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CSF1R_HUMAN_539_921

Macrophage colony-stimulating factor 1 receptor [Protein kinase superfamily. Tyr protein kinase family. CSF-1/PDGF receptor subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CSF1R_HUMAN):D: Protein kinase (586:589, 596, 614:616, 633, 636, 637, 640, 646, 647, 661, 663:670, 673, 677, 769, 774:777, 782, 783, 785, 794:802)
R: Activation loop (796:802)
548:551, 559, 586:589, 596, 614:616, 633, 636, 637, 640, 646, 647, 661, 663:670, 673, 677, 769, 774:777, 782, 783, 785, 794:802

Full PDB list

2i0v, 2i0y, 2i1m, 2ogv, 3bea, 3dpk, 3krj, 3krl, 3lcd, 3lco, 4hw7, 4r7h, 4r7i (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
5
5
0
K
5
8
6
T
5
8
7
L
5
8
8
G
5
8
9
V
5
9
6
A
6
1
4
K
6
1
6
E
6
3
3
I
6
3
6
M
6
3
7
L
6
4
0
V
6
4
7
V
6
6
1
T
6
6
3
E
6
6
4
Y
6
6
5
C
6
6
6
C
6
6
7
Y
6
6
8
G
6
6
9
D
6
7
0
N
6
7
3
C
7
7
4
I
7
7
5
H
7
7
6
R
7
7
7
R
7
8
2
N
7
8
3
L
7
8
5
I
7
9
4
G
7
9
5
D
7
9
6
F
7
9
7
A
8
0
0
R
8
0
1
[1]2i0v.a 6c324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2i1m.a 5cn25 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2ogv.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3bea.a ixh38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3dpk.a 8c536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3krj.a krj28 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3krl.a krl29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4r7h.a p3129 . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . .
[2]3lcd.a bdy36 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3lco.a lc033 - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4hw7.a 64m30 - . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . .
[2]4r7i.a sti37 - . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . .

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
V
5
4
8
R
5
4
9
W
5
5
0
K
5
5
1
N
5
5
9
K
5
8
6
T
5
8
7
L
5
8
8
G
5
8
9
V
5
9
6
A
6
1
4
V
6
1
5
K
6
1
6
E
6
3
3
I
6
3
6
M
6
3
7
L
6
4
0
I
6
4
6
V
6
4
7
V
6
6
1
T
6
6
3
E
6
6
4
Y
6
6
5
C
6
6
6
C
6
6
7
Y
6
6
8
G
6
6
9
D
6
7
0
N
6
7
3
R
6
7
7
L
7
6
9
C
7
7
4
I
7
7
5
H
7
7
6
R
7
7
7
R
7
8
2
N
7
8
3
L
7
8
5
I
7
9
4
G
7
9
5
D
7
9
6
F
7
9
7
G
7
9
8
L
7
9
9
A
8
0
0
R
8
0
1
D
8
0
2
[1]2i0v.a . * * . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]2i1m.a . * * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . .
[1]2ogv.a . * * . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]3bea.a . * * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . .
[1]3dpk.a . * * * - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . . . . .
[1]3krj.a . * * . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . * .
[1]3krl.a * * * . - . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . * .
[1]4r7h.a . * * . - . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . * . . . . .
[2]3lcd.a - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * * . * * * .
[2]3lco.a - - - - K . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[2]4hw7.a - - - - - . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . * . . . . .
[2]4r7i.a - - - - - . . . . . . . . . . . . . . . . . . . T . . . . . . . . . . . . . . . . * . . . . .

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
2i0v.a:6c3
2i1m.a:5cn
2ogv.a is apo
3bea.a:ixh
3dpk.a:8c5
3krj.a:krj
3krl.a:krl
4r7h.a:p31
3lcd.a:bdy
3lco.a:lc0
4hw7.a:64m
4r7i.a:sti
[1] 2i0v.a
0
0.8 - 1.3 1.5 0.1 0 1.7 2.6 6.7 4.0 11
[1] 2i1m.a 0.1
0
- 0.4 0.3 0.4 0.2 4.5 1.1 8.2 6.2 10
[1] 2ogv.a 3.9 4.0
-
5.3 5.5 2.4 3.1 4.9 4.7 5.0 4.4 13
[1] 3bea.a 0.1 0.4 -
0
0.4 0.4 0.2 3.3 1.0 7.5 5.2 9.2
[1] 3dpk.a 0.5 0.1 - 0.1
0.1
0.5 0.4 3.8 1.0 7.2 5.7 9.5
[1] 3krj.a 0 0.7 - 2.5 1.2
0
0 2.2 2.6 6.6 3.9 11
[1] 3krl.a 0.5 0.3 - 2.1 1.6 0.6
0.1
3.7 2.5 7.5 4.6 11
[1] 4r7h.a 1.9 3.8 - 2.5 2.9 1.5 2.4
0
3.2 4.4 2.8 9.2
[2] 3lcd.a 0.2 0 - 0.2 0.2 0.2 0.3 4.9
0
6.1 5.3 9.3
[2] 3lco.a 1.1 2.8 - 2.2 2.8 0.7 1.6 0.6 2.9
0.1
0.4 1.1
[2] 4hw7.a 1.8 3.5 - 2.5 2.9 1.3 2.1 0 3.1 0.9
0.1
0.6
[2] 4r7i.a 1.3 3.7 - 2.0 2.7 0.9 1.9 0.1 2.4 0.3 0.2
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
2i0v.a
2i1m.a
2ogv.a
3bea.a
3dpk.a
3krj.a
3krl.a
4r7h.a
3lcd.a
3lco.a
4hw7.a
4r7i.a
[1] 2i0v.a
0
.16 .13 .16 .19 .07 .07 .12 .43 .28 .29 .30
[1] 2i1m.a .16
0
.21 .08 .05 .17 .20 .13 .41 .28 .28 .29
[1] 2ogv.a .13 .21
0
.20 .23 .14 .13 .10 .41 .32 .28 .29
[1] 3bea.a .16 .08 .20
0
.06 .18 .19 .15 .37 .24 .25 .27
[1] 3dpk.a .19 .05 .23 .06
0
.20 .22 .14 .39 .26 .26 .26
[1] 3krj.a .07 .17 .14 .18 .20
0
.11 .12 .44 .29 .29 .31
[1] 3krl.a .07 .20 .13 .19 .22 .11
0
.14 .46 .31 .32 .33
[1] 4r7h.a .12 .13 .10 .15 .14 .12 .14
0
.37 .25 .21 .20
[2] 3lcd.a .43 .41 .41 .37 .39 .44 .46 .37
0
.21 .19 .18
[2] 3lco.a .28 .28 .32 .24 .26 .29 .31 .25 .21
0
.05 .05
[2] 4hw7.a .29 .28 .28 .25 .26 .29 .32 .21 .19 .05
0
.02
[2] 4r7i.a .30 .29 .29 .27 .26 .31 .33 .20 .18 .05 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
2i0v.a
2i1m.a
2ogv.a
3bea.a
3dpk.a
3krj.a
3krl.a
4r7h.a
3lcd.a
3lco.a
4hw7.a
4r7i.a
[1] 2i0v.a
0
1.2 2.7 1.2 1.4 0.4 0.5 0.9 6.6 2.7 0.9 0.9
[1] 2i1m.a 1.2
0
2.7 0.7 0.6 1.3 1.2 1.2 6.2 2.7 0.8 0.8
[1] 2ogv.a 2.7 2.7
0
2.7 1.6 2.6 0.6 1.0 6.6 2.9 0.9 1.1
[1] 3bea.a 1.2 0.7 2.7
0
0.6 1.3 1.2 1.4 6.3 2.6 1.0 1.0
[1] 3dpk.a 1.4 0.6 1.6 0.6
0
1.5 1.4 1.3 5.3 1.0 0.9 0.9
[1] 3krj.a 0.4 1.3 2.6 1.3 1.5
0
0.5 0.9 6.7 2.7 0.8 1.0
[1] 3krl.a 0.5 1.2 0.6 1.2 1.4 0.5
0
0.8 5.9 1.1 0.7 0.9
[1] 4r7h.a 0.9 1.2 1.0 1.4 1.3 0.9 0.8
0
5.6 0.8 0.2 0.3
[2] 3lcd.a 6.6 6.2 6.6 6.3 5.3 6.7 5.9 5.6
0
6.5 5.6 5.5
[2] 3lco.a 2.7 2.7 2.9 2.6 1.0 2.7 1.1 0.8 6.5
0
0.8 0.8
[2] 4hw7.a 0.9 0.8 0.9 1.0 0.9 0.8 0.7 0.2 5.6 0.8
0
0.3
[2] 4r7i.a 0.9 0.8 1.1 1.0 0.9 1.0 0.9 0.3 5.5 0.8 0.3
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
2i0v.a
2i1m.a
2ogv.a
3bea.a
3dpk.a
3krj.a
3krl.a
4r7h.a
3lcd.a
3lco.a
4hw7.a
4r7i.a
[1] 2i0v.a
0
1.8 3.1 2.0 1.8 1.1 0.9 1.7 6.9 3.2 1.8 1.8
[1] 2i1m.a 1.8
0
3.2 1.2 1.1 1.8 1.7 2.0 6.5 2.9 1.6 1.5
[1] 2ogv.a 3.1 3.2
0
3.1 2.2 3.1 1.3 1.4 6.9 2.9 1.4 1.3
[1] 3bea.a 2.0 1.2 3.1
0
1.1 2.0 1.9 2.0 6.6 2.9 1.6 1.5
[1] 3dpk.a 1.8 1.1 2.2 1.1
0
2.0 1.8 1.9 5.6 1.8 1.7 1.5
[1] 3krj.a 1.1 1.8 3.1 2.0 2.0
0
1.2 1.5 7.0 3.0 1.5 1.6
[1] 3krl.a 0.9 1.7 1.3 1.9 1.8 1.2
0
1.5 6.1 1.9 1.6 1.5
[1] 4r7h.a 1.7 2.0 1.4 2.0 1.9 1.5 1.5
0
5.9 1.2 0.8 0.5
[2] 3lcd.a 6.9 6.5 6.9 6.6 5.6 7.0 6.1 5.9
0
6.1 5.9 5.8
[2] 3lco.a 3.2 2.9 2.9 2.9 1.8 3.0 1.9 1.2 6.1
0
1.2 1.2
[2] 4hw7.a 1.8 1.6 1.4 1.6 1.7 1.5 1.6 0.8 5.9 1.2
0
0.8
[2] 4r7i.a 1.8 1.5 1.3 1.5 1.5 1.6 1.5 0.5 5.8 1.2 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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