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DYR_MOUSE_2_187

Dihydrofolate reductase [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR_MOUSE):D: DHFR (8:10, 21:23, 31, 32, 35, 36, 57, 60:62, 65, 68, 69, 71, 116, 122, 137)
R: Substrate binding (31, 32, 35, 36)
8:10, 21:23, 31, 32, 35, 36, 57, 60:62, 65, 68, 69, 71, 116, 122, 137
Cofactors (cF):ndp

Full PDB list

1u70, 2fzj, 3d80, 3d84, 3k45, 3k47

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
8
V
9
A
1
0
G
2
1
D
2
2
L
2
3
E
3
1
F
3
2
F
3
5
Q
3
6
T
5
7
S
6
0
I
6
1
P
6
2
N
6
5
L
6
8
K
6
9
R
7
1
V
1
1
6
Y
1
2
2
T
1
3
7
[1]1u70.a mtx33 . . . . . R . . . . . . . . . . . . . . . ndp
[1]2fzj.a dh327 . . . . . . . . . . . . . . . . . . . . . ndp
[1]3d80.a q2229 . . . . . . . . . . . . . . . . . . . . . ndp
[1]3d84.x none . . . . . . . . . . . . . . . . . . . . . ndp
[1]3k45.a 51p21 . . . . . . . . . . . . . . . . . . . . . ndp
[1]3k47.a d0922 . . . . . . . . . . . . . . . . . . . . . ndp

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 cF
I
8
V
9
A
1
0
G
2
1
D
2
2
L
2
3
E
3
1
F
3
2
F
3
5
Q
3
6
T
5
7
S
6
0
I
6
1
P
6
2
N
6
5
L
6
8
K
6
9
R
7
1
V
1
1
6
Y
1
2
2
T
1
3
7
[1]1u70.a . . . . . R . . . . . . . . . . . . . . . ndp
[1]2fzj.a . . . . . . . . . . . . . . . . . . . . . ndp
[1]3d80.a . . . . . . . . . . . . . . . . . . . . . ndp
[1]3d84.x . . . . . . . * . * . . . . . . . . . . . ndp
[1]3k45.a . . . . . . . . . * . . . . . . . . . . . ndp
[1]3k47.a . . . . . . . * . * . . . . . . . . . . . ndp

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
1u70.a:mtx
2fzj.a:dh3
3d80.a:q22
3d84.x is apo
3k45.a:51p
3k47.a:d09
[1] 1u70.a
0.1
1.5 2.4 - 0.1 0.2
[1] 2fzj.a 0.4
0.1
0.1 - 0.1 0.1
[1] 3d80.a 0 0
0
- 0 0
[1] 3d84.x 3.6 4.1 0.3
-
0 0.1
[1] 3k45.a 1.4 2.0 0.3 -
0.1
0.2
[1] 3k47.a 3.3 3.3 0.3 - 0
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
1u70.a
2fzj.a
3d80.a
3d84.x
3k45.a
3k47.a
[1] 1u70.a
0
.14 .13 .30 .20 .26
[1] 2fzj.a .14
0
.03 .22 .14 .18
[1] 3d80.a .13 .03
0
.21 .11 .17
[1] 3d84.x .30 .22 .21
0
.12 .05
[1] 3k45.a .20 .14 .11 .12
0
.11
[1] 3k47.a .26 .18 .17 .05 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1u70.a
2fzj.a
3d80.a
3d84.x
3k45.a
3k47.a
[1] 1u70.a
0
0.6 0.5 0.5 0.6 0.5
[1] 2fzj.a 0.6
0
0.3 0.3 0.6 0.5
[1] 3d80.a 0.5 0.3
0
0.2 0.4 0.3
[1] 3d84.x 0.5 0.3 0.2
0
0.5 0.3
[1] 3k45.a 0.6 0.6 0.4 0.5
0
0.3
[1] 3k47.a 0.5 0.5 0.3 0.3 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1u70.a
2fzj.a
3d80.a
3d84.x
3k45.a
3k47.a
[1] 1u70.a
0
0.8 1.1 1.1 0.8 1.1
[1] 2fzj.a 0.8
0
1.1 1.0 0.9 1.1
[1] 3d80.a 1.1 1.1
0
1.3 0.8 1.4
[1] 3d84.x 1.1 1.0 1.3
0
0.8 0.5
[1] 3k45.a 0.8 0.9 0.8 0.8
0
0.8
[1] 3k47.a 1.1 1.1 1.4 0.5 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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