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OPRD_HUMAN_36_339

Delta-type opioid receptor [G-protein coupled receptor 1 family]

Composition of the binding site

Protein chains monomer
A1 (OPRD_HUMAN):105, 108, 125, 128, 129, 132, 199, 200, 214, 217, 274, 277, 278, 281, 284, 300, 304, 307, 308105, 108, 125, 128, 129, 132, 199, 200, 214, 217, 274, 277, 278, 281, 284, 300, 304, 307, 308

Full PDB list

4ej4, 4n6h, 4rwa, 4rwd (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
L
1
2
5
D
1
2
8
Y
1
2
9
M
1
3
2
M
1
9
9
L
2
0
0
K
2
1
4
V
2
1
7
W
2
7
4
I
2
7
7
V
2
8
1
W
2
8
4
L
3
0
0
I
3
0
4
G
3
0
7
Y
3
0
8
[1]4ej4.a ej431 . . . . . . . . . . . . . . . .
[1]4rwa.a di7.di8FFnh249 . . . . . . . . . . . . . . . .

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
Q
1
0
5
K
1
0
8
L
1
2
5
D
1
2
8
Y
1
2
9
M
1
3
2
M
1
9
9
L
2
0
0
K
2
1
4
V
2
1
7
W
2
7
4
I
2
7
7
H
2
7
8
V
2
8
1
W
2
8
4
L
3
0
0
I
3
0
4
G
3
0
7
Y
3
0
8
[1]4ej4.a . . . . . . . . . . . . . . . . . . .
[1]4rwa.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
4ej4.a:ej4
4rwa.a:di7.di8FFnh2
[1] 4ej4.a
0
0.5
[1] 4rwa.a 0.7
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
4ej4.a
4rwa.a
[1] 4ej4.a
0
.06
[1] 4rwa.a .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
4ej4.a
4rwa.a
[1] 4ej4.a
0
0.6
[1] 4rwa.a 0.6
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

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
4ej4.a
4rwa.a
[1] 4ej4.a
0
0.9
[1] 4rwa.a 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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