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CHS2_MEDSA_1_389

Chalcone synthase 2 [Chalcone/stilbene synthases family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CHS2_MEDSA):R: Coenzyme A binding (55, 58, 59, 62)
R: Substrate binding (216, 217)
63, 132, 133, 163, 164, 192:194, 196, 197, 206, 207, 210, 214, 215, 254:256, 263:265, 267:269, 271, 272, 303, 305:309, 336:338, 373:375
55, 58, 59, 62, 63, 132, 133, 163, 164, 192:194, 196, 197, 206, 207, 210, 214:217, 254:256, 263:265, 267:269, 271, 272, 303, 305:309, 336:338, 373:375

Full PDB list

1bi5, 1bq6, 1cgk, 1cgz, 1chw, 1cml, 1d6f, 1d6h, 1d6i, 1i86, 1i88, 1i89, 1i8b, 1jwx, 1u0v, 1u0w

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
5
5
R
5
8
M
5
9
K
6
2
S
6
3
T
1
3
2
S
1
3
3
G
1
6
3
C
1
6
4
E
1
9
2
V
1
9
3
T
1
9
4
V
1
9
6
T
1
9
7
L
2
0
6
V
2
1
0
L
2
1
4
F
2
1
5
G
2
1
6
D
2
1
7
I
2
5
4
D
2
5
5
G
2
5
6
L
2
6
3
T
2
6
4
F
2
6
5
L
2
6
7
V
2
7
1
P
2
7
2
H
3
0
3
G
3
0
5
G
3
0
6
P
3
0
7
A
3
0
8
I
3
0
9
N
3
3
6
M
3
3
7
S
3
3
8
F
3
7
3
G
3
7
4
P
3
7
5
[1]1bi5.a none . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1bq6.a coa48 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1cgk.a nar20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1cgz.a stl17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1chw.a hxc55 . . . . . . . . S . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1cml.a mlc51 . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1d6f.a b3p19 . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1d6h.a coa48 . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . A . . . . .
[1]1d6i.a none . . . . . . . . * . . . . . . . . . . . . . . . . . . . . Q . . . . . . . . . . .
[1]1i86.a none . . . . . . . . * . . . . . . . . . . . . . A . . . . . . . . . . . . . . . . . .
[1]1i88.b none . . . . . . . . * . . . . . . . . . . . . . V . . . . . . . . . . . . . . . . . .
[1]1i89.b none . . . . . . . . * . . . . . . . . . . . . . L . . . . . . . . . . . . . . . . . .
[1]1i8b.a none . . . . . . . . * . . . . . . . . . . . . . F . . . . . . . . . . . . . . . . . .
[1]1jwx.a none . . . . . . . . * . . . . . . . . S . . . . . . . . . . . . . . . . . . . . . . .
[1]1u0v.b none . . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1u0w.c stl17 . . . . . . T . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
K
5
5
R
5
8
M
5
9
K
6
2
S
6
3
T
1
3
2
S
1
3
3
G
1
6
3
C
1
6
4
E
1
9
2
V
1
9
3
T
1
9
4
V
1
9
6
T
1
9
7
L
2
0
6
D
2
0
7
V
2
1
0
L
2
1
4
F
2
1
5
G
2
1
6
D
2
1
7
I
2
5
4
D
2
5
5
G
2
5
6
L
2
6
3
T
2
6
4
F
2
6
5
L
2
6
7
L
2
6
8
K
2
6
9
V
2
7
1
P
2
7
2
H
3
0
3
G
3
0
5
G
3
0
6
P
3
0
7
A
3
0
8
I
3
0
9
N
3
3
6
M
3
3
7
S
3
3
8
F
3
7
3
G
3
7
4
P
3
7
5
[1]1bi5.a . . . * . . . . csd . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1bq6.a . . . . . . . . csd . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1cgk.a . * . * . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1cgz.a . * . * . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1chw.a . . . . . . . . S . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1cml.a . . . . . . . . A . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1d6f.a . . . . . . . . A . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1d6h.a . . . . . . . . csd . . . . . . . . . . . . . . . . . * . . . . . . . . . . . A . . . . .
[1]1d6i.a . * . * . . . . csd . . . . . . . . . . . . . . . . . * . . . . . Q . . . . . . . . . . .
[1]1i86.a . * . * . . . . csd . . . . . . . . . . . . . . A . . * . . . . . . . . . . . . . . . . .
[1]1i88.b . * . * . . . . csd . . . . . . . . . . . . . . V . . * . . . . . . . . . . . . . . . . .
[1]1i89.b . * . * . . . . csd . . . . . . . . . . . . . . L . . * . . . . . . . . . . . . . . . . .
[1]1i8b.a . * . * . . . . csd . . . . . . . . . . . . . . F . . * . . . . . . . . . . . . . . . . .
[1]1jwx.a . * . * . . . . csd . . . . . . . . . S . . . . . . . * . . . . . . . . . . . . . . . . .
[1]1u0v.b . . . * . . T . . . . . . . . . . . . . . . . . . . * * K G . . . . . . . . . . . . . .
[1]1u0w.c * * . * . . T . . . . . . . . . . . . . . . . . . . * . K G . . . . . . . . . . . . . .

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
1bi5.a is apo
1bq6.a:coa
1cgk.a:nar
1cgz.a:stl
1chw.a:hxc
1cml.a:mlc
1d6f.a:b3p
1d6h.a:coa
1d6i.a is apo
1i86.a is apo
1i88.b is apo
1i89.b is apo
1i8b.a is apo
1jwx.a is apo
1u0v.b is apo
1u0w.c:stl
[1] 1bi5.a
-
1.6 0.6 0.6 3.2 5.4 1.4 2.7 - - - - - - - 0.8
[1] 1bq6.a -
0
0.5 0.6 1.3 3.4 1.4 1.1 - - - - - - - 0.7
[1] 1cgk.a - 2.5
0
0.2 3.0 5.8 0.5 3.9 - - - - - - - 0.5
[1] 1cgz.a - 2.6 0.2
0.1
2.9 5.4 0.5 3.9 - - - - - - - 0.2
[1] 1chw.a - 0 3.8 4.2
0
0.4 0.3 0.1 - - - - - - - 4.1
[1] 1cml.a - 0.1 3.1 3.1 0
0.1
0.1 0 - - - - - - - 2.6
[1] 1d6f.a - 0.3 3.1 3.1 0 0.4
0.1
0.1 - - - - - - - 2.8
[1] 1d6h.a - 0.4 3.8 3.1 1.4 0.5 1.0
0.1
- - - - - - - 2.8
[1] 1d6i.a - 3.5 0.6 0.7 5.6 7.0 1.4 5.3
-
- - - - - - 0.6
[1] 1i86.a - 2.4 0.7 1.1 4.2 5.9 1.3 3.4 -
-
- - - - - 1.3
[1] 1i88.b - 2.1 0.8 1.3 4.0 5.8 1.2 3.7 - -
-
- - - - 1.6
[1] 1i89.b - 2.4 2.1 2.8 4.2 5.7 1.7 3.7 - - -
-
- - - 3.1
[1] 1i8b.a - 2.3 4.3 4.4 4.3 5.6 1.3 3.4 - - - -
-
- - 5.0
[1] 1jwx.a - 2.3 3.6 3.4 4.2 3.0 1.9 2.8 - - - - -
-
- 3.4
[1] 1u0v.b - 1.1 3.0 3.2 1.8 2.4 0.4 1.6 - - - - - -
-
2.8
[1] 1u0w.c - 2.8 0.2 0 3.7 6.2 0.5 3.6 - - - - - - -
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
1bi5.a
1bq6.a
1cgk.a
1cgz.a
1chw.a
1cml.a
1d6f.a
1d6h.a
1d6i.a
1i86.a
1i88.b
1i89.b
1i8b.a
1jwx.a
1u0v.b
1u0w.c
[1] 1bi5.a
0
.06 .06 .05 .10 .10 .10 .09 .05 .04 .06 .09 .13 .05 .10 .11
[1] 1bq6.a .06
0
.10 .10 .07 .07 .07 .06 .10 .09 .12 .13 .18 .10 .13 .11
[1] 1cgk.a .06 .10
0
.02 .12 .10 .10 .14 .07 .05 .07 .10 .14 .07 .10 .11
[1] 1cgz.a .05 .10 .02
0
.12 .10 .09 .13 .07 .05 .07 .11 .14 .06 .08 .09
[1] 1chw.a .10 .07 .12 .12
0
.04 .05 .06 .15 .14 .16 .19 .23 .12 .10 .15
[1] 1cml.a .10 .07 .10 .10 .04
0
.02 .06 .15 .14 .14 .19 .23 .11 .08 .13
[1] 1d6f.a .10 .07 .10 .09 .05 .02
0
.05 .15 .14 .14 .18 .22 .12 .08 .11
[1] 1d6h.a .09 .06 .14 .13 .06 .06 .05
0
.14 .13 .13 .17 .21 .09 .11 .14
[1] 1d6i.a .05 .10 .07 .07 .15 .15 .15 .14
0
.05 .08 .11 .16 .08 .14 .16
[1] 1i86.a .04 .09 .05 .05 .14 .14 .14 .13 .05
0
.05 .07 .11 .07 .13 .13
[1] 1i88.b .06 .12 .07 .07 .16 .14 .14 .13 .08 .05
0
.07 .10 .07 .13 .15
[1] 1i89.b .09 .13 .10 .11 .19 .19 .18 .17 .11 .07 .07
0
.06 .10 .18 .18
[1] 1i8b.a .13 .18 .14 .14 .23 .23 .22 .21 .16 .11 .10 .06
0
.14 .22 .22
[1] 1jwx.a .05 .10 .07 .06 .12 .11 .12 .09 .08 .07 .07 .10 .14
0
.10 .13
[1] 1u0v.b .10 .13 .10 .08 .10 .08 .08 .11 .14 .13 .13 .18 .22 .10
0
.09
[1] 1u0w.c .11 .11 .11 .09 .15 .13 .11 .14 .16 .13 .15 .18 .22 .13 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1bi5.a
1bq6.a
1cgk.a
1cgz.a
1chw.a
1cml.a
1d6f.a
1d6h.a
1d6i.a
1i86.a
1i88.b
1i89.b
1i8b.a
1jwx.a
1u0v.b
1u0w.c
[1] 1bi5.a
0
0.1 0.2 0.2 0.2 0.3 0.3 0.3 0.2 0.2 0.3 0.2 0.2 0.2 1.1 1.0
[1] 1bq6.a 0.1
0
0.2 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.3 0.2 0.2 0.2 1.1 1.1
[1] 1cgk.a 0.2 0.2
0
0.2 0.3 0.3 0.3 0.3 0.2 0.1 0.3 0.2 0.2 0.3 1.1 1.1
[1] 1cgz.a 0.2 0.2 0.2
0
0.3 0.3 0.3 0.3 0.3 0.2 0.3 0.2 0.2 0.3 1.1 1.1
[1] 1chw.a 0.2 0.2 0.3 0.3
0
0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3 0.2 1.1 1.1
[1] 1cml.a 0.3 0.3 0.3 0.3 0.2
0
0.1 0.3 0.3 0.3 0.3 0.3 0.3 0.2 1.1 1.1
[1] 1d6f.a 0.3 0.3 0.3 0.3 0.2 0.1
0
0.3 0.3 0.3 0.3 0.3 0.3 0.2 1.1 1.1
[1] 1d6h.a 0.3 0.2 0.3 0.3 0.2 0.3 0.3
0
0.3 0.3 0.3 0.3 0.3 0.3 1.2 1.1
[1] 1d6i.a 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.3
0
0.2 0.3 0.2 0.2 0.3 1.1 1.0
[1] 1i86.a 0.2 0.2 0.1 0.2 0.3 0.3 0.3 0.3 0.2
0
0.2 0.1 0.2 0.2 1.1 1.1
[1] 1i88.b 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.2
0
0.2 0.3 0.2 1.1 1.1
[1] 1i89.b 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.1 0.2
0
0.2 0.2 1.1 1.1
[1] 1i8b.a 0.2 0.2 0.2 0.2 0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.2
0
0.3 1.1 1.0
[1] 1jwx.a 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.3 0.3 0.2 0.2 0.2 0.3
0
1.1 1.1
[1] 1u0v.b 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.2 1.1 1.1 1.1 1.1 1.1 1.1
0
0.5
[1] 1u0w.c 1.0 1.1 1.1 1.1 1.1 1.1 1.1 1.1 1.0 1.1 1.1 1.1 1.0 1.1 0.5
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

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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
1bi5.a
1bq6.a
1cgk.a
1cgz.a
1chw.a
1cml.a
1d6f.a
1d6h.a
1d6i.a
1i86.a
1i88.b
1i89.b
1i8b.a
1jwx.a
1u0v.b
1u0w.c
[1] 1bi5.a
0
0.7 0.5 0.4 1.1 1.2 1.2 1.1 0.5 0.5 0.5 0.3 0.3 0.8 1.6 1.3
[1] 1bq6.a 0.7
0
0.9 0.9 0.8 0.9 0.9 0.9 0.6 0.9 0.8 0.8 0.8 1.1 1.4 1.4
[1] 1cgk.a 0.5 0.9
0
0.3 1.2 1.2 1.2 1.2 0.7 0.6 0.5 0.5 0.5 0.9 1.6 1.2
[1] 1cgz.a 0.4 0.9 0.3
0
1.2 1.2 1.2 1.1 0.7 0.5 0.5 0.5 0.5 0.8 1.6 1.2
[1] 1chw.a 1.1 0.8 1.2 1.2
0
0.7 0.8 0.7 1.0 1.2 1.2 1.1 1.2 1.1 1.3 1.6
[1] 1cml.a 1.2 0.9 1.2 1.2 0.7
0
0.7 0.8 1.1 1.3 1.2 1.2 1.3 1.1 1.3 1.6
[1] 1d6f.a 1.2 0.9 1.2 1.2 0.8 0.7
0
0.6 1.1 1.2 1.2 1.2 1.3 0.9 1.3 1.5
[1] 1d6h.a 1.1 0.9 1.2 1.1 0.7 0.8 0.6
0
1.0 1.1 1.2 1.2 1.2 0.9 1.3 1.5
[1] 1d6i.a 0.5 0.6 0.7 0.7 1.0 1.1 1.1 1.0
0
0.7 0.7 0.6 0.6 1.0 1.4 1.3
[1] 1i86.a 0.5 0.9 0.6 0.5 1.2 1.3 1.2 1.1 0.7
0
0.5 0.4 0.5 0.8 1.6 1.3
[1] 1i88.b 0.5 0.8 0.5 0.5 1.2 1.2 1.2 1.2 0.7 0.5
0
0.4 0.5 0.9 1.6 1.3
[1] 1i89.b 0.3 0.8 0.5 0.5 1.1 1.2 1.2 1.2 0.6 0.4 0.4
0
0.3 0.8 1.6 1.3
[1] 1i8b.a 0.3 0.8 0.5 0.5 1.2 1.3 1.3 1.2 0.6 0.5 0.5 0.3
0
0.9 1.6 1.3
[1] 1jwx.a 0.8 1.1 0.9 0.8 1.1 1.1 0.9 0.9 1.0 0.8 0.9 0.8 0.9
0
1.5 1.4
[1] 1u0v.b 1.6 1.4 1.6 1.6 1.3 1.3 1.3 1.3 1.4 1.6 1.6 1.6 1.6 1.5
0
1.2
[1] 1u0w.c 1.3 1.4 1.2 1.2 1.6 1.6 1.5 1.5 1.3 1.3 1.3 1.3 1.3 1.4 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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