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P2RY1_HUMAN_2_373_TM

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

Composition of the binding site

Protein chains monomer
A1 (P2RY1_HUMAN):41, 42, 44, 46, 195, 201, 203:205, 283, 286, 287, 291, 299, 303, 306, 31041, 42, 44, 46, 195, 201, 203:205, 283, 286, 287, 291, 299, 303, 306, 310

Full PDB list

4xnv, 4xnw

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
C
4
2
L
4
4
K
4
6
R
1
9
5
T
2
0
1
Y
2
0
3
D
2
0
4
T
2
0
5
N
2
8
3
A
2
8
6
R
2
8
7
Q
2
9
1
N
2
9
9
Y
3
0
3
Y
3
0
6
R
3
1
0
[1]4xnv.a none . . . . . . . . . . . . . . . .
[1]4xnw.c 2id29 . . . . . . . . . . . . . . . .

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
K
4
1
C
4
2
L
4
4
K
4
6
R
1
9
5
T
2
0
1
Y
2
0
3
D
2
0
4
T
2
0
5
N
2
8
3
A
2
8
6
R
2
8
7
Q
2
9
1
N
2
9
9
Y
3
0
3
Y
3
0
6
R
3
1
0
[1]4xnv.a . . . . . . . . . . . . . . . . .
[1]4xnw.c . . . . . . . . . . . . . . . . .

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 is apo
4xnw.c:2id
[1] 4xnv.a
-
1.0
[1] 4xnw.c -
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
4xnv.a
4xnw.c
[1] 4xnv.a
0
.05
[1] 4xnw.c .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
4xnv.a
4xnw.c
[1] 4xnv.a
0
1.1
[1] 4xnw.c 1.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
4xnv.a
4xnw.c
[1] 4xnv.a
0
1.8
[1] 4xnw.c 1.8
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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