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DYR_MYCTU_4_161

Dihydrofolate reductase [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR_MYCTU):D: DHFR (7:9, 18:22, 25, 29:31, 33, 34, 44, 48, 51:53, 55, 56, 59, 62, 96, 97, 102, 115)
R: Substrate binding (7:9)
7:9, 18:22, 25, 29:31, 33, 34, 44, 48, 51:53, 55, 56, 59, 62, 96, 97, 102, 115
Cofactors (cF):1dg/atr/nap/ndp

Full PDB list

1df7, 1dg5, 1dg7, 1dg8, 2cig, 4kl9, 4klx, 4km0, 4km2, 4kne, 4m2x, 5ja3, 5u26, 5u27, 5ujf (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
I
7
W
8
A
9
G
1
9
D
2
1
I
2
2
R
2
5
D
2
9
Q
3
0
A
3
1
F
3
3
R
3
4
M
4
4
T
4
8
S
5
1
L
5
2
P
5
3
K
5
5
V
5
6
L
5
9
R
6
2
I
9
6
G
9
7
Y
1
0
2
T
1
1
5
[1]1df7.a mtx33 . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]1dg7.a wrb22 . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]2cig.a none . . . . . . . . . . . . . V . . . . . . . . . . . 1dg
[1]4kl9.a none . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]4km0.a cp617 . . . . . . . . . . . . . . . . . . . . . . . . . atr
[1]4km2.a top21 . . . . . . . . . . . . . . . . . . . . . . . . . atr
[1]4kne.a 1cy17 . . . . . . . . . . . . . . . . . . . . . . . . . atr
[1]4m2x.a tmq27 . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]5ja3.b u0630 . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]5u27.a p6523 . . . . . . . . . . . . . . . . . . . . . . . . . nap
[1]5ujf.a mmv26 . . . . . . . . . . . . . . . . . . . . . . . . .

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
7
W
8
A
9
R
1
8
G
1
9
G
2
0
D
2
1
I
2
2
R
2
5
D
2
9
Q
3
0
A
3
1
F
3
3
R
3
4
M
4
4
T
4
8
S
5
1
L
5
2
P
5
3
K
5
5
V
5
6
L
5
9
R
6
2
I
9
6
G
9
7
Y
1
0
2
T
1
1
5
[1]1df7.a . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]1dg7.a . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]2cig.a . . . . . . . . . . . . . . . V . . . . . . . . . . . 1dg
[1]4kl9.a . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]4km0.a . . . . . . . . . . . . . * . . . . . . . . . . . . . atr
[1]4km2.a . . . . . . . . . . . . . . . . . . . . . . . . . . . atr
[1]4kne.a . . . . . . . . . . . . . . . . . . . . . . . . . . . atr
[1]4m2x.a . . . . . . . . . . . . . . . . . . . . . . . . . . . ndp
[1]5ja3.b . . . . . . . . . . . . . * . . . . . . . . . . . . . ndp
[1]5u27.a . . . . . . . . . . . . . * . . . . . . . . . . . . . nap
[1]5ujf.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
1df7.a:mtx
1dg7.a:wrb
2cig.a is apo
4kl9.a is apo
4km0.a:cp6
4km2.a:top
4kne.a:1cy
4m2x.a:tmq
5ja3.b:u06
5u27.a:p65
5ujf.a:mmv
[1] 1df7.a
0
0 - - 0.5 0.8 0.2 0.5 0 0.1 0.2
[1] 1dg7.a 0.1
0
- - 0.6 0.7 0.3 0.2 0.3 0 0.4
[1] 2cig.a 0.6 0
-
- 0.3 0.6 0.2 0.1 0 0 0.1
[1] 4kl9.a 0.2 0 -
-
0.5 0.6 0.2 0.3 0.1 0 0.2
[1] 4km0.a 1.2 0.1 - -
0
0.4 0.1 0.5 0.1 0.5 0
[1] 4km2.a 0.4 0 - - 0.1
0
0.1 0.3 0 0 0
[1] 4kne.a 0.1 0 - - 0.2 0.7
0
0.2 0.3 0.4 0.3
[1] 4m2x.a 0 0 - - 0.5 0.5 0.5
0
0 0 0
[1] 5ja3.b 3.8 0 - - 0.3 0.8 0.4 0.4
0.2
0.1 1.0
[1] 5u27.a 1.4 0.4 - - 0.3 1.1 0.3 0.9 0.8
0
0.3
[1] 5ujf.a 2.7 0 - - 0.4 0.5 0.4 1.0 3.2 0.6
0.1
[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
1df7.a
1dg7.a
2cig.a
4kl9.a
4km0.a
4km2.a
4kne.a
4m2x.a
5ja3.b
5u27.a
5ujf.a
[1] 1df7.a
0
0 .03 .02 .08 .05 .03 .02 .14 .08 .20
[1] 1dg7.a 0
0
.03 .02 .07 .05 .03 .03 .14 .08 .21
[1] 2cig.a .03 .03
0
.03 .07 .02 .05 .03 .13 .07 .20
[1] 4kl9.a .02 .02 .03
0
.09 .04 .03 .03 .16 .09 .23
[1] 4km0.a .08 .07 .07 .09
0
.06 .07 .10 .12 .09 .19
[1] 4km2.a .05 .05 .02 .04 .06
0
.05 .04 .15 .10 .22
[1] 4kne.a .03 .03 .05 .03 .07 .05
0
.04 .15 .09 .21
[1] 4m2x.a .02 .03 .03 .03 .10 .04 .04
0
.16 .10 .22
[1] 5ja3.b .14 .14 .13 .16 .12 .15 .15 .16
0
.13 .20
[1] 5u27.a .08 .08 .07 .09 .09 .10 .09 .10 .13
0
.19
[1] 5ujf.a .20 .21 .20 .23 .19 .22 .21 .22 .20 .19
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
1df7.a
1dg7.a
2cig.a
4kl9.a
4km0.a
4km2.a
4kne.a
4m2x.a
5ja3.b
5u27.a
5ujf.a
[1] 1df7.a
0
0.2 0.6 1.0 1.4 1.2 1.3 0.4 0.5 0.5 2.8
[1] 1dg7.a 0.2
0
0.6 0.9 1.4 1.2 1.2 0.4 0.5 0.5 2.7
[1] 2cig.a 0.6 0.6
0
0.6 1.4 1.2 1.3 0.7 0.7 0.8 2.8
[1] 4kl9.a 1.0 0.9 0.6
0
1.4 1.3 1.3 1.0 0.9 1.1 2.8
[1] 4km0.a 1.4 1.4 1.4 1.4
0
0.6 0.3 1.5 1.5 1.7 3.0
[1] 4km2.a 1.2 1.2 1.2 1.3 0.6
0
0.5 1.3 1.3 1.6 2.9
[1] 4kne.a 1.3 1.2 1.3 1.3 0.3 0.5
0
1.4 1.4 1.6 2.9
[1] 4m2x.a 0.4 0.4 0.7 1.0 1.5 1.3 1.4
0
0.5 0.4 2.7
[1] 5ja3.b 0.5 0.5 0.7 0.9 1.5 1.3 1.4 0.5
0
0.6 2.6
[1] 5u27.a 0.5 0.5 0.8 1.1 1.7 1.6 1.6 0.4 0.6
0
2.7
[1] 5ujf.a 2.8 2.7 2.8 2.8 3.0 2.9 2.9 2.7 2.6 2.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.2 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
1df7.a
1dg7.a
2cig.a
4kl9.a
4km0.a
4km2.a
4kne.a
4m2x.a
5ja3.b
5u27.a
5ujf.a
[1] 1df7.a
0
1.4 1.4 1.9 2.3 1.7 1.7 1.5 1.6 1.6 2.9
[1] 1dg7.a 1.4
0
1.6 1.9 2.4 1.5 2.0 1.5 1.8 1.7 3.0
[1] 2cig.a 1.4 1.6
0
1.4 2.0 1.7 1.8 1.1 1.3 1.1 3.1
[1] 4kl9.a 1.9 1.9 1.4
0
2.1 2.1 1.8 1.3 1.7 1.4 3.2
[1] 4km0.a 2.3 2.4 2.0 2.1
0
1.6 1.6 2.1 2.2 1.9 3.2
[1] 4km2.a 1.7 1.5 1.7 2.1 1.6
0
1.6 1.9 1.9 2.0 3.2
[1] 4kne.a 1.7 2.0 1.8 1.8 1.6 1.6
0
1.7 1.8 1.9 3.1
[1] 4m2x.a 1.5 1.5 1.1 1.3 2.1 1.9 1.7
0
1.3 0.9 3.1
[1] 5ja3.b 1.6 1.8 1.3 1.7 2.2 1.9 1.8 1.3
0
0.9 3.0
[1] 5u27.a 1.6 1.7 1.1 1.4 1.9 2.0 1.9 0.9 0.9
0
3.1
[1] 5ujf.a 2.9 3.0 3.1 3.2 3.2 3.2 3.1 3.1 3.0 3.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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