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RIPK1_HUMAN_1_294

Receptor-interacting serine/threonine-protein kinase 1 [Protein kinase superfamily. TKL Ser/Thr protein kinase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (RIPK1_HUMAN):D: Protein kinase (23:31, 33, 43:45, 60:68, 70, 75:78, 81, 90:95, 129, 134, 136, 145, 154:157, 159, 161, 162, 165)23:31, 33, 43:45, 60:68, 70, 75:78, 81, 90:95, 129, 134, 136, 145, 154:157, 159, 161, 162, 165

Full PDB list

4ith, 4iti, 4itj, 4neu, 5hx6, 5tx5, 6c3e, 6c4d

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
3
F
2
8
V
3
1
I
4
3
M
4
4
K
4
5
E
6
3
A
6
4
M
6
7
N
6
8
L
7
0
V
7
5
V
7
6
K
7
7
L
7
8
L
9
0
M
9
2
E
9
3
Y
9
4
M
9
5
L
1
2
9
V
1
3
4
H
1
3
6
L
1
4
5
I
1
5
4
A
1
5
5
D
1
5
6
L
1
5
7
L
1
5
9
S
1
6
1
F
1
6
2
W
1
6
5
[1]4ith.b rcm19 . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4iti.a 1hw31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4itj.b 1hx21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5hx6.a 65u28 . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tx5.a 7mj28 . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6c3e.a ejy19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]6c4d.a ejp33 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4neu.a q1a30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
2
3
D
2
4
S
2
5
G
2
6
G
2
7
F
2
8
G
2
9
K
3
0
V
3
1
L
3
3
I
4
3
M
4
4
K
4
5
L
6
0
L
6
1
E
6
2
E
6
3
A
6
4
K
6
5
M
6
6
M
6
7
N
6
8
L
7
0
V
7
5
V
7
6
K
7
7
L
7
8
V
8
1
L
9
0
V
9
1
M
9
2
E
9
3
Y
9
4
M
9
5
L
1
2
9
V
1
3
4
H
1
3
6
L
1
4
5
I
1
5
4
A
1
5
5
D
1
5
6
L
1
5
7
L
1
5
9
S
1
6
1
F
1
6
2
W
1
6
5
[1]4ith.b . - - - - - - . * . * . . . . . . . . . . . . . . . * . . . * . . . . . . . . . . . . . . .
[1]4iti.a . . . . . * . . * . * . * . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . .
[1]4itj.b . . . * . . . . . . . . * . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . * .
[1]5hx6.a . . . - - - . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . * .
[1]5tx5.a . . . . - - . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . * .
[1]6c3e.a . . . . . . . . * . . . * . . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . . .
[1]6c4d.a - - - - . * . . . . . . . . . . . . . . * . . . . . . . . . * . . . . . . . . . . . . . * .
[2]4neu.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
4ith.b:rcm
4iti.a:1hw
4itj.b:1hx
5hx6.a:65u
5tx5.a:7mj
6c3e.a:ejy
6c4d.a:ejp
4neu.a:q1a
[1] 4ith.b
0.1
2.2 2.0 4.7 3.8 1.9 4.0 3.0
[1] 4iti.a 0.2
0.2
1.0 4.4 4.1 0.8 4.2 4.3
[1] 4itj.b 0.8 1.7
0
2.3 2.3 0.5 3.9 2.9
[1] 5hx6.a 1.2 3.5 0.4
0
0 0.2 0.2 2.2
[1] 5tx5.a 1.5 3.4 0.4 0
0
0.2 0.4 2.4
[1] 6c3e.a 1.4 4.6 0.8 2.5 2.1
0
3.3 2.8
[1] 6c4d.a 0.9 2.5 0.3 0 0.2 0
0
5.2
[2] 4neu.a 1.5 8.1 2.3 3.1 2.8 1.6 3.9
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 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
4ith.b
4iti.a
4itj.b
5hx6.a
5tx5.a
6c3e.a
6c4d.a
4neu.a
[1] 4ith.b
0
.17 .22 .17 .18 .20 .21 .31
[1] 4iti.a .17
0
.18 .22 .22 .19 .22 .34
[1] 4itj.b .22 .18
0
.14 .15 .23 .22 .29
[1] 5hx6.a .17 .22 .14
0
.03 .19 .11 .25
[1] 5tx5.a .18 .22 .15 .03
0
.19 .10 .24
[1] 6c3e.a .20 .19 .23 .19 .19
0
.25 .23
[1] 6c4d.a .21 .22 .22 .11 .10 .25
0
.32
[2] 4neu.a .31 .34 .29 .25 .24 .23 .32
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
4ith.b
4iti.a
4itj.b
5hx6.a
5tx5.a
6c3e.a
6c4d.a
4neu.a
[1] 4ith.b
0
1.7 1.2 1.6 1.7 1.4 1.4 3.2
[1] 4iti.a 1.7
0
4.1 2.4 2.5 2.6 2.2 6.1
[1] 4itj.b 1.2 4.1
0
1.8 2.1 3.1 2.6 3.4
[1] 5hx6.a 1.6 2.4 1.8
0
0.5 1.9 1.1 3.6
[1] 5tx5.a 1.7 2.5 2.1 0.5
0
2.0 1.0 4.0
[1] 6c3e.a 1.4 2.6 3.1 1.9 2.0
0
2.2 5.0
[1] 6c4d.a 1.4 2.2 2.6 1.1 1.0 2.2
0
4.4
[2] 4neu.a 3.2 6.1 3.4 3.6 4.0 5.0 4.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.1 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
4ith.b
4iti.a
4itj.b
5hx6.a
5tx5.a
6c3e.a
6c4d.a
4neu.a
[1] 4ith.b
0
1.7 1.5 1.8 1.9 1.7 1.8 4.4
[1] 4iti.a 1.7
0
4.1 2.4 2.4 2.6 2.6 6.5
[1] 4itj.b 1.5 4.1
0
1.8 2.0 3.6 3.1 4.5
[1] 5hx6.a 1.8 2.4 1.8
0
0.5 2.0 1.4 4.6
[1] 5tx5.a 1.9 2.4 2.0 0.5
0
2.0 1.3 4.7
[1] 6c3e.a 1.7 2.6 3.6 2.0 2.0
0
2.3 5.8
[1] 6c4d.a 1.8 2.6 3.1 1.4 1.3 2.3
0
5.3
[2] 4neu.a 4.4 6.5 4.5 4.6 4.7 5.8 5.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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