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DDR1_HUMAN_598_913

Epithelial discoidin domain-containing receptor 1 [Protein kinase superfamily. Tyr protein kinase family. Insulin receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DDR1_HUMAN):D: Protein kinase (616, 620, 621, 624, 653:655, 672, 675, 676, 679, 684, 685, 699:707, 711, 757, 762:765, 773, 782:787, 789)616, 620, 621, 624, 653:655, 672, 675, 676, 679, 684, 685, 699:707, 711, 757, 762:765, 773, 782:787, 789

Full PDB list

3zos, 4bkj, 4ckr, 5bvk, 5bvn, 5bvo, 5bvw, 5fdp, 5fdx

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
6
1
6
V
6
2
4
A
6
5
3
V
6
5
4
K
6
5
5
E
6
7
2
I
6
7
5
M
6
7
6
L
6
7
9
I
6
8
4
I
6
8
5
M
6
9
9
T
7
0
1
D
7
0
2
Y
7
0
3
M
7
0
4
E
7
0
5
N
7
0
6
G
7
0
7
L
7
5
7
F
7
6
2
V
7
6
3
H
7
6
4
R
7
6
5
L
7
7
3
I
7
8
2
A
7
8
3
D
7
8
4
F
7
8
5
M
7
8
7
[1]3zos.a 0li39 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4bkj.b sti37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ckr.a di140 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bvk.a 4vc18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bvn.a 4vd31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bvo.a 4ve32 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5bvw.a 1n133 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . -
[1]5fdp.a 5wr38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5fdx.b 5x138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
L
6
1
6
Q
6
2
0
F
6
2
1
V
6
2
4
A
6
5
3
V
6
5
4
K
6
5
5
E
6
7
2
I
6
7
5
M
6
7
6
L
6
7
9
I
6
8
4
I
6
8
5
M
6
9
9
I
7
0
0
T
7
0
1
D
7
0
2
Y
7
0
3
M
7
0
4
E
7
0
5
N
7
0
6
G
7
0
7
Q
7
1
1
L
7
5
7
F
7
6
2
V
7
6
3
H
7
6
4
R
7
6
5
L
7
7
3
I
7
8
2
A
7
8
3
D
7
8
4
F
7
8
5
G
7
8
6
M
7
8
7
R
7
8
9
[1]3zos.a . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4bkj.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ckr.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]5bvk.a . . . . . . . . . . . . . . . . . . * . . . . . * . . * . . . * . . . .
[1]5bvn.a . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . * . . . .
[1]5bvo.a . - . . . . . . . . . . . . . . . . . . . . . . * . . * . . . * . . . .
[1]5bvw.a . . . . . . . . . . . . . . . . . . * . . . . . * . . . . . . * . . - -
[1]5fdp.a . . . . . . . . . . . . . . . . . . * . . . . . * . . * . . . * . . . .
[1]5fdx.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
3zos.a:0li
4bkj.b:sti
4ckr.a:di1
5bvk.a:4vc
5bvn.a:4vd
5bvo.a:4ve
5bvw.a:1n1
5fdp.a:5wr
5fdx.b:5x1
[1] 3zos.a
0
2.1 2.4 1.1 1.2 1.0 0.6 1.8 2.3
[1] 4bkj.b 1.7
0
0.3 0.4 0.3 0.7 1.1 0.5 0.6
[1] 4ckr.a 1.5 0
0
0.5 0.4 1.1 0.3 0.3 1.0
[1] 5bvk.a 2.5 2.5 4.3
0
0.3 0.6 0.5 0.7 0.7
[1] 5bvn.a 2.2 1.4 2.4 0.2
0
0.2 0.4 0.6 0.5
[1] 5bvo.a 2.2 2.1 3.5 0 0
0
0 0.6 0.6
[1] 5bvw.a 3.2 3.1 4.3 1.8 2.0 2.2
0
2.4 2.4
[1] 5fdp.a 2.8 2.8 4.0 0.5 0.4 0.6 0.7
0
0
[1] 5fdx.b 2.5 1.9 2.6 0.5 0.5 0.8 0.3 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
3zos.a
4bkj.b
4ckr.a
5bvk.a
5bvn.a
5bvo.a
5bvw.a
5fdp.a
5fdx.b
[1] 3zos.a
0
.16 .14 .18 .15 .16 .19 .21 .17
[1] 4bkj.b .16
0
.06 .17 .12 .14 .18 .17 .14
[1] 4ckr.a .14 .06
0
.15 .11 .13 .17 .16 .13
[1] 5bvk.a .18 .17 .15
0
.08 .06 .12 .06 .11
[1] 5bvn.a .15 .12 .11 .08
0
.09 .10 .10 .07
[1] 5bvo.a .16 .14 .13 .06 .09
0
.12 .09 .11
[1] 5bvw.a .19 .18 .17 .12 .10 .12
0
.15 .11
[1] 5fdp.a .21 .17 .16 .06 .10 .09 .15
0
.07
[1] 5fdx.b .17 .14 .13 .11 .07 .11 .11 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.3 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
3zos.a
4bkj.b
4ckr.a
5bvk.a
5bvn.a
5bvo.a
5bvw.a
5fdp.a
5fdx.b
[1] 3zos.a
0
2.0 2.4 1.9 2.0 1.7 1.4 1.6 1.6
[1] 4bkj.b 2.0
0
1.0 2.5 2.6 2.3 2.1 2.1 2.1
[1] 4ckr.a 2.4 1.0
0
2.6 2.7 2.6 2.2 2.5 2.5
[1] 5bvk.a 1.9 2.5 2.6
0
1.7 1.5 0.6 2.0 2.0
[1] 5bvn.a 2.0 2.6 2.7 1.7
0
0.5 1.2 1.7 1.7
[1] 5bvo.a 1.7 2.3 2.6 1.5 0.5
0
1.0 1.1 1.0
[1] 5bvw.a 1.4 2.1 2.2 0.6 1.2 1.0
0
1.8 1.8
[1] 5fdp.a 1.6 2.1 2.5 2.0 1.7 1.1 1.8
0
0.4
[1] 5fdx.b 1.6 2.1 2.5 2.0 1.7 1.0 1.8 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.7 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
3zos.a
4bkj.b
4ckr.a
5bvk.a
5bvn.a
5bvo.a
5bvw.a
5fdp.a
5fdx.b
[1] 3zos.a
0
2.3 3.0 2.9 2.6 1.9 1.9 1.8 2.0
[1] 4bkj.b 2.3
0
1.9 3.4 3.2 2.7 2.6 2.4 2.4
[1] 4ckr.a 3.0 1.9
0
3.1 3.2 3.0 2.5 3.0 3.1
[1] 5bvk.a 2.9 3.4 3.1
0
2.5 2.3 1.1 2.8 3.0
[1] 5bvn.a 2.6 3.2 3.2 2.5
0
0.9 1.5 2.0 2.4
[1] 5bvo.a 1.9 2.7 3.0 2.3 0.9
0
1.2 1.2 1.1
[1] 5bvw.a 1.9 2.6 2.5 1.1 1.5 1.2
0
2.1 2.3
[1] 5fdp.a 1.8 2.4 3.0 2.8 2.0 1.2 2.1
0
0.8
[1] 5fdx.b 2.0 2.4 3.1 3.0 2.4 1.1 2.3 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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