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5HT2B_HUMAN_27_404

5-hydroxytryptamine receptor 2B [G-protein coupled receptor 1 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (5HT2B_HUMAN):R: Agonist binding (135, 136, 139, 140)
R: Agonist binding (337, 340, 341)
131, 132, 207:211, 217, 218, 221, 225, 344, 347, 348, 359, 360, 362, 363, 366, 370
131, 132, 135, 136, 139, 140, 207:211, 217, 218, 221, 225, 337, 340, 341, 344, 347, 348, 359, 360, 362, 363, 366, 370

Full PDB list

4ib4, 4nc3, 5tud, 5tvn (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
W
1
3
1
L
1
3
2
D
1
3
5
V
1
3
6
S
1
3
9
T
1
4
0
V
2
0
8
L
2
0
9
T
2
1
0
K
2
1
1
F
2
1
7
M
2
1
8
G
2
2
1
A
2
2
5
W
3
3
7
F
3
4
0
F
3
4
1
N
3
4
4
L
3
4
7
V
3
4
8
Q
3
5
9
L
3
6
2
E
3
6
3
V
3
6
6
Y
3
7
0
[1]4ib4.a erm43 . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tvn.a 7ld24 . . . . . . . . . . . . . . . . . . . . . . . . .

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
W
1
3
1
L
1
3
2
D
1
3
5
V
1
3
6
S
1
3
9
T
1
4
0
C
2
0
7
V
2
0
8
L
2
0
9
T
2
1
0
K
2
1
1
F
2
1
7
M
2
1
8
G
2
2
1
A
2
2
5
W
3
3
7
F
3
4
0
F
3
4
1
N
3
4
4
L
3
4
7
V
3
4
8
Q
3
5
9
M
3
6
0
L
3
6
2
E
3
6
3
V
3
6
6
Y
3
7
0
[1]4ib4.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5tvn.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
4ib4.a:erm
5tvn.a:7ld
[1] 4ib4.a
0
0.2
[1] 5tvn.a 5.5
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
4ib4.a
5tvn.a
[1] 4ib4.a
0
.20
[1] 5tvn.a .20
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
4ib4.a
5tvn.a
[1] 4ib4.a
0
0.7
[1] 5tvn.a 0.7
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
4ib4.a
5tvn.a
[1] 4ib4.a
0
1.1
[1] 5tvn.a 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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