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PTGDS_HUMAN_25_190

Prostaglandin-H2 D-isomerase [Calycin superfamily. Lipocalin family]

Composition of the binding site

Protein chains monomer
A1 (PTGDS_HUMAN):45, 48, 51, 52, 54, 55, 58, 59, 62, 64, 65, 67, 79, 81, 83, 85, 91:94, 96, 107, 109:112, 114, 116, 118, 131, 133, 139:143, 145, 147, 149, 18045, 48, 51, 52, 54, 55, 58, 59, 62, 64, 65, 67, 79, 81, 83, 85, 91:94, 96, 107, 109:112, 114, 116, 118, 131, 133, 139:143, 145, 147, 149, 180

Full PDB list

2wwp, 3o19, 3o22, 3o2y, 4imn, 4imo, 4orr, 4ors, 4oru, 4orw, 4orx, 4ory, 4os0, 4os3, 4os8, 5wy9 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
S
4
5
L
4
8
N
5
1
S
5
2
W
5
4
L
5
5
K
5
8
K
5
9
L
6
2
M
6
4
S
6
7
L
7
9
S
8
1
F
8
3
T
9
1
R
9
2
T
9
3
M
9
4
Y
1
0
7
S
1
0
9
W
1
1
2
Y
1
1
6
V
1
1
8
S
1
3
3
P
1
3
9
G
1
4
0
D
1
4
2
F
1
4
3
M
1
4
5
T
1
4
7
Y
1
4
9
L
1
8
0
[1]2wwp.a none . . . . . . - - . . . . . . . . . . . . . . . . . . . . . . . .
[1]3o22.a ola,ola,plm,plm76 . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . .
[1]3o2y.a ola,plm38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4imn.a 1pg17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4imo.a pwz,pwz50 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4orr.a pe340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ors.b none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oru.b peu76 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4orx.b peu76 . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . .
[1]4ory.d none . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . . .
[1]5wy9.a 1pg,pg0,pg033 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4os0.a none . . . . F . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4os3.a none . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . .
[2]4os8.a none . . . . F . . . . . . . . . . . . . . . F . . . . . . . . . . .

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
S
4
5
L
4
8
N
5
1
S
5
2
W
5
4
L
5
5
K
5
8
K
5
9
L
6
2
M
6
4
C
6
5
S
6
7
L
7
9
S
8
1
F
8
3
R
8
5
T
9
1
R
9
2
T
9
3
M
9
4
L
9
6
Y
1
0
7
S
1
0
9
P
1
1
0
H
1
1
1
W
1
1
2
S
1
1
4
Y
1
1
6
V
1
1
8
L
1
3
1
S
1
3
3
P
1
3
9
G
1
4
0
E
1
4
1
D
1
4
2
F
1
4
3
M
1
4
5
T
1
4
7
Y
1
4
9
L
1
8
0
[1]2wwp.a . . . . * . - - . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]3o22.a . . . . * . . * * . A . . . . . . . . . . . . . - - . . . . . . . . . . . . . .
[1]3o2y.a . . . . . . . * * . A . . . . . . . . . . . . . . * . . . . . . . . . . . . . .
[1]4imn.a . . . . * . . * * . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]4imo.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4orr.a . . . . * . . * * . A . . . . . . . . . . . . . . . . . . . . . . . . * . . . .
[1]4ors.b . . . . * . . * * . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4oru.b . . . . . . . * * . A . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4orx.b . . . . . . . A * . A . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]4ory.d . . . . . . . A * . A . . . . . . * . . . . . . . * . . . . . . . . . . . . . .
[1]5wy9.a . . . . * . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4os0.a . . . . F . . . . . A . . . . * . . . . . . . . . . . . . . . * . . . . . . . .
[2]4os3.a . . . . . . . . . . A . . . . . . * . . . . . . . F . . . . . . . . . . . . . .
[2]4os8.a . . . . F . . . . . A . . . . * . * . . . . . . . F . . . . . * . . . . . . . .

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
2wwp.a is apo
3o22.a:ola,plm
3o2y.a:ola,plm
4imn.a:1pg
4imo.a:pwz
4orr.a:pe3
4ors.b is apo
4oru.b:peu
4orx.b:peu
4ory.d is apo
5wy9.a:1pg,pg0
4os0.a is apo
4os3.a is apo
4os8.a is apo
[1] 2wwp.a
-
1.0 0.1 0 2.6 1.2 - 1.0 1.3 - 0.1 - - -
[1] 3o22.a -
0.2
0.4 0 4.1 0.1 - 0.8 2.7 - 0.6 - - -
[1] 3o2y.a - 1.4
0.1
0.3 3.8 2.2 - 0.4 2.3 - 0.6 - - -
[1] 4imn.a - 1.0 0.5
0
3.4 1.5 - 1.0 3.1 - 0.1 - - -
[1] 4imo.a - 0.6 0 0
0
0.8 - 0 0.1 - 0.1 - - -
[1] 4orr.a - 3.9 3.2 0.4 5.7
0.1
- 3.6 5.4 - 0.6 - - -
[1] 4ors.b - 0.3 0.4 0.1 4.0 0.1
-
0.5 2.6 - 0.4 - - -
[1] 4oru.b - 1.4 0.6 0.1 2.8 2.9 -
0.1
2.1 - 0.6 - - -
[1] 4orx.b - 4.3 1.5 0.1 2.9 3.7 - 0.6
0.1
- 1.6 - - -
[1] 4ory.d - 4.2 1.4 1.4 3.8 3.3 - 1.3 0.8
-
2.4 - - -
[1] 5wy9.a - 0.8 0.4 0.1 4.1 1.4 - 0.4 2.6 -
0
- - -
[2] 4os0.a - 1.8 0.8 0.1 3.6 2.1 - 1.1 0 - 1.0
-
- -
[2] 4os3.a - 3.8 1.1 0.2 2.3 1.8 - 1.0 0.2 - 2.1 -
-
-
[2] 4os8.a - 2.7 1.7 0.2 4.3 2.4 - 1.7 0.2 - 1.9 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
2wwp.a
3o22.a
3o2y.a
4imn.a
4imo.a
4orr.a
4ors.b
4oru.b
4orx.b
4ory.d
5wy9.a
4os0.a
4os3.a
4os8.a
[1] 2wwp.a
0
.17 .23 .10 .10 .25 .14 .20 .23 .24 .14 .19 .22 .24
[1] 3o22.a .17
0
.14 .10 .18 .12 .07 .15 .28 .23 .09 .27 .30 .32
[1] 3o2y.a .23 .14
0
.15 .19 .20 .18 .09 .20 .16 .11 .27 .30 .32
[1] 4imn.a .10 .10 .15
0
.17 .17 .09 .13 .25 .23 .05 .26 .30 .31
[1] 4imo.a .10 .18 .19 .17
0
.27 .17 .16 .17 .19 .18 .14 .15 .17
[1] 4orr.a .25 .12 .20 .17 .27
0
.18 .22 .35 .30 .15 .36 .40 .41
[1] 4ors.b .14 .07 .18 .09 .17 .18
0
.17 .27 .26 .07 .26 .29 .31
[1] 4oru.b .20 .15 .09 .13 .16 .22 .17
0
.15 .19 .12 .21 .24 .26
[1] 4orx.b .23 .28 .20 .25 .17 .35 .27 .15
0
.13 .25 .24 .18 .23
[1] 4ory.d .24 .23 .16 .23 .19 .30 .26 .19 .13
0
.24 .28 .23 .28
[1] 5wy9.a .14 .09 .11 .05 .18 .15 .07 .12 .25 .24
0
.27 .31 .33
[2] 4os0.a .19 .27 .27 .26 .14 .36 .26 .21 .24 .28 .27
0
.10 .06
[2] 4os3.a .22 .30 .30 .30 .15 .40 .29 .24 .18 .23 .31 .10
0
.08
[2] 4os8.a .24 .32 .32 .31 .17 .41 .31 .26 .23 .28 .33 .06 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.0 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
2wwp.a
3o22.a
3o2y.a
4imn.a
4imo.a
4orr.a
4ors.b
4oru.b
4orx.b
4ory.d
5wy9.a
4os0.a
4os3.a
4os8.a
[1] 2wwp.a
0
1.4 1.2 0.7 0.9 1.4 2.0 1.2 1.2 1.3 0.9 1.4 1.4 1.4
[1] 3o22.a 1.4
0
0.8 1.3 2.1 0.3 1.2 0.9 0.9 0.7 1.1 2.3 2.0 2.2
[1] 3o2y.a 1.2 0.8
0
1.1 1.8 0.8 1.5 0.6 0.6 0.8 0.8 2.0 1.9 1.9
[1] 4imn.a 0.7 1.3 1.1
0
1.5 1.3 2.0 1.0 1.0 1.1 0.7 2.0 1.8 1.9
[1] 4imo.a 0.9 2.1 1.8 1.5
0
2.0 2.4 1.7 1.7 1.8 1.6 1.3 1.4 1.3
[1] 4orr.a 1.4 0.3 0.8 1.3 2.0
0
1.6 0.8 0.8 0.6 1.1 2.2 2.0 2.1
[1] 4ors.b 2.0 1.2 1.5 2.0 2.4 1.6
0
1.8 1.8 1.8 1.8 2.4 2.3 2.4
[1] 4oru.b 1.2 0.9 0.6 1.0 1.7 0.8 1.8
0
0.2 0.6 0.7 2.0 1.8 1.9
[1] 4orx.b 1.2 0.9 0.6 1.0 1.7 0.8 1.8 0.2
0
0.6 0.7 2.0 1.8 1.8
[1] 4ory.d 1.3 0.7 0.8 1.1 1.8 0.6 1.8 0.6 0.6
0
0.8 2.0 1.8 1.9
[1] 5wy9.a 0.9 1.1 0.8 0.7 1.6 1.1 1.8 0.7 0.7 0.8
0
2.1 1.9 2.0
[2] 4os0.a 1.4 2.3 2.0 2.0 1.3 2.2 2.4 2.0 2.0 2.0 2.1
0
0.7 0.6
[2] 4os3.a 1.4 2.0 1.9 1.8 1.4 2.0 2.3 1.8 1.8 1.8 1.9 0.7
0
0.3
[2] 4os8.a 1.4 2.2 1.9 1.9 1.3 2.1 2.4 1.9 1.8 1.9 2.0 0.6 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.4 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
2wwp.a
3o22.a
3o2y.a
4imn.a
4imo.a
4orr.a
4ors.b
4oru.b
4orx.b
4ory.d
5wy9.a
4os0.a
4os3.a
4os8.a
[1] 2wwp.a
0
1.8 1.8 0.8 1.3 2.0 2.5 1.8 2.0 2.0 1.4 2.0 2.0 2.0
[1] 3o22.a 1.8
0
1.1 1.7 2.9 1.0 1.5 1.3 1.5 1.3 1.4 2.9 2.9 2.9
[1] 3o2y.a 1.8 1.1
0
1.6 2.6 1.6 2.0 1.2 1.3 1.4 1.4 2.8 2.7 2.8
[1] 4imn.a 0.8 1.7 1.6
0
2.2 1.9 2.5 1.7 1.8 1.9 1.2 2.7 2.7 2.7
[1] 4imo.a 1.3 2.9 2.6 2.2
0
2.9 3.2 2.5 2.3 2.4 2.4 1.9 1.9 1.9
[1] 4orr.a 2.0 1.0 1.6 1.9 2.9
0
2.3 1.4 1.6 1.6 1.7 3.0 3.0 3.0
[1] 4ors.b 2.5 1.5 2.0 2.5 3.2 2.3
0
2.3 2.4 2.2 2.3 3.2 3.1 3.1
[1] 4oru.b 1.8 1.3 1.2 1.7 2.5 1.4 2.3
0
0.8 1.2 1.3 2.7 2.7 2.7
[1] 4orx.b 2.0 1.5 1.3 1.8 2.3 1.6 2.4 0.8
0
1.1 1.6 2.5 2.3 2.3
[1] 4ory.d 2.0 1.3 1.4 1.9 2.4 1.6 2.2 1.2 1.1
0
1.6 2.6 2.4 2.4
[1] 5wy9.a 1.4 1.4 1.4 1.2 2.4 1.7 2.3 1.3 1.6 1.6
0
2.9 2.8 2.8
[2] 4os0.a 2.0 2.9 2.8 2.7 1.9 3.0 3.2 2.7 2.5 2.6 2.9
0
1.2 1.0
[2] 4os3.a 2.0 2.9 2.7 2.7 1.9 3.0 3.1 2.7 2.3 2.4 2.8 1.2
0
0.9
[2] 4os8.a 2.0 2.9 2.8 2.7 1.9 3.0 3.1 2.7 2.3 2.4 2.8 1.0 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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