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DPYD_PIG_1_1025_uracil

Dihydropyrimidine dehydrogenase [NADP(+)] [Dihydropyrimidine dehydrogenase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DPYD_PIG):R: Substrate binding (668, 670)
R: Substrate binding (736, 737)
609, 611:613, 671:673, 675, 764
609, 611:613, 668, 670:673, 675, 736, 737, 764
Cofactors (cF):fmn

Full PDB list

1gt8, 1gte, 1gth, 1h7w, 1h7x (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
N
6
0
9
E
6
1
1
L
6
1
2
I
6
1
3
N
6
6
8
S
6
7
0
C
6
7
1
P
6
7
2
H
6
7
3
M
6
7
5
N
7
3
6
T
7
3
7
G
7
6
4
[1]1gt8.b uaa12 . . . . . . . . . . . . . fmn
[1]1gth.a idh8 . . . . . . * . . . . . . fmn
[1]1gth.c iur9 . . . . . . . . . . . . . fmn
[1]1gth.d ura8 . . . . . . . . . . . . . fmn
[1]1h7w.a none . . . . . . . . . . . . . fmn
[1]1h7x.a urf9 . . . . . . A . . - . . . fmn

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

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PDB.ch
A1 cF
N
6
0
9
E
6
1
1
L
6
1
2
I
6
1
3
N
6
6
8
S
6
7
0
C
6
7
1
P
6
7
2
H
6
7
3
M
6
7
5
N
7
3
6
T
7
3
7
G
7
6
4
[1]1gt8.b . . . . . . . . . . . . . fmn
[1]1gth.a . . . . . . * . . . . . . fmn
[1]1gth.c . . . . . . . . . . . . . fmn
[1]1gth.d . . . . . . . . . . . . . fmn
[1]1h7w.a . . . . . . . . . . . . . fmn
[1]1h7x.a . . . . . . A . . - . . . fmn

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
1gt8.b:uaa
1gth.a:idh
1gth.c:iur
1gth.d:ura
1h7w.a is apo
1h7x.a:urf
[1] 1gt8.b
0
0 0.1 0 - 0
[1] 1gth.a 1.6
0.4
0.4 0.1 - 0.1
[1] 1gth.c 1.2 0.1
0.2
0 - 0
[1] 1gth.d 1.3 0.1 0.2
0
- 0
[1] 1h7w.a 0.3 0 0.1 0
-
0
[1] 1h7x.a 0.3 0 0.1 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
1gt8.b
1gth.a
1gth.c
1gth.d
1h7w.a
1h7x.a
[1] 1gt8.b
0
.12 .09 .10 .02 .02
[1] 1gth.a .12
0
.03 .02 .10 .10
[1] 1gth.c .09 .03
0
.01 .07 .07
[1] 1gth.d .10 .02 .01
0
.08 .08
[1] 1h7w.a .02 .10 .07 .08
0
0
[1] 1h7x.a .02 .10 .07 .08 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.9 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
1gt8.b
1gth.a
1gth.c
1gth.d
1h7w.a
1h7x.a
[1] 1gt8.b
0
6.2 6.2 6.2 1.2 0.8
[1] 1gth.a 6.2
0
0.1 0.1 6.2 5.1
[1] 1gth.c 6.2 0.1
0
0.1 6.2 5.1
[1] 1gth.d 6.2 0.1 0.1
0
6.2 5.2
[1] 1h7w.a 1.2 6.2 6.2 6.2
0
0.1
[1] 1h7x.a 0.8 5.1 5.1 5.2 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 3.2 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
1gt8.b
1gth.a
1gth.c
1gth.d
1h7w.a
1h7x.a
[1] 1gt8.b
0
7.9 8.0 7.9 1.4 0.7
[1] 1gth.a 7.9
0
0.2 0.1 7.9 6.5
[1] 1gth.c 8.0 0.2
0
0.2 7.9 6.5
[1] 1gth.d 7.9 0.1 0.2
0
7.9 6.5
[1] 1h7w.a 1.4 7.9 7.9 7.9
0
0.2
[1] 1h7x.a 0.7 6.5 6.5 6.5 0.2
0
[Binding site full-atom RMSD matrix]







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