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LYN_HUMAN_235_512

Tyrosine-protein kinase Lyn [Protein kinase superfamily. Tyr protein kinase family. SRC subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (LYN_HUMAN):D: Protein kinase (253, 254, 256, 258, 261, 273, 275, 290, 294, 303, 317, 319:326, 371, 374, 384, 385)253, 254, 256, 258, 261, 273, 275, 290, 294, 303, 317, 319:326, 371, 374, 384, 385

Full PDB list

2zv7, 2zv8, 2zv9, 2zva, 3a4o, 5xy1

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
2
5
3
V
2
6
1
A
2
7
3
K
2
7
5
E
2
9
0
M
2
9
4
V
3
0
3
I
3
1
7
T
3
1
9
E
3
2
0
Y
3
2
1
M
3
2
2
A
3
2
3
K
3
2
4
G
3
2
5
S
3
2
6
A
3
7
1
L
3
7
4
A
3
8
4
D
3
8
5
[1]2zv7.a none . . . . . . . . . . F . . . . . . . . .
[1]2zv8.a anp31 . . . . . . . . . . F . . . . . . . . .
[1]2zv9.a pp221 . . . . . . . . . . F . . . . . . . . .
[1]2zva.a 1n133 . . . . . . . . . . F . . . . . . . . .
[1]3a4o.x stu35 . . . . . . . . . . . . . . . . . . . .
[1]5xy1.a 8h030 . . . . . . . . . . . . . . . . . . . .

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
5
3
G
2
5
4
G
2
5
6
F
2
5
8
V
2
6
1
A
2
7
3
K
2
7
5
E
2
9
0
M
2
9
4
V
3
0
3
I
3
1
7
T
3
1
9
E
3
2
0
Y
3
2
1
M
3
2
2
A
3
2
3
K
3
2
4
G
3
2
5
S
3
2
6
A
3
7
1
L
3
7
4
A
3
8
4
D
3
8
5
[1]2zv7.a . . . . . . * . . . . . . F . . . . . . . . .
[1]2zv8.a . . . . . . . . . . . . . F . . . . . . . . .
[1]2zv9.a . . . . . . . . . . . . . F . . . . . . . . .
[1]2zva.a . . . . . . . . . . . . . F . . . . . . . . .
[1]3a4o.x . . . . . . . . . . . . . . . . . . . . . . .
[1]5xy1.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
2zv7.a is apo
2zv8.a:anp
2zv9.a:pp2
2zva.a:1n1
3a4o.x:stu
5xy1.a:8h0
[1] 2zv7.a
-
0.1 0.2 1.0 1.1 0.7
[1] 2zv8.a -
0
0 0.4 0.6 0.2
[1] 2zv9.a - 0
0
0.4 0.7 0.5
[1] 2zva.a - 0 0
0
0.2 0
[1] 3a4o.x - 0 0 0.2
0.1
0
[1] 5xy1.a - 0 0.1 0.3 0.1
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
2zv7.a
2zv8.a
2zv9.a
2zva.a
3a4o.x
5xy1.a
[1] 2zv7.a
0
.05 .04 .07 .08 .09
[1] 2zv8.a .05
0
.03 .03 .05 .06
[1] 2zv9.a .04 .03
0
.04 .05 .06
[1] 2zva.a .07 .03 .04
0
.02 .03
[1] 3a4o.x .08 .05 .05 .02
0
.02
[1] 5xy1.a .09 .06 .06 .03 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2zv7.a
2zv8.a
2zv9.a
2zva.a
3a4o.x
5xy1.a
[1] 2zv7.a
0
0.6 0.6 0.7 1.1 0.8
[1] 2zv8.a 0.6
0
0.4 0.3 0.8 0.5
[1] 2zv9.a 0.6 0.4
0
0.4 0.8 0.6
[1] 2zva.a 0.7 0.3 0.4
0
0.7 0.5
[1] 3a4o.x 1.1 0.8 0.8 0.7
0
0.8
[1] 5xy1.a 0.8 0.5 0.6 0.5 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
2zv7.a
2zv8.a
2zv9.a
2zva.a
3a4o.x
5xy1.a
[1] 2zv7.a
0
0.8 0.8 1.0 1.2 1.0
[1] 2zv8.a 0.8
0
0.6 0.5 0.9 0.6
[1] 2zv9.a 0.8 0.6
0
0.7 1.1 0.8
[1] 2zva.a 1.0 0.5 0.7
0
0.9 0.6
[1] 3a4o.x 1.2 0.9 1.1 0.9
0
0.9
[1] 5xy1.a 1.0 0.6 0.8 0.6 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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