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KIT_HUMAN_550_935

Mast/stem cell growth factor receptor Kit [Protein kinase superfamily. Tyr protein kinase family. CSF-1/PDGF receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (KIT_HUMAN):D: Protein kinase (593, 595:601, 603, 621:623, 640, 643, 644, 647, 653, 654, 668, 670:677, 684, 783, 788:791, 796, 797, 799, 808:815)
553, 556:558
553, 556:558, 593, 595:601, 603, 621:623, 640, 643, 644, 647, 653, 654, 668, 670:677, 684, 783, 788:791, 796, 797, 799, 808:815

Full PDB list

1pkg, 1t45, 1t46, 3g0e, 3g0f, 4hvs, 4u0i (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
5
5
7
L
5
9
5
G
5
9
6
A
5
9
7
G
5
9
8
A
5
9
9
F
6
0
0
G
6
0
1
V
6
0
3
A
6
2
1
V
6
2
2
K
6
2
3
E
6
4
0
V
6
4
3
L
6
4
4
L
6
4
7
I
6
5
3
V
6
5
4
V
6
6
8
T
6
7
0
E
6
7
1
Y
6
7
2
C
6
7
3
C
6
7
4
G
6
7
6
D
6
7
7
L
7
8
3
C
7
8
8
I
7
8
9
H
7
9
0
R
7
9
1
R
7
9
6
N
7
9
7
L
7
9
9
I
8
0
8
C
8
0
9
D
8
1
0
F
8
1
1
[1]1t45.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3g0e.a b4922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4hvs.a 64728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1pkg.b adp,mg28 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]1t46.a sti37 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4u0i.a 0li39 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
Y
5
5
3
Q
5
5
6
W
5
5
7
K
5
5
8
K
5
9
3
L
5
9
5
G
5
9
6
A
5
9
7
G
5
9
8
A
5
9
9
F
6
0
0
G
6
0
1
V
6
0
3
A
6
2
1
V
6
2
2
K
6
2
3
E
6
4
0
V
6
4
3
L
6
4
4
L
6
4
7
I
6
5
3
V
6
5
4
V
6
6
8
T
6
7
0
E
6
7
1
Y
6
7
2
C
6
7
3
C
6
7
4
Y
6
7
5
G
6
7
6
D
6
7
7
R
6
8
4
L
7
8
3
C
7
8
8
I
7
8
9
H
7
9
0
R
7
9
1
R
7
9
6
N
7
9
7
L
7
9
9
I
8
0
8
C
8
0
9
D
8
1
0
F
8
1
1
G
8
1
2
L
8
1
3
A
8
1
4
R
8
1
5
[1]1t45.a . * * * . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . .
[1]3g0e.a . * * . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . * * * . * .
[1]4hvs.a . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . .
[2]1pkg.b - - - - . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . * . * * .
[2]1t46.a - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . .
[2]4u0i.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
1t45.a is apo
3g0e.a:b49
4hvs.a:647
1pkg.b:adp,mg
1t46.a:sti
4u0i.a:0li
[1] 1t45.a
-
1.6 4.5 10 12 12
[1] 3g0e.a -
0
4.2 9.2 9.2 11
[1] 4hvs.a - 0.1
0
9.2 6.9 7.0
[2] 1pkg.b - 0.2 5.5
0.2
9.1 12
[2] 1t46.a - 0.1 0.6 8.9
0
0.3
[2] 4u0i.a - 0.5 0.5 8.2 0.5
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
1t45.a
3g0e.a
4hvs.a
1pkg.b
1t46.a
4u0i.a
[1] 1t45.a
0
.10 .14 .36 .32 .30
[1] 3g0e.a .10
0
.15 .35 .30 .29
[1] 4hvs.a .14 .15
0
.32 .20 .19
[2] 1pkg.b .36 .35 .32
0
.15 .16
[2] 1t46.a .32 .30 .20 .15
0
.03
[2] 4u0i.a .30 .29 .19 .16 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.6 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
1t45.a
3g0e.a
4hvs.a
1pkg.b
1t46.a
4u0i.a
[1] 1t45.a
0
0.6 1.3 5.3 1.1 1.0
[1] 3g0e.a 0.6
0
1.4 5.1 0.9 0.9
[1] 4hvs.a 1.3 1.4
0
5.1 0.8 0.6
[2] 1pkg.b 5.3 5.1 5.1
0
4.7 4.9
[2] 1t46.a 1.1 0.9 0.8 4.7
0
0.4
[2] 4u0i.a 1.0 0.9 0.6 4.9 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1t45.a
3g0e.a
4hvs.a
1pkg.b
1t46.a
4u0i.a
[1] 1t45.a
0
1.2 2.4 5.4 1.6 1.6
[1] 3g0e.a 1.2
0
2.4 5.4 1.7 1.7
[1] 4hvs.a 2.4 2.4
0
5.3 1.0 0.8
[2] 1pkg.b 5.4 5.4 5.3
0
5.0 5.2
[2] 1t46.a 1.6 1.7 1.0 5.0
0
0.5
[2] 4u0i.a 1.6 1.7 0.8 5.2 0.5
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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