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P2RY1_HUMAN_2_373_alloEH123

P2Y purinoceptor 1 [G-protein coupled receptor 1 family]

Composition of the binding site

Protein chains monomer
A1 (P2RY1_HUMAN):62, 66, 102, 103, 105, 106, 119, 123, 126, 127, 13062, 66, 102, 103, 105, 106, 119, 123, 126, 127, 130

Full PDB list

4xnv, 4xnw

Pocket contact map

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PDB.ch
   
ligand
A1
F
6
2
F
6
6
L
1
0
2
T
1
0
3
P
1
0
5
A
1
0
6
F
1
1
9
M
1
2
3
L
1
2
6
Q
1
2
7
I
1
3
0
[1]4xnv.a bur32 . . . . . . . . . . .
[1]4xnw.a none . . . . . . . . . . .

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
F
6
2
F
6
6
L
1
0
2
T
1
0
3
P
1
0
5
A
1
0
6
F
1
1
9
M
1
2
3
L
1
2
6
Q
1
2
7
I
1
3
0
[1]4xnv.a . . . . . . . . . . .
[1]4xnw.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
4xnv.a:bur
4xnw.a is apo
[1] 4xnv.a
0
-
[1] 4xnw.a 0.3
-
[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
4xnv.a
4xnw.a
[1] 4xnv.a
0
.03
[1] 4xnw.a .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
4xnv.a
4xnw.a
[1] 4xnv.a
0
0.3
[1] 4xnw.a 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
4xnv.a
4xnw.a
[1] 4xnv.a
0
0.7
[1] 4xnw.a 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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