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DPYD_PIG_1_1025_NADPH

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

Composition of the binding site

Protein chains monomer
A1 (DPYD_PIG):131, 289, 291, 339:343, 364, 365, 371, 393, 437:439, 481, 484:488131, 289, 291, 339:343, 364, 365, 371, 393, 437:439, 481, 484:488
Cofactors (cF):fad/sf4

Full PDB list

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

Pocket contact map

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PDB.ch
   
ligand
A1 cF
D
2
9
1
G
3
3
9
A
3
4
0
G
3
4
1
T
3
4
3
R
3
6
4
K
3
6
5
R
3
7
1
P
3
9
3
A
4
3
7
F
4
3
8
D
4
8
1
N
4
8
7
[1]1h7w.a none . . . . . . . . . . . . . fad,sf4
[1]1h7x.a ndp39 . . . . . . . . . . . . . fad,sf4

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
P
1
3
1
K
2
8
9
D
2
9
1
G
3
3
9
A
3
4
0
G
3
4
1
D
3
4
2
T
3
4
3
R
3
6
4
K
3
6
5
R
3
7
1
P
3
9
3
A
4
3
7
F
4
3
8
G
4
3
9
D
4
8
1
G
4
8
4
M
4
8
5
A
4
8
6
N
4
8
7
T
4
8
8
[1]1h7w.a . . . . . . . . . . * . . . . . . . . * . fad,sf4
[1]1h7x.a . . . . . . . . . . . . . . . . . . . . . fad,sf4

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
1h7w.a is apo
1h7x.a:ndp
[1] 1h7w.a
-
3.4
[1] 1h7x.a -
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
1h7w.a
1h7x.a
[1] 1h7w.a
0
.15
[1] 1h7x.a .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1h7w.a
1h7x.a
[1] 1h7w.a
0
0.5
[1] 1h7x.a 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1h7w.a
1h7x.a
[1] 1h7w.a
0
1.3
[1] 1h7x.a 1.3
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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