1 4.2 5.3 4.8 5.5 1.7 3.0
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2qo7.a
2qo9.a
2qob.a
2qok.a
2qon.a
2qoo.a
3fy2.a
4g2f.a
4gk2.a
4gk3.a
4gk4.a
4p4c.a
4p5q.a
4p5z.a
4twn.a
4two.a
3dzq.a
[1] 2qo7.a
0
.07 .06 .03 .07 .04 .06 .05 .06 .07 .05 .06 .03 .14 .18 .06 .34
[1] 2qo9.a .07
0
.02 .06 .03 .08 .01 .05 .08 .05 .04 .07 .05 .12 .17 .04 .33
[1] 2qob.a .06 .02
0
.05 .03 .07 .02 .06 .09 .07 .05 .08 .05 .14 .18 .05 .33
[1] 2qok.a .03 .06 .05
0
.05 .03 .05 .04 .06 .06 .05 .05 .02 .13 .17 .04 .33
[1] 2qon.a .07 .03 .03 .05
0
.07 .03 .05 .07 .05 .03 .09 .05 .15 .18 .03 .35
[1] 2qoo.a .04 .08 .07 .03 .07
0
.07 .07 .09 .09 .08 .04 .05 .12 .15 .07 .32
[1] 3fy2.a .06 .01 .02 .05 .03 .07
0
.05 .08 .05 .04 .08 .05 .12 .16 .04 .33
[1] 4g2f.a .05 .05 .06 .04 .05 .07 .05
0
.03 .04 .02 .07 .02 .15 .19 .03 .35
[1] 4gk2.a .06 .08 .09 .06 .07 .09 .08 .03
0
.05 .05 .07 .05 .16 .20 .05 .35
[1] 4gk3.a .07 .05 .07 .06 .05 .09 .05 .04 .05
0
.03 .08 .04 .13 .18 .03 .33
[1] 4gk4.a .05 .04 .05 .05 .03 .08 .04 .02 .05 .03
0
.07 .03 .14 .18 .01 .33
[1] 4p4c.a .06 .07 .08 .05 .09 .04 .08 .07 .07 .08 .07
0
.05 .11 .15 .07 .30
[1] 4p5q.a .03 .05 .05 .02 .05 .05 .05 .02 .05 .04 .03 .05
0
.14 .17 .03 .34
[1] 4p5z.a .14 .12 .14 .13 .15 .12 .12 .15 .16 .13 .14 .11 .14
0
.11 .14 .23
[1] 4twn.a .18 .17 .18 .17 .18 .15 .16 .19 .20 .18 .18 .15 .17 .11
0
.17 .29
[1] 4two.a .06 .04 .05 .04 .03 .07 .04 .03 .05 .03 .01 .07 .03 .14 .17
0
.33
[2] 3dzq.a .34 .33 .33 .33 .35 .32 .33 .35 .35 .33 .33 .30 .34 .23 .29 .33
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

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
2qo7.a
2qo9.a
2qob.a
2qok.a
2qon.a
2qoo.a
3fy2.a
4g2f.a
4gk2.a
4gk3.a
4gk4.a
4p4c.a
4p5q.a
4p5z.a
4twn.a
4two.a
3dzq.a
[1] 2qo7.a
0
0.3 0.6 0.8 0.9 0.8 0.5 0.4 0.5 0.4 0.4 0.2 0.3 1.1 2.4 0.4 2.9
[1] 2qo9.a 0.3
0
0.4 0.8 0.8 0.8 0.3 0.4 0.5 0.3 0.4 0.3 0.3 1.1 4.2 0.3 3.3
[1] 2qob.a 0.6 0.4
0
0.5 0.5 0.5 0.3 0.4 0.6 0.6 0.3 0.5 0.4 1.1 4.1 0.3 3.2
[1] 2qok.a 0.8 0.8 0.5
0
0.3 0.1 0.6 0.8 0.9 0.9 0.7 0.8 0.7 1.3 4.0 0.7 3.4
[1] 2qon.a 0.9 0.8 0.5 0.3
0
0.3 0.6 0.8 0.9 0.9 0.7 0.9 0.7 1.3 4.0 0.7 3.4
[1] 2qoo.a 0.8 0.8 0.5 0.1 0.3
0
0.7 0.8 0.9 1.0 0.8 0.8 0.7 1.3 1.9 0.7 3.0
[1] 3fy2.a 0.5 0.3 0.3 0.6 0.6 0.7
0
0.3 0.5 0.4 0.3 0.4 0.3 1.1 4.1 0.3 3.3
[1] 4g2f.a 0.4 0.4 0.4 0.8 0.8 0.8 0.3
0
0.3 0.3 0.2 0.3 0.2 1.1 4.1 0.3 3.1
[1] 4gk2.a 0.5 0.5 0.6 0.9 0.9 0.9 0.5 0.3
0
0.4 0.4 0.5 0.4 1.1 2.7 0.4 3.2
[1] 4gk3.a 0.4 0.3 0.6 0.9 0.9 1.0 0.4 0.3 0.4
0
0.3 0.3 0.3 1.1 4.1 0.4 3.2
[1] 4gk4.a 0.4 0.4 0.3 0.7 0.7 0.8 0.3 0.2 0.4 0.3
0
0.4 0.2 1.1 4.1 0.2 3.2
[1] 4p4c.a 0.2 0.3 0.5 0.8 0.9 0.8 0.4 0.3 0.5 0.3 0.4
0
0.3 1.1 2.1 0.4 2.8
[1] 4p5q.a 0.3 0.3 0.4 0.7 0.7 0.7 0.3 0.2 0.4 0.3 0.2 0.3
0
1.1 4.1 0.2 3.2
[1] 4p5z.a 1.1 1.1 1.1 1.3 1.3 1.3 1.1 1.1 1.1 1.1 1.1 1.1 1.1
0
1.9 1.1 2.5
[1] 4twn.a 2.4 4.2 4.1 4.0 4.0 1.9 4.1 4.1 2.7 4.1 4.1 2.1 4.1 1.9
0
4.1 3.5
[1] 4two.a 0.4 0.3 0.3 0.7 0.7 0.7 0.3 0.3 0.4 0.4 0.2 0.4 0.2 1.1 4.1
0
3.2
[2] 3dzq.a 2.9 3.3 3.2 3.4 3.4 3.0 3.3 3.1 3.2 3.2 3.2 2.8 3.2 2.5 3.5 3.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
2qo7.a
2qo9.a
2qob.a
2qok.a
2qon.a
2qoo.a
3fy2.a
4g2f.a
4gk2.a
4gk3.a
4gk4.a
4p4c.a
4p5q.a
4p5z.a
4twn.a
4two.a
3dzq.a
[1] 2qo7.a
0
0.6 1.1 0.8 1.0 0.8 0.9 0.9 0.8 1.2 1.0 0.8 0.5 1.8 3.0 1.0 3.9
[1] 2qo9.a 0.6
0
1.0 0.9 0.9 0.9 1.1 0.9 0.8 1.2 1.0 0.8 0.7 1.9 4.1 0.9 4.0
[1] 2qob.a 1.1 1.0
0
1.1 0.9 1.1 1.0 0.8 1.1 1.1 0.7 1.2 1.1 1.9 4.1 0.5 4.0
[1] 2qok.a 0.8 0.9 1.1
0
0.5 0.3 1.1 1.1 1.0 1.4 1.1 1.0 0.8 1.9 4.0 1.1 4.1
[1] 2qon.a 1.0 0.9 0.9 0.5
0
0.5 0.9 0.9 1.0 1.2 0.9 1.1 0.9 2.0 4.0 0.9 4.1
[1] 2qoo.a 0.8 0.9 1.1 0.3 0.5
0
1.0 1.1 1.0 1.4 1.1 1.0 0.8 1.9 2.7 1.1 3.9
[1] 3fy2.a 0.9 1.1 1.0 1.1 0.9 1.0
0
0.9 1.0 1.1 0.9 1.1 1.0 1.9 4.1 0.6 4.0
[1] 4g2f.a 0.9 0.9 0.8 1.1 0.9 1.1 0.9
0
0.9 1.0 0.5 1.1 0.9 1.9 4.1 0.7 4.0
[1] 4gk2.a 0.8 0.8 1.1 1.0 1.0 1.0 1.0 0.9
0
1.1 0.9 0.8 0.6 1.8 3.0 1.0 4.0
[1] 4gk3.a 1.2 1.2 1.1 1.4 1.2 1.4 1.1 1.0 1.1
0
1.0 1.1 1.1 1.9 4.0 0.9 3.7
[1] 4gk4.a 1.0 1.0 0.7 1.1 0.9 1.1 0.9 0.5 0.9 1.0
0
1.1 1.0 1.9 4.1 0.6 4.0
[1] 4p4c.a 0.8 0.8 1.2 1.0 1.1 1.0 1.1 1.1 0.8 1.1 1.1
0
0.7 1.8 2.8 1.1 3.9
[1] 4p5q.a 0.5 0.7 1.1 0.8 0.9 0.8 1.0 0.9 0.6 1.1 1.0 0.7
0
1.8 4.0 0.8 3.9
[1] 4p5z.a 1.8 1.9 1.9 1.9 2.0 1.9 1.9 1.9 1.8 1.9 1.9 1.8 1.8
0
2.1 1.9 3.2
[1] 4twn.a 3.0 4.1 4.1 4.0 4.0 2.7 4.1 4.1 3.0 4.0 4.1 2.8 4.0 2.1
0
4.1 3.9
[1] 4two.a 1.0 0.9 0.5 1.1 0.9 1.1 0.6 0.7 1.0 0.9 0.6 1.1 0.8 1.9 4.1
0
4.0
[2] 3dzq.a 3.9 4.0 4.0 4.1 4.1 3.9 4.0 4.0 4.0 3.7 4.0 3.9 3.9 3.2 3.9 4.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...