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ADRB1_MELGA_31_367_TM

Beta-1 adrenergic receptor [G-protein coupled receptor 1 family. Adrenergic receptor subfamily. ADRB1 sub-subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ADRB1_MELGA):R: Agonist and antagonist binding (201, 203, 207, 208, 211, 212, 215)
R: Agonist and antagonist binding (303, 306, 307, 310)
R: Agonist and antagonist binding (329, 330, 333)
98, 101, 102, 117, 118, 121, 122, 125, 199, 200, 322, 325, 326
98, 101, 102, 117, 118, 121, 122, 125, 199:201, 203, 207, 208, 211, 212, 215, 303, 306, 307, 310, 322, 325, 326, 329, 330, 333
Cofactors (cF):2cv
Metals (Me):Na

Full PDB list

2vt4, 2y00, 2y01, 2y02, 2y03, 2y04, 2ycw, 2ycx, 2ycy, 2ycz, 3zpq, 3zpr, 4ami, 4amj, 4bvn, 4gpo, 5a8e, 5f8u (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
1
0
1
V
1
0
2
W
1
1
7
T
1
1
8
D
1
2
1
V
1
2
2
V
1
2
5
C
1
9
9
D
2
0
0
F
2
0
1
T
2
0
3
Y
2
0
7
A
2
0
8
S
2
1
1
S
2
1
5
W
3
0
3
F
3
0
6
F
3
0
7
N
3
1
0
F
3
2
5
V
3
2
6
N
3
2
9
W
3
3
0
Y
3
3
3
[1]2vt4.a p3221 . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]2y00.a y0022 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2y02.a whj27 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2y03.b 5fw15 . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]2y04.b 68h17 . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]2ycw.a cau22 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2ycz.a i3222 . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zpq.a xf515 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]3zpr.a 3wc17 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]4ami.b g9027 . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]4amj.a cvd30 . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]4bvn.a p3221 . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]4gpo.a none . . . . . . . . . . . . . . . . . . . . . . . .
[1]5a8e.a xtk22 . . . . . . . . . . . . . . . . . . . . . . . . Na

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 Me
G
9
8
L
1
0
1
V
1
0
2
W
1
1
7
T
1
1
8
D
1
2
1
V
1
2
2
V
1
2
5
C
1
9
9
D
2
0
0
F
2
0
1
T
2
0
3
Y
2
0
7
A
2
0
8
S
2
1
1
S
2
1
2
S
2
1
5
W
3
0
3
F
3
0
6
F
3
0
7
N
3
1
0
D
3
2
2
F
3
2
5
V
3
2
6
N
3
2
9
W
3
3
0
Y
3
3
3
[1]2vt4.a . . . . . . . . . . . . . . . . . . . . . . . . . . . Na
[1]2y00.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2y02.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2y03.b . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]2y04.b . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]2ycw.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]2ycz.a . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3zpq.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]3zpr.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]4ami.b . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv
[1]4amj.a . . . . . . . . . . . . . . . . . . . . . . . . . . . 2cv Na
[1]4bvn.a . . . . . . . . . . . . . . . . . . . . . K * . . . . Na
[1]4gpo.a . . . . . . . . . . . . . . * . . . . . . . . . . . .
[1]5a8e.a . . . . . . . . . . . . . . . . . . . . . . * . . . . Na

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
2vt4.a:p32
2y00.a:y00
2y02.a:whj
2y03.b:5fw
2y04.b:68h
2ycw.a:cau
2ycz.a:i32
3zpq.a:xf5
3zpr.a:3wc
4ami.b:g90
4amj.a:cvd
4bvn.a:p32
4gpo.a is apo
5a8e.a:xtk
[1] 2vt4.a
0
0.3 0 0 0 0.3 0.3 0.1 0.1 0 0.1 0.1 - 0.2
[1] 2y00.a 0.7
0
0.2 0.1 0.2 0.8 1.1 0.8 0.8 0.2 0.6 0.6 - 0.8
[1] 2y02.a 0.6 0.3
0
0.1 0.2 0.6 0.8 0.4 0.5 0.6 0.5 0.5 - 0.6
[1] 2y03.b 0.8 0.2 0.3
0
0 0.5 1.0 0.4 0.8 0.5 0.8 0.8 - 0.6
[1] 2y04.b 0.3 0.1 0.5 0
0.1
0.4 0.7 0.4 0.3 0.3 0.6 0.3 - 0.6
[1] 2ycw.a 0.1 0.1 0.2 0 0
0.2
0.3 0.3 0.2 0.2 0.2 0 - 0.3
[1] 2ycz.a 0 0.2 0.2 0 0 0.2
0
0 0.1 0.1 0 0 - 0.3
[1] 3zpq.a 0.1 0 0.1 0 0 0.4 0.3
0
0.1 0.1 0.1 0.1 - 0.4
[1] 3zpr.a 0 0.1 0.1 0 0 0.3 0.1 0
0
0.1 0 0.1 - 0.4
[1] 4ami.b 0.2 0.1 0.5 0 0.1 0.5 0.5 0.3 0.4
0
0.2 0.1 - 0.4
[1] 4amj.a 0.1 0.1 0 0 0 0.2 0.2 0.1 0 0.1
0
0 - 0.2
[1] 4bvn.a 0 0 0.9 0 0 0.3 0.2 0.2 0.2 0.3 0.7
0
- 0.2
[1] 4gpo.a 1.4 0.7 1.0 0.4 0.5 1.6 1.5 1.4 1.4 0.9 1.5 1.6
-
1.6
[1] 5a8e.a 0 0 1.1 0 0 0.2 0.2 0.1 0.1 0.2 0.6 0 -
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
2vt4.a
2y00.a
2y02.a
2y03.b
2y04.b
2ycw.a
2ycz.a
3zpq.a
3zpr.a
4ami.b
4amj.a
4bvn.a
4gpo.a
5a8e.a
[1] 2vt4.a
0
.07 .04 .06 .04 .04 .03 .03 .01 .03 .03 .06 .13 .07
[1] 2y00.a .07
0
.05 .07 .05 .06 .07 .06 .06 .06 .07 .09 .10 .11
[1] 2y02.a .04 .05
0
.04 .04 .04 .05 .03 .03 .04 .04 .07 .13 .09
[1] 2y03.b .06 .07 .04
0
.04 .04 .04 .06 .05 .06 .06 .07 .10 .09
[1] 2y04.b .04 .05 .04 .04
0
.05 .04 .05 .04 .03 .06 .05 .11 .07
[1] 2ycw.a .04 .06 .04 .04 .05
0
.03 .04 .03 .04 .03 .06 .11 .06
[1] 2ycz.a .03 .07 .05 .04 .04 .03
0
.04 .03 .04 .03 .06 .12 .06
[1] 3zpq.a .03 .06 .03 .06 .05 .04 .04
0
.01 .04 .03 .06 .14 .06
[1] 3zpr.a .01 .06 .03 .05 .04 .03 .03 .01
0
.03 .02 .05 .13 .06
[1] 4ami.b .03 .06 .04 .06 .03 .04 .04 .04 .03
0
.04 .04 .11 .05
[1] 4amj.a .03 .07 .04 .06 .06 .03 .03 .03 .02 .04
0
.07 .13 .05
[1] 4bvn.a .06 .09 .07 .07 .05 .06 .06 .06 .05 .04 .07
0
.14 .03
[1] 4gpo.a .13 .10 .13 .10 .11 .11 .12 .14 .13 .11 .13 .14
0
.15
[1] 5a8e.a .07 .11 .09 .09 .07 .06 .06 .06 .06 .05 .05 .03 .15
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2vt4.a
2y00.a
2y02.a
2y03.b
2y04.b
2ycw.a
2ycz.a
3zpq.a
3zpr.a
4ami.b
4amj.a
4bvn.a
4gpo.a
5a8e.a
[1] 2vt4.a
0
0.7 0.8 0.6 0.5 0.4 0.3 0.7 0.6 0.4 0.7 0.4 0.8 0.4
[1] 2y00.a 0.7
0
0.5 0.4 0.4 0.5 0.7 0.3 0.3 0.4 0.4 0.8 0.8 0.8
[1] 2y02.a 0.8 0.5
0
0.6 0.6 0.7 0.8 0.5 0.5 0.6 0.5 0.9 0.9 0.9
[1] 2y03.b 0.6 0.4 0.6
0
0.3 0.4 0.6 0.5 0.5 0.3 0.6 0.6 0.7 0.6
[1] 2y04.b 0.5 0.4 0.6 0.3
0
0.4 0.5 0.4 0.4 0.2 0.5 0.6 0.7 0.6
[1] 2ycw.a 0.4 0.5 0.7 0.4 0.4
0
0.4 0.5 0.5 0.3 0.5 0.5 0.7 0.5
[1] 2ycz.a 0.3 0.7 0.8 0.6 0.5 0.4
0
0.6 0.6 0.4 0.7 0.5 0.7 0.5
[1] 3zpq.a 0.7 0.3 0.5 0.5 0.4 0.5 0.6
0
0.2 0.4 0.2 0.7 0.8 0.7
[1] 3zpr.a 0.6 0.3 0.5 0.5 0.4 0.5 0.6 0.2
0
0.4 0.2 0.7 0.8 0.7
[1] 4ami.b 0.4 0.4 0.6 0.3 0.2 0.3 0.4 0.4 0.4
0
0.5 0.5 0.7 0.5
[1] 4amj.a 0.7 0.4 0.5 0.6 0.5 0.5 0.7 0.2 0.2 0.5
0
0.8 0.9 0.8
[1] 4bvn.a 0.4 0.8 0.9 0.6 0.6 0.5 0.5 0.7 0.7 0.5 0.8
0
0.8 0.2
[1] 4gpo.a 0.8 0.8 0.9 0.7 0.7 0.7 0.7 0.8 0.8 0.7 0.9 0.8
0
0.8
[1] 5a8e.a 0.4 0.8 0.9 0.6 0.6 0.5 0.5 0.7 0.7 0.5 0.8 0.2 0.8
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
2vt4.a
2y00.a
2y02.a
2y03.b
2y04.b
2ycw.a
2ycz.a
3zpq.a
3zpr.a
4ami.b
4amj.a
4bvn.a
4gpo.a
5a8e.a
[1] 2vt4.a
0
1.0 1.1 0.9 0.8 0.8 0.8 0.9 0.9 0.8 1.0 0.9 1.1 0.8
[1] 2y00.a 1.0
0
0.4 0.6 0.7 0.7 0.9 0.5 0.5 0.6 0.6 0.9 1.0 0.9
[1] 2y02.a 1.1 0.4
0
0.7 0.8 0.8 1.0 0.6 0.6 0.7 0.7 1.0 1.1 1.1
[1] 2y03.b 0.9 0.6 0.7
0
0.5 0.6 0.8 0.6 0.7 0.7 0.8 0.7 1.0 0.8
[1] 2y04.b 0.8 0.7 0.8 0.5
0
0.6 0.7 0.7 0.7 0.6 0.8 0.7 1.0 0.7
[1] 2ycw.a 0.8 0.7 0.8 0.6 0.6
0
0.7 0.6 0.6 0.8 0.7 0.6 1.0 0.8
[1] 2ycz.a 0.8 0.9 1.0 0.8 0.7 0.7
0
0.9 0.9 0.7 1.0 0.8 0.9 0.8
[1] 3zpq.a 0.9 0.5 0.6 0.6 0.7 0.6 0.9
0
0.2 0.7 0.5 0.8 1.1 0.9
[1] 3zpr.a 0.9 0.5 0.6 0.7 0.7 0.6 0.9 0.2
0
0.7 0.4 0.8 1.0 0.9
[1] 4ami.b 0.8 0.6 0.7 0.7 0.6 0.8 0.7 0.7 0.7
0
0.8 0.8 0.9 0.7
[1] 4amj.a 1.0 0.6 0.7 0.8 0.8 0.7 1.0 0.5 0.4 0.8
0
0.9 1.1 0.9
[1] 4bvn.a 0.9 0.9 1.0 0.7 0.7 0.6 0.8 0.8 0.8 0.8 0.9
0
1.1 0.5
[1] 4gpo.a 1.1 1.0 1.1 1.0 1.0 1.0 0.9 1.1 1.0 0.9 1.1 1.1
0
1.0
[1] 5a8e.a 0.8 0.9 1.1 0.8 0.7 0.8 0.8 0.9 0.9 0.7 0.9 0.5 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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