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FYN_HUMAN_80_144_pep

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

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (FYN_HUMAN):D: SH3 (91:97, 99, 100, 115:119, 132, 134:137)91:97, 99, 100, 115:119, 132, 134:137

Full PDB list

1avz, 1efn, 1fyn, 1g83, 1m27, 1shf, 3cqt, 3h0f, 3h0h, 3h0i, 3ua6, 3ua7, 3uf4, 4d8d, 4eik, 4znx (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
Y
9
1
Y
9
3
E
9
4
R
9
6
T
9
7
D
9
9
D
1
0
0
E
1
1
6
G
1
1
7
D
1
1
8
W
1
1
9
Y
1
3
2
P
1
3
4
N
1
3
6
Y
1
3
7
[1]1avz.c TPQVPLRP-GY79 . . . . . . . . . . . . . . .
[1]1efn.a RPQVPLRP-HTQGY109 . . . I . . . . . . . . . . .
[1]1efn.c RPQVPLRP-GY83 . . . I . . . . . . . . . . .
[1]1fyn.a PPAYPPPPVP72 . . . . . . . . . . . . . . .
[1]4d8d.a PVTPQVPLRP-TQGY109 . . . W . . . . . . . . . . .
[1]4d8d.c VTPQVPLRP-GY86 . . . W . . . . . . . . . . .
[2]1shf.b none . . . . . . . . . . . . . . .
[2]3h0i.b none . . . I . . . . . . . . . . .
[2]3ua7.a aceAPPIPPPR62 . . . . . . . . . . . . . . .
[2]4eik.a SLARRPLPPLP86 . . . . . . . . . . . . . . .
[2]4znx.a APPLPPRNRP78 . . . . . . . . . . . . . . .
[2]4znx.c APPLPPRNR65 . . . . . . . . . . . . . . .
[3]1m27.c MD-TGS-RK,V-S-LQYPV109 . . . . . . . . . . . . . . .
[3]3cqt.a none . . . . . . . . . . . . . I .
[3]3h0f.a pg512 . . . W . . . . . . . . . . .
[4]3ua7.d APPIPPPR59 . . . . . . . . . . . . . . .

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
9
1
D
9
2
Y
9
3
E
9
4
A
9
5
R
9
6
T
9
7
D
9
9
D
1
0
0
S
1
1
5
E
1
1
6
G
1
1
7
D
1
1
8
W
1
1
9
Y
1
3
2
P
1
3
4
S
1
3
5
N
1
3
6
Y
1
3
7
[1]1avz.c . . . . . . . . . . . . . . . . . . .
[1]1efn.a . . . . . I . . . . . . . . . . . . .
[1]1efn.c . . . . . I . . . . . . . . . . . . .
[1]1fyn.a . . . . . * . . . . * . * . . . . . .
[1]4d8d.a . . . . . W . . . . . . . . . . . . .
[1]4d8d.c . . . . . W . . . . . . . . . . . . .
[2]1shf.b * . . . . * . . . . . . * . . . . . .
[2]3h0i.b * . . . . I . . . . . . . . . . . . .
[2]3ua7.a * . . . . * . . . . * . . . * . . . .
[2]4eik.a . . . . . * . . . . . . . . . . . . .
[2]4znx.a . . . . . * . . . . . . . . . . . . .
[2]4znx.c . . . . . * . . . . . . . . . . . . .
[3]1m27.c * . . . . * . . . . * . . . . . . . .
[3]3cqt.a . . . . . * * . . . * . . * . . . I .
[3]3h0f.a . . . . . W . . . . * . . . . . . . .
[4]3ua7.d . . . . . * . . . . * . . . * . . . .

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
1avz.c:TPQVPLRP-GY
1efn.a:RPQVPLRP-HTQGY
1efn.c:RPQVPLRP-GY
1fyn.a:PPAYPPPPVP
4d8d.a:PVTPQVPLRP-TQGY
4d8d.c:VTPQVPLRP-GY
1shf.b is apo
3h0i.b is apo
3ua7.a:aceAPPIPPPR
4eik.a:SLARRPLPPLP
4znx.a:APPLPPRNRP
4znx.c:APPLPPRNR
1m27.c:MD-TGS-RK,V-S-LQYPV
3cqt.a is apo
3h0f.a:pg5
3ua7.d:APPIPPPR
[1] 1avz.c
0
0.5 0.2 1.8 0.2 0.4 - - 0.1 0.6 0.1 0.1 0.9 - 0 0.3
[1] 1efn.a 0.3
0.1
0.1 2.0 0.1 0.1 - - 0.1 0.8 0.4 0.3 1.0 - 0 0.2
[1] 1efn.c 0.2 0.3
0
1.4 0.2 0.1 - - 0.1 0.7 0.2 0.2 0.9 - 0 0.3
[1] 1fyn.a 1.9 1.1 1.2
0.6
2.4 1.3 - - 0.1 3.4 2.1 2.1 1.7 - 0 0.5
[1] 4d8d.a 0.3 0.4 0 1.9
0.1
0.2 - - 0.1 0.4 0.2 0.2 1.2 - 0 0.2
[1] 4d8d.c 0.3 0.3 0 1.8 0.2
0.1
- - 0.1 0.4 0.1 0.2 1.1 - 0 0.3
[2] 1shf.b 1.0 3.8 0.6 1.9 3.0 0.6
-
- 0.7 0.6 0.6 0.6 1.0 - 0 0.5
[2] 3h0i.b 0.9 2.5 0.8 2.5 3.2 0.6 -
-
0.2 0.8 0.4 0.5 1.0 - 0.1 0.6
[2] 3ua7.a 1.0 3.6 0.5 2.0 2.4 0.3 - -
0
1.2 0.2 0.2 1.7 - 0 0.3
[2] 4eik.a 0.5 4.3 0.5 1.5 3.8 0.7 - - 0.7
0
1.1 1.1 1.1 - 0 0.3
[2] 4znx.a 0.4 3.3 0.2 1.6 2.5 0.2 - - 0.2 0.6
0
0.1 0.5 - 0 0.2
[2] 4znx.c 0.3 3.7 0.1 1.8 2.8 0.2 - - 0.1 0.6 0
0
0.5 - 0 0.2
[3] 1m27.c 1.7 4.9 1.0 1.7 4.7 1.2 - - 2.6 3.6 1.4 1.3
0
- 0 0.4
[3] 3cqt.a 1.9 4.9 1.1 2.7 5.2 1.5 - - 1.2 2.8 1.3 1.3 0.8
-
0 1.3
[3] 3h0f.a 2.0 4.6 1.4 3.9 5.5 1.1 - - 0.6 1.8 0.6 0.5 1.4 -
0
0.4
[4] 3ua7.d 0.7 3.6 0.5 2.8 4.0 0.6 - - 0.4 3.1 1.9 1.8 1.0 - 0
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 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
1avz.c
1efn.a
1efn.c
1fyn.a
4d8d.a
4d8d.c
1shf.b
3h0i.b
3ua7.a
4eik.a
4znx.a
4znx.c
1m27.c
3cqt.a
3h0f.a
3ua7.d
[1] 1avz.c
0
.05 .06 .26 .07 .04 .23 .21 .30 .28 .23 .24 .41 .45 .37 .37
[1] 1efn.a .05
0
.06 .23 .07 .04 .25 .24 .28 .29 .23 .24 .41 .42 .35 .38
[1] 1efn.c .06 .06
0
.22 .07 .04 .26 .25 .32 .29 .20 .23 .44 .42 .36 .43
[1] 1fyn.a .26 .23 .22
0
.25 .25 .32 .36 .44 .42 .34 .37 .39 .28 .32 .41
[1] 4d8d.a .07 .07 .07 .25
0
.05 .22 .22 .32 .25 .24 .25 .43 .45 .35 .43
[1] 4d8d.c .04 .04 .04 .25 .05
0
.22 .22 .31 .27 .23 .24 .43 .45 .37 .41
[2] 1shf.b .23 .25 .26 .32 .22 .22
0
.10 .23 .19 .16 .17 .28 .33 .25 .31
[2] 3h0i.b .21 .24 .25 .36 .22 .22 .10
0
.15 .18 .16 .17 .24 .31 .23 .28
[2] 3ua7.a .30 .28 .32 .44 .32 .31 .23 .15
0
.22 .18 .17 .17 .31 .24 .22
[2] 4eik.a .28 .29 .29 .42 .25 .27 .19 .18 .22
0
.14 .11 .30 .27 .22 .28
[2] 4znx.a .23 .23 .20 .34 .24 .23 .16 .16 .18 .14
0
.03 .29 .27 .21 .23
[2] 4znx.c .24 .24 .23 .37 .25 .24 .17 .17 .17 .11 .03
0
.26 .26 .19 .21
[3] 1m27.c .41 .41 .44 .39 .43 .43 .28 .24 .17 .30 .29 .26
0
.25 .16 .27
[3] 3cqt.a .45 .42 .42 .28 .45 .45 .33 .31 .31 .27 .27 .26 .25
0
.18 .32
[3] 3h0f.a .37 .35 .36 .32 .35 .37 .25 .23 .24 .22 .21 .19 .16 .18
0
.28
[4] 3ua7.d .37 .38 .43 .41 .43 .41 .31 .28 .22 .28 .23 .21 .27 .32 .28
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
1avz.c
1efn.a
1efn.c
1fyn.a
4d8d.a
4d8d.c
1shf.b
3h0i.b
3ua7.a
4eik.a
4znx.a
4znx.c
1m27.c
3cqt.a
3h0f.a
3ua7.d
[1] 1avz.c
0
0.8 0.6 1.0 0.6 0.5 1.2 1.1 0.8 0.6 0.8 0.7 1.0 1.0 1.0 1.0
[1] 1efn.a 0.8
0
0.7 1.4 0.7 0.7 1.5 1.4 1.0 1.0 1.0 1.0 1.3 1.3 1.5 1.3
[1] 1efn.c 0.6 0.7
0
1.1 0.4 0.3 1.3 1.3 0.9 0.8 0.8 0.8 1.2 1.0 1.1 1.1
[1] 1fyn.a 1.0 1.4 1.1
0
1.1 1.1 0.9 0.9 1.0 0.9 1.0 1.0 0.6 1.1 0.5 0.6
[1] 4d8d.a 0.6 0.7 0.4 1.1
0
0.3 1.3 1.2 0.9 0.8 0.8 0.8 1.1 1.1 1.1 1.0
[1] 4d8d.c 0.5 0.7 0.3 1.1 0.3
0
1.3 1.3 0.9 0.8 0.8 0.8 1.2 1.1 1.1 1.1
[2] 1shf.b 1.2 1.5 1.3 0.9 1.3 1.3
0
0.8 1.2 1.1 1.2 1.2 0.9 1.3 1.0 1.1
[2] 3h0i.b 1.1 1.4 1.3 0.9 1.2 1.3 0.8
0
0.9 0.9 1.0 0.9 0.8 1.0 0.9 0.8
[2] 3ua7.a 0.8 1.0 0.9 1.0 0.9 0.9 1.2 0.9
0
0.6 0.5 0.4 0.9 0.6 1.1 0.8
[2] 4eik.a 0.6 1.0 0.8 0.9 0.8 0.8 1.1 0.9 0.6
0
0.6 0.6 0.9 0.8 1.1 0.9
[2] 4znx.a 0.8 1.0 0.8 1.0 0.8 0.8 1.2 1.0 0.5 0.6
0
0.1 1.0 0.5 1.1 0.8
[2] 4znx.c 0.7 1.0 0.8 1.0 0.8 0.8 1.2 0.9 0.4 0.6 0.1
0
1.0 0.5 1.1 0.8
[3] 1m27.c 1.0 1.3 1.2 0.6 1.1 1.2 0.9 0.8 0.9 0.9 1.0 1.0
0
1.0 0.8 0.7
[3] 3cqt.a 1.0 1.3 1.0 1.1 1.1 1.1 1.3 1.0 0.6 0.8 0.5 0.5 1.0
0
1.1 0.8
[3] 3h0f.a 1.0 1.5 1.1 0.5 1.1 1.1 1.0 0.9 1.1 1.1 1.1 1.1 0.8 1.1
0
0.6
[4] 3ua7.d 1.0 1.3 1.1 0.6 1.0 1.1 1.1 0.8 0.8 0.9 0.8 0.8 0.7 0.8 0.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.9 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
1avz.c
1efn.a
1efn.c
1fyn.a
4d8d.a
4d8d.c
1shf.b
3h0i.b
3ua7.a
4eik.a
4znx.a
4znx.c
1m27.c
3cqt.a
3h0f.a
3ua7.d
[1] 1avz.c
0
1.0 0.6 1.4 0.8 0.7 1.7 1.2 1.2 1.3 1.1 1.2 2.0 1.8 1.3 1.4
[1] 1efn.a 1.0
0
1.1 1.6 1.2 1.2 1.9 1.7 1.2 1.4 1.2 1.2 1.9 1.7 1.7 1.5
[1] 1efn.c 0.6 1.1
0
1.4 0.7 0.8 1.8 1.5 1.0 1.0 0.9 0.9 1.8 1.4 1.4 1.2
[1] 1fyn.a 1.4 1.6 1.4
0
1.5 1.6 1.6 1.3 1.3 1.5 1.2 1.4 1.5 1.6 0.8 0.9
[1] 4d8d.a 0.8 1.2 0.7 1.5
0
0.6 1.8 1.4 1.1 1.1 1.0 1.0 1.8 1.4 1.7 1.4
[1] 4d8d.c 0.7 1.2 0.8 1.6 0.6
0
1.7 1.4 1.1 1.0 1.0 1.0 1.8 1.5 1.8 1.5
[2] 1shf.b 1.7 1.9 1.8 1.6 1.8 1.7
0
1.1 1.8 1.7 1.3 1.8 2.0 2.1 1.4 1.7
[2] 3h0i.b 1.2 1.7 1.5 1.3 1.4 1.4 1.1
0
1.2 1.1 1.0 1.2 1.6 1.5 1.2 1.1
[2] 3ua7.a 1.2 1.2 1.0 1.3 1.1 1.1 1.8 1.2
0
1.2 0.9 0.8 1.6 1.3 1.3 1.2
[2] 4eik.a 1.3 1.4 1.0 1.5 1.1 1.0 1.7 1.1 1.2
0
0.8 0.9 1.7 1.4 1.4 1.4
[2] 4znx.a 1.1 1.2 0.9 1.2 1.0 1.0 1.3 1.0 0.9 0.8
0
0.2 1.7 1.4 1.2 1.1
[2] 4znx.c 1.2 1.2 0.9 1.4 1.0 1.0 1.8 1.2 0.8 0.9 0.2
0
1.7 1.3 1.4 1.2
[3] 1m27.c 2.0 1.9 1.8 1.5 1.8 1.8 2.0 1.6 1.6 1.7 1.7 1.7
0
1.8 1.5 1.4
[3] 3cqt.a 1.8 1.7 1.4 1.6 1.4 1.5 2.1 1.5 1.3 1.4 1.4 1.3 1.8
0
1.5 1.5
[3] 3h0f.a 1.3 1.7 1.4 0.8 1.7 1.8 1.4 1.2 1.3 1.4 1.2 1.4 1.5 1.5
0
0.9
[4] 3ua7.d 1.4 1.5 1.2 0.9 1.4 1.5 1.7 1.1 1.2 1.4 1.1 1.2 1.4 1.5 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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