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P2Y12_HUMAN_1_342

P2Y purinoceptor 12 [G-protein coupled receptor 1 family]

Composition of the binding site

Protein chains monomer
A1 (P2Y12_HUMAN):19, 93, 97, 98, 101, 102, 105, 106, 109, 155, 156, 159, 173:175, 179, 187, 190, 191, 194, 252, 255, 256, 258:260, 263, 276, 277, 279, 280, 28319, 93, 97, 98, 101, 102, 105, 106, 109, 155, 156, 159, 173:175, 179, 187, 190, 191, 194, 252, 255, 256, 258:260, 263, 276, 277, 279, 280, 283
Cofactors (cF):olc

Full PDB list

4ntj, 4pxz, 4py0

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
R
9
3
C
9
7
S
1
0
1
V
1
0
2
Y
1
0
5
F
1
0
6
Y
1
0
9
L
1
5
5
S
1
5
6
N
1
5
9
K
1
7
3
K
1
7
4
C
1
7
5
K
1
7
9
H
1
8
7
V
1
9
0
N
1
9
1
C
1
9
4
F
2
5
2
R
2
5
6
Y
2
5
9
Q
2
6
3
L
2
7
6
K
2
8
0
[1]4pxz.a 6ad29 . . . . . . . . . . . . . . . . . . . . . . . . olc
[1]4py0.a 6at33 . . . . . . . . . . . . . . . . . . . . . . . . olc
[2]4ntj.a azj33 . . . . . . . . . . - - - . . . . . . . . . . .

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

[download in TSV format]
   
PDB.ch
A1 cF
R
1
9
R
9
3
C
9
7
Q
9
8
S
1
0
1
V
1
0
2
Y
1
0
5
F
1
0
6
Y
1
0
9
L
1
5
5
S
1
5
6
N
1
5
9
K
1
7
3
K
1
7
4
C
1
7
5
K
1
7
9
H
1
8
7
V
1
9
0
N
1
9
1
C
1
9
4
F
2
5
2
A
2
5
5
R
2
5
6
P
2
5
8
Y
2
5
9
T
2
6
0
Q
2
6
3
L
2
7
6
F
2
7
7
V
2
7
9
K
2
8
0
T
2
8
3
[1]4pxz.a . . . . . . . . . . . . . . . . . . . . . * * . * . . . . . . . olc
[1]4py0.a . . . . . . . . . . . . . . . . . . . . . . * . * . . . . . . . olc
[2]4ntj.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
4pxz.a:6ad
4py0.a:6at
4ntj.a:azj
[1] 4pxz.a
0.1
0.8 10
[1] 4py0.a 0
0.1
9.4
[2] 4ntj.a 0.9 1.2
0
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4pxz.a
4py0.a
4ntj.a
[1] 4pxz.a
0
.05 .37
[1] 4py0.a .05
0
.34
[2] 4ntj.a .37 .34
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
4pxz.a
4py0.a
4ntj.a
[1] 4pxz.a
0
0.5 3.7
[1] 4py0.a 0.5
0
3.5
[2] 4ntj.a 3.7 3.5
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

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
4pxz.a
4py0.a
4ntj.a
[1] 4pxz.a
0
0.7 3.9
[1] 4py0.a 0.7
0
3.7
[2] 4ntj.a 3.9 3.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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