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BPHD_PARXL_2_286

2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase [AB hydrolase superfamily. BphD family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (BPHD_PARXL):R: Substrate binding (42, 43)
40, 41, 46, 47, 50, 51, 111:113, 138, 139, 153, 156, 171, 172, 175, 176, 181, 182, 186, 190, 213, 216, 239, 240, 265, 266, 269
40:43, 46, 47, 50, 51, 111:113, 138, 139, 153, 156, 171, 172, 175, 176, 181, 182, 186, 190, 213, 216, 239, 240, 265, 266, 269

Full PDB list

2og1, 2pu5, 2pu7, 2puh, 2puj, 2rht, 2rhw, 2ri6, 3v1k, 3v1l, 3v1m, 3v1n

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
H
4
0
G
4
1
G
4
2
G
4
3
A
4
6
G
4
7
S
5
0
N
5
1
N
1
1
1
S
1
1
2
M
1
1
3
G
1
3
8
G
1
3
9
I
1
5
3
L
1
5
6
M
1
7
1
L
1
7
2
F
1
7
5
L
1
7
6
L
1
8
1
L
1
8
6
R
1
9
0
L
2
1
3
W
2
1
6
F
2
3
9
V
2
4
0
H
2
6
5
W
2
6
6
W
2
6
9
[1]2og1.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2pu5.b mli7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2pu7.a mli7 . . . . . . . . . A . . . . . . . . . . . . . . . . A . .
[1]2puh.a hpk16 . . . . . . . . . A . . . . . . . . . . . . . . . . . . .
[1]2puj.a hpz16 . . . . . . . . . A . . . . . . . . . . . . . . . . A . .
[1]2rht.a c1e17 . . . . . . . . . A . . . . . . . . . . . . . . . . . . .
[1]2rhw.a c0e,mli25 . . . . . . . . . A . . . . . . . . . . . . . . . . . . .
[1]2ri6.a mli7 . . . . . . . . . A . . . . . . . . . . . . . . . . . . .
[1]3v1k.a mla7 . . . . . . . . . . . . . . . . . . . . . . . . . . Q . .
[1]3v1k.b none . . . . . . . . . . . . . . . . . . . . . . . . . . Q . .
[1]3v1l.a none . . . . . . . . . A . . . . . . . . . . . . . . . . Q . .
[1]3v1m.a hpk16 . . . . . . . . . A . . . . . . . . . . . . . . . . Q . .
[1]3v1n.a bez,hpk24 . . . . . . . . . * . . . . . . . . . . . . . . . . Q . .

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
H
4
0
G
4
1
G
4
2
G
4
3
A
4
6
G
4
7
S
5
0
N
5
1
N
1
1
1
S
1
1
2
M
1
1
3
G
1
3
8
G
1
3
9
I
1
5
3
L
1
5
6
M
1
7
1
L
1
7
2
F
1
7
5
L
1
7
6
L
1
8
1
I
1
8
2
L
1
8
6
R
1
9
0
L
2
1
3
W
2
1
6
F
2
3
9
V
2
4
0
H
2
6
5
W
2
6
6
W
2
6
9
[1]2og1.a . . . . . . . * . * . . . . . . . . . . . * . . . * . . . .
[1]2pu5.b . . . . . . . * . * . . . . . . . . . . . * . . . * . . . .
[1]2pu7.a . . . . . . . . . A . . . . . . . . . . . * . . . * . A . .
[1]2puh.a . . . . . . . * . A . . . . . . . . . . . * . . . . . . . .
[1]2puj.a . . . . . . . . . A . . . . . . . . . . . * . . . . . A * .
[1]2rht.a . . . . . . . * . A . . . . . . . . . . . * . . . . . . * .
[1]2rhw.a . . . . . . . * . A . . . . . . . . . . . * . . . . . . * .
[1]2ri6.a . . . . . . . * . A . . . . . . . . . . . * . . . . . . * .
[1]3v1k.a . . . . . . . * . * . . . . . . . . . . . * . . . * . Q . .
[1]3v1k.b . . . . . . . * . * . . . . . . . . . . . * . . . * . Q . .
[1]3v1l.a . . . . . . . . . A . . . . . . . . . . . * . . . * . Q . .
[1]3v1m.a . . . . . . . . . A . . . . . . . * . . . * . . . . . Q . .
[1]3v1n.a . . . . . . . . . * . . . . . . . * . . . . . . . . . Q . .

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
2og1.a is apo
2pu5.b:mli
2pu7.a:mli
2puh.a:hpk
2puj.a:hpz
2rht.a:c1e
2rhw.a:c0e,mli
2ri6.a:mli
3v1k.a:mla
3v1k.b is apo
3v1l.a is apo
3v1m.a:hpk
3v1n.a:bez,hpk
[1] 2og1.a
-
0.3 0.4 1.6 1.3 2.0 2.0 1.4 0.4 - - 1.3 3.7
[1] 2pu5.b -
0.1
0.2 1.7 1.3 1.6 2.0 1.1 0.6 - - 1.2 5.0
[1] 2pu7.a - 0.1
0.1
1.5 1.6 2.0 1.5 1.1 0.2 - - 1.6 3.8
[1] 2puh.a - 0.5 0.6
0
0.9 0.9 0.3 0.1 0.4 - - 0.9 3.7
[1] 2puj.a - 0.2 0.3 0.2
0
0.2 0.1 0 0.4 - - 0.1 3.7
[1] 2rht.a - 0.2 0.6 0.4 0
0.1
0 0 0.4 - - 0 4.7
[1] 2rhw.a - 0.1 0.7 0.4 0 0.2
0
0 0.4 - - 0.1 5.7
[1] 2ri6.a - 0.1 0.6 0.4 0.2 0.4 0.1
0
0.4 - - 0.3 5.2
[1] 3v1k.a - 0.5 0.5 1.4 1.9 2.3 1.8 1.2
0.1
- - 1.9 5.2
[1] 3v1k.b - 0.4 0.4 1.4 2.1 2.6 2.0 1.3 0.3
-
- 2.0 4.3
[1] 3v1l.a - 0.1 0.1 1.3 1.7 2.1 1.7 0.9 0.1 -
-
1.8 3.5
[1] 3v1m.a - 0.3 0.6 0 0.8 1.1 0.5 0 0.3 - -
0.5
2.0
[1] 3v1n.a - 0.3 0.6 0.1 0.9 1.2 0.5 0.2 0.2 - - 0.8
0.6
[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
2og1.a
2pu5.b
2pu7.a
2puh.a
2puj.a
2rht.a
2rhw.a
2ri6.a
3v1k.a
3v1k.b
3v1l.a
3v1m.a
3v1n.a
[1] 2og1.a
0
.08 .10 .11 .16 .16 .19 .17 .06 .04 .06 .13 .15
[1] 2pu5.b .08
0
.15 .12 .19 .17 .19 .18 .13 .10 .11 .17 .21
[1] 2pu7.a .10 .15
0
.16 .12 .17 .17 .15 .07 .10 .05 .12 .19
[1] 2puh.a .11 .12 .16
0
.12 .09 .11 .11 .15 .12 .12 .08 .16
[1] 2puj.a .16 .19 .12 .12
0
.07 .10 .08 .16 .18 .13 .09 .17
[1] 2rht.a .16 .17 .17 .09 .07
0
.04 .03 .16 .18 .17 .14 .22
[1] 2rhw.a .19 .19 .17 .11 .10 .04
0
.03 .15 .20 .18 .16 .24
[1] 2ri6.a .17 .18 .15 .11 .08 .03 .03
0
.13 .17 .16 .15 .22
[1] 3v1k.a .06 .13 .07 .15 .16 .16 .15 .13
0
.08 .08 .17 .20
[1] 3v1k.b .04 .10 .10 .12 .18 .18 .20 .17 .08
0
.06 .15 .17
[1] 3v1l.a .06 .11 .05 .12 .13 .17 .18 .16 .08 .06
0
.11 .17
[1] 3v1m.a .13 .17 .12 .08 .09 .14 .16 .15 .17 .15 .11
0
.10
[1] 3v1n.a .15 .21 .19 .16 .17 .22 .24 .22 .20 .17 .17 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.1 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
2og1.a
2pu5.b
2pu7.a
2puh.a
2puj.a
2rht.a
2rhw.a
2ri6.a
3v1k.a
3v1k.b
3v1l.a
3v1m.a
3v1n.a
[1] 2og1.a
0
0.5 0.6 0.4 0.6 0.6 0.7 0.7 0.4 0.6 0.6 0.6 0.6
[1] 2pu5.b 0.5
0
0.8 0.5 0.8 0.7 0.8 0.8 0.6 0.6 0.8 0.7 0.8
[1] 2pu7.a 0.6 0.8
0
0.6 0.3 0.4 0.4 0.4 0.5 0.6 0.3 0.4 0.5
[1] 2puh.a 0.4 0.5 0.6
0
0.5 0.5 0.6 0.6 0.5 0.6 0.5 0.4 0.5
[1] 2puj.a 0.6 0.8 0.3 0.5
0
0.2 0.3 0.2 0.4 0.6 0.2 0.2 0.4
[1] 2rht.a 0.6 0.7 0.4 0.5 0.2
0
0.2 0.3 0.5 0.6 0.4 0.3 0.5
[1] 2rhw.a 0.7 0.8 0.4 0.6 0.3 0.2
0
0.2 0.6 0.7 0.3 0.4 0.5
[1] 2ri6.a 0.7 0.8 0.4 0.6 0.2 0.3 0.2
0
0.5 0.7 0.3 0.4 0.5
[1] 3v1k.a 0.4 0.6 0.5 0.5 0.4 0.5 0.6 0.5
0
0.4 0.4 0.4 0.5
[1] 3v1k.b 0.6 0.6 0.6 0.6 0.6 0.6 0.7 0.7 0.4
0
0.6 0.6 0.7
[1] 3v1l.a 0.6 0.8 0.3 0.5 0.2 0.4 0.3 0.3 0.4 0.6
0
0.2 0.4
[1] 3v1m.a 0.6 0.7 0.4 0.4 0.2 0.3 0.4 0.4 0.4 0.6 0.2
0
0.2
[1] 3v1n.a 0.6 0.8 0.5 0.5 0.4 0.5 0.5 0.5 0.5 0.7 0.4 0.2
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
2og1.a
2pu5.b
2pu7.a
2puh.a
2puj.a
2rht.a
2rhw.a
2ri6.a
3v1k.a
3v1k.b
3v1l.a
3v1m.a
3v1n.a
[1] 2og1.a
0
0.7 1.0 0.9 1.4 1.3 1.6 1.3 0.7 0.8 1.0 1.2 1.4
[1] 2pu5.b 0.7
0
1.1 1.1 1.6 1.5 1.7 1.4 0.9 0.8 1.1 1.3 1.6
[1] 2pu7.a 1.0 1.1
0
1.1 1.1 1.2 1.5 1.3 0.8 1.0 0.5 0.8 1.2
[1] 2puh.a 0.9 1.1 1.1
0
1.1 0.9 1.3 1.0 1.0 1.1 1.1 0.8 1.1
[1] 2puj.a 1.4 1.6 1.1 1.1
0
0.6 1.1 0.7 1.2 1.4 1.2 0.9 1.2
[1] 2rht.a 1.3 1.5 1.2 0.9 0.6
0
0.9 0.6 1.2 1.4 1.2 1.0 1.3
[1] 2rhw.a 1.6 1.7 1.5 1.3 1.1 0.9
0
0.9 1.5 1.6 1.4 1.3 1.6
[1] 2ri6.a 1.3 1.4 1.3 1.0 0.7 0.6 0.9
0
1.2 1.4 1.3 1.1 1.4
[1] 3v1k.a 0.7 0.9 0.8 1.0 1.2 1.2 1.5 1.2
0
0.8 0.9 1.2 1.4
[1] 3v1k.b 0.8 0.8 1.0 1.1 1.4 1.4 1.6 1.4 0.8
0
0.9 1.1 1.4
[1] 3v1l.a 1.0 1.1 0.5 1.1 1.2 1.2 1.4 1.3 0.9 0.9
0
0.9 1.2
[1] 3v1m.a 1.2 1.3 0.8 0.8 0.9 1.0 1.3 1.1 1.2 1.1 0.9
0
0.8
[1] 3v1n.a 1.4 1.6 1.2 1.1 1.2 1.3 1.6 1.4 1.4 1.4 1.2 0.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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