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ADCY2_RAT_870_1082

Adenylate cyclase type 2 [Adenylyl cyclase class-4/guanylyl cyclase family]

Composition of the binding site

Protein chains monomer
A1 (ADCY2_RAT):889, 938, 940, 945, 1018:1022, 1024, 1025, 1028, 1029, 1065889, 938, 940, 945, 1018:1022, 1024, 1025, 1028, 1029, 1065
Cofactors (cF):fkp/fok
Metals (Me):Ca/Mg/Mn

Full PDB list

1ab8, 1azs, 1cjk, 1cjt, 1cju, 1cjv, 1cs4, 1cul, 1tl7, 1u0h, 2gvd, 2gvz, 3c14, 3c15, 3c16, 3g82, 3maa (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
F
8
8
9
K
9
3
8
I
9
4
0
M
9
4
5
D
1
0
1
8
I
1
0
1
9
W
1
0
2
0
G
1
0
2
1
N
1
0
2
2
V
1
0
2
4
N
1
0
2
5
S
1
0
2
8
R
1
0
2
9
K
1
0
6
5
[1]1ab8.a fok29 . . . . . . . . . . . . . -
[1]1azs.b none . . . . . . . . . . . . . . fkp
[1]1cjk.b F-A-D,tat55 . . . . . . . . . . . . . . fok Mg,Mn
[1]1cjt.b dad,GF-A-L-D65 . . . . . . . . . . . . . . fok Mg,Mn
[1]1cs4.b 101,GF-A-L-D58 . . . . . . . . . . . . . . fok Mg
[1]1cul.b 103,3po,GF-A-L-D70 . . . . . . . . . . . . . . fok Mg
[1]1u0h.b onm42 . . . . . . . . . . . . . . fok Mg
[1]2gvd.b 12846 . . . . . . . . . . . . . . fkp Mn
[1]2gvz.b ona41 . . . . . . . . . . . . . . fkp Mn
[1]3c16.b atp31 . . . . . . . . . . . . . . fok Ca
[1]3g82.b mi341 . . . . . . . . . . . . . . fok Mn
[1]3maa.b tat31 . . . . . . . . . . . . . . fkp

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 cF Me
F
8
8
9
K
9
3
8
I
9
4
0
M
9
4
5
D
1
0
1
8
I
1
0
1
9
W
1
0
2
0
G
1
0
2
1
N
1
0
2
2
V
1
0
2
4
N
1
0
2
5
S
1
0
2
8
R
1
0
2
9
K
1
0
6
5
[1]1ab8.a . . . . . . . . . . * . . -
[1]1azs.b . . . . . . . . . . * . . * fkp
[1]1cjk.b . . . . . . . . . . * . * . fok Mg,Mn
[1]1cjt.b . . . . . . . . . . * . * . fok Mg,Mn
[1]1cs4.b . . . . . . . . . . * . * . fok Mg
[1]1cul.b . . . . . . . . . . * . * . fok Mg
[1]1u0h.b . . . . . . . . . . . . . . fok Mg
[1]2gvd.b . . . . . . . . . . . . . * fkp Mn
[1]2gvz.b . . . . . . . . . . . . . . fkp Mn
[1]3c16.b . . . . . . . . . . * . . . fok Ca
[1]3g82.b . . . . . . . . . . . . . . fok Mn
[1]3maa.b . . . . . . . . . . * . . . fkp

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
1ab8.a:fok
1azs.b is apo
1cjk.b:F-A-D,tat
1cjt.b:GF-A-L-D,dad
1cs4.b:101,GF-A-L-D
1cul.b:103,3po,GF-A-L-D
1u0h.b:onm
2gvd.b:128
2gvz.b:ona
3c16.b:atp
3g82.b:mi3
3maa.b:tat
[1] 1ab8.a
0
- 0.8 1.5 1.5 1.7 1.4 0.6 1.0 0.1 1.6 0.4
[1] 1azs.b 0.1
-
1.6 1.3 0.4 0.8 1.4 1.7 2.1 1.1 2.0 1.3
[1] 1cjk.b 0.4 -
0
0.1 0 0.2 1.4 1.5 1.0 0 0.9 1.3
[1] 1cjt.b 0.1 - 0
0
0 0.1 1.5 1.2 1.2 0 1.2 1.4
[1] 1cs4.b 0.1 - 0 0.1
0
0 1.5 1.5 1.2 0 1.1 1.4
[1] 1cul.b 0.1 - 0 0.1 0
0.1
1.3 1.0 1.1 0 0.9 1.4
[1] 1u0h.b 0 - 0.3 0.4 0.6 0.4
0.1
0.1 0.1 0.1 0.4 0.3
[1] 2gvd.b 0 - 0.5 0.7 0.9 0.8 0.5
0.1
0.1 0.6 0.4 0.6
[1] 2gvz.b 0 - 0.5 0.6 0.4 0.5 0.5 0.5
0
0 0.4 0.2
[1] 3c16.b 0.1 - 0.1 0.2 0 0 1.6 1.6 1.2
0
1.3 0
[1] 3g82.b 0 - 0.3 0.5 0.1 0.4 0.1 0.3 0.1 0.2
0.1
0.3
[1] 3maa.b 0.1 - 0.1 0.1 0.1 0.1 1.2 1.2 1.2 0 0.8
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
1ab8.a
1azs.b
1cjk.b
1cjt.b
1cs4.b
1cul.b
1u0h.b
2gvd.b
2gvz.b
3c16.b
3g82.b
3maa.b
[1] 1ab8.a
0
.30 .31 .31 .34 .31 .19 .21 .14 .21 .20 .19
[1] 1azs.b .30
0
.25 .27 .25 .24 .15 .14 .21 .14 .17 .14
[1] 1cjk.b .31 .25
0
.05 .06 .05 .21 .23 .20 .15 .22 .13
[1] 1cjt.b .31 .27 .05
0
.02 .03 .22 .25 .21 .17 .23 .14
[1] 1cs4.b .34 .25 .06 .02
0
.04 .23 .26 .21 .15 .22 .14
[1] 1cul.b .31 .24 .05 .03 .04
0
.19 .22 .19 .16 .20 .12
[1] 1u0h.b .19 .15 .21 .22 .23 .19
0
.03 .07 .14 .04 .09
[1] 2gvd.b .21 .14 .23 .25 .26 .22 .03
0
.10 .15 .05 .11
[1] 2gvz.b .14 .21 .20 .21 .21 .19 .07 .10
0
.14 .08 .09
[1] 3c16.b .21 .14 .15 .17 .15 .16 .14 .15 .14
0
.13 .05
[1] 3g82.b .20 .17 .22 .23 .22 .20 .04 .05 .08 .13
0
.09
[1] 3maa.b .19 .14 .13 .14 .14 .12 .09 .11 .09 .05 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1ab8.a
1azs.b
1cjk.b
1cjt.b
1cs4.b
1cul.b
1u0h.b
2gvd.b
2gvz.b
3c16.b
3g82.b
3maa.b
[1] 1ab8.a
0
0.6 0.6 0.5 0.5 0.5 0.7 0.6 0.6 0.5 0.5 0.6
[1] 1azs.b 0.6
0
0.8 0.9 0.9 0.9 0.5 0.3 0.6 0.3 0.5 0.6
[1] 1cjk.b 0.6 0.8
0
0.3 0.3 0.3 0.8 0.8 0.8 0.8 0.6 1.0
[1] 1cjt.b 0.5 0.9 0.3
0
0.2 0.2 0.8 0.9 0.9 0.9 0.6 1.1
[1] 1cs4.b 0.5 0.9 0.3 0.2
0
0.1 0.8 0.9 0.9 0.9 0.6 1.1
[1] 1cul.b 0.5 0.9 0.3 0.2 0.1
0
0.8 0.9 0.9 0.9 0.6 1.1
[1] 1u0h.b 0.7 0.5 0.8 0.8 0.8 0.8
0
0.4 0.5 0.5 0.5 0.8
[1] 2gvd.b 0.6 0.3 0.8 0.9 0.9 0.9 0.4
0
0.6 0.3 0.5 0.6
[1] 2gvz.b 0.6 0.6 0.8 0.9 0.9 0.9 0.5 0.6
0
0.5 0.7 0.8
[1] 3c16.b 0.5 0.3 0.8 0.9 0.9 0.9 0.5 0.3 0.5
0
0.5 0.7
[1] 3g82.b 0.5 0.5 0.6 0.6 0.6 0.6 0.5 0.5 0.7 0.5
0
0.7
[1] 3maa.b 0.6 0.6 1.0 1.1 1.1 1.1 0.8 0.6 0.8 0.7 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
1ab8.a
1azs.b
1cjk.b
1cjt.b
1cs4.b
1cul.b
1u0h.b
2gvd.b
2gvz.b
3c16.b
3g82.b
3maa.b
[1] 1ab8.a
0
1.6 1.5 1.6 1.6 1.6 1.5 1.6 1.5 1.6 1.5 1.6
[1] 1azs.b 1.6
0
1.3 1.2 1.2 1.2 0.9 1.0 1.0 0.9 0.9 1.0
[1] 1cjk.b 1.5 1.3
0
0.6 0.7 0.7 1.4 1.5 1.4 1.2 1.3 1.2
[1] 1cjt.b 1.6 1.2 0.6
0
0.5 0.6 1.3 1.5 1.3 1.2 1.2 1.2
[1] 1cs4.b 1.6 1.2 0.7 0.5
0
0.4 1.3 1.5 1.3 1.2 1.2 1.1
[1] 1cul.b 1.6 1.2 0.7 0.6 0.4
0
1.4 1.6 1.3 1.1 1.2 1.1
[1] 1u0h.b 1.5 0.9 1.4 1.3 1.3 1.4
0
0.8 0.6 1.1 0.8 1.2
[1] 2gvd.b 1.6 1.0 1.5 1.5 1.5 1.6 0.8
0
0.9 1.2 1.0 1.3
[1] 2gvz.b 1.5 1.0 1.4 1.3 1.3 1.3 0.6 0.9
0
1.0 0.9 1.1
[1] 3c16.b 1.6 0.9 1.2 1.2 1.2 1.1 1.1 1.2 1.0
0
0.8 0.9
[1] 3g82.b 1.5 0.9 1.3 1.2 1.2 1.2 0.8 1.0 0.9 0.8
0
1.1
[1] 3maa.b 1.6 1.0 1.2 1.2 1.1 1.1 1.2 1.3 1.1 0.9 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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