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EST1_HUMAN_20_559

Liver carboxylesterase 1 [Type-B carboxylesterase/lipase family]

Composition of the binding site

Protein chains monomer
A1 (EST1_HUMAN):90, 92, 93, 96, 97, 101, 141:143, 145, 146, 220:222, 247, 248, 252, 254, 255, 298, 299, 302:305, 316:318, 358, 359, 361:365, 388, 425, 426, 46890, 92, 93, 96, 97, 101, 141:143, 145, 146, 220:222, 247, 248, 252, 254, 255, 298, 299, 302:305, 316:318, 358, 359, 361:365, 388, 425, 426, 468

Full PDB list

1mx1, 1mx5, 1ya4, 1ya8, 1yah, 2dqy, 2dqz, 2dr0, 2h7c, 2hrq, 2hrr, 3k9b, 4ab1, 5a7f, 5a7g, 5a7h (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
9
0
K
9
2
A
9
3
L
9
6
L
9
7
F
1
0
1
G
1
4
1
G
1
4
2
G
1
4
3
V
1
4
6
S
2
2
1
A
2
2
2
T
2
5
2
V
2
5
4
L
2
5
5
L
2
9
9
K
3
0
2
F
3
0
3
L
3
0
4
S
3
0
5
P
3
1
7
L
3
1
8
L
3
5
8
I
3
5
9
Q
3
6
2
L
3
6
3
M
3
6
4
L
3
8
8
M
4
2
5
F
4
2
6
H
4
6
8
[1]1mx1.c tha15 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]1mx5.b htq20 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]1ya4.c ctx28 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]1ya8.b smb7 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]1yah.b eee6 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]2dqz.b plm11 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]2dr0.a tch35 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]2h7c.b coa48 . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]2hrq.b gd710 . . . . . . . . . . * . . . . . . . . . . . . . - . . . . . .
[1]2hrr.b ntj8 . . . . . . . . . . * . . . . . . . . . . . . . - . . . . . .
[1]3k9b.a ww210 . . . . . . . . . . * . . . . . . . - - - - . . - . . . . . .
[1]3k9b.b ww210 . . . . . . . . . . * . . . . . . - - - S . . . - . . . . . .
[1]3k9b.c ww210 . . . . . . . . . . * . - . . . . - - - - . . . L - - - . . .
[1]5a7f.a none . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . .
[1]5a7g.a none . . . . . . . . . . A . . . . . . . . . - . . . - . . . . . .

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
D
9
0
K
9
2
A
9
3
L
9
6
L
9
7
F
1
0
1
G
1
4
1
G
1
4
2
G
1
4
3
M
1
4
5
V
1
4
6
E
2
2
0
S
2
2
1
A
2
2
2
S
2
4
7
G
2
4
8
T
2
5
2
V
2
5
4
L
2
5
5
T
2
9
8
L
2
9
9
K
3
0
2
F
3
0
3
L
3
0
4
S
3
0
5
Q
3
1
6
P
3
1
7
L
3
1
8
L
3
5
8
I
3
5
9
M
3
6
1
Q
3
6
2
L
3
6
3
M
3
6
4
S
3
6
5
L
3
8
8
M
4
2
5
F
4
2
6
H
4
6
8
[1]1mx1.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]1mx5.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]1ya4.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]1ya8.b . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . - . . . . . . .
[1]1yah.b . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . - . . . . . . .
[1]2dqz.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]2dr0.a . . . . . . . . . . . . * . . . . . . . . . . * . . . . . . . - . . . . . . .
[1]2h7c.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]2hrq.b . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . - * . . . . . .
[1]2hrr.b . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . - . . . . . . .
[1]3k9b.a . . . . . . . . . . . . * . . . . . . . . . . - - - - - . . . - . . . . . . .
[1]3k9b.b . . . . . . . . . . . . * . . . . . . . . . - - - L S . . . . - . . . . . . .
[1]3k9b.c . . . . . . . . . . . . * . . . - . . . . . - - - - - . . . . L - - - - . . .
[1]5a7f.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - * . . . . . .
[1]5a7g.a . . . . . . . . . . . . A . . . . . . . . . . . . - - . . . . - . . . . . . .

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
1mx1.c:tha
1mx5.b:htq
1ya4.c:ctx
1ya8.b:smb
1yah.b:eee
2dqz.b:plm
2dr0.a:tch
2h7c.b:coa
2hrq.b:gd7
2hrr.b:ntj
3k9b.a:ww2
3k9b.b:ww2
3k9b.c:ww2
5a7f.a is apo
5a7g.a is apo
[1] 1mx1.c
0
0.3 0.7 0 0 0.1 1.8 1.1 0.5 0.2 0.3 0.4 0.6 - -
[1] 1mx5.b 0.1
0
0.8 0 0 0 1.8 0.8 0.6 0.4 0.6 0.8 1.0 - -
[1] 1ya4.c 0.4 0.2
0
0 0 0 1.4 1.1 0.6 0.4 0.5 0.6 0.7 - -
[1] 1ya8.b 0.1 0.3 0.2
0
0 0 1.1 1.2 0.7 0.4 0.5 0.7 0.7 - -
[1] 1yah.b 0.1 0.6 2.0 0.3
0
0.3 2.3 2.7 0.6 0.4 0.8 0.9 0.7 - -
[1] 2dqz.b 0.1 0.3 0.6 0 0
0
1.3 0.6 0.6 0.4 0.5 0.7 0.8 - -
[1] 2dr0.a 0.1 0.1 1.8 0 0 0
0.6
1.4 0.8 0.6 0.8 0.8 0.9 - -
[1] 2h7c.b 0.2 0.4 1.1 0.1 0 0 1.8
0.4
0.7 0.4 0.5 0.8 1.0 - -
[1] 2hrq.b 0.5 0.8 1.0 0 0 0 2.0 1.1
0.5
0.4 0.5 0.7 0.9 - -
[1] 2hrr.b 0.1 0.7 0.5 0.1 0 0.1 1.5 1.1 0.8
0.4
0.7 0.7 0.8 - -
[1] 3k9b.a 0.1 0.1 0 0 0 0 1.1 0.9 0.7 0.6
0.8
0.9 0.9 - -
[1] 3k9b.b 0.1 0.1 0.3 0 0 0 1.2 1.5 0.7 0.6 0.8
0.9
0.8 - -
[1] 3k9b.c 0.1 0.1 0 0 0 0 1.0 0.3 0.7 0.6 0.8 0.9
0.9
- -
[1] 5a7f.a 0.2 1.1 1.2 0 0 0.4 3.7 3.0 0.7 0.5 0.6 0.9 0.9
-
-
[1] 5a7g.a 0.1 0.6 0.4 0 0 0 1.3 0.9 0.3 0.1 0.1 0.3 0.4 -
-
[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
1mx1.c
1mx5.b
1ya4.c
1ya8.b
1yah.b
2dqz.b
2dr0.a
2h7c.b
2hrq.b
2hrr.b
3k9b.a
3k9b.b
3k9b.c
5a7f.a
5a7g.a
[1] 1mx1.c
0
.04 .04 .07 .09 .05 .11 .04 .07 .06 .07 .11 .08 .10 .07
[1] 1mx5.b .04
0
.04 .06 .07 .04 .09 .04 .05 .04 .07 .10 .07 .08 .06
[1] 1ya4.c .04 .04
0
.05 .07 .03 .09 .05 .06 .06 .05 .08 .06 .09 .06
[1] 1ya8.b .07 .06 .05
0
.05 .02 .06 .06 .05 .05 .06 .07 .06 .11 .06
[1] 1yah.b .09 .07 .07 .05
0
.05 .04 .08 .07 .06 .09 .11 .09 .12 .07
[1] 2dqz.b .05 .04 .03 .02 .05
0
.06 .04 .04 .03 .05 .07 .05 .10 .05
[1] 2dr0.a .11 .09 .09 .06 .04 .06
0
.11 .09 .07 .09 .11 .08 .15 .09
[1] 2h7c.b .04 .04 .05 .06 .08 .04 .11
0
.05 .05 .06 .09 .07 .11 .07
[1] 2hrq.b .07 .05 .06 .05 .07 .04 .09 .05
0
.04 .08 .10 .09 .10 .05
[1] 2hrr.b .06 .04 .06 .05 .06 .03 .07 .05 .04
0
.05 .08 .06 .11 .05
[1] 3k9b.a .07 .07 .05 .06 .09 .05 .09 .06 .08 .05
0
.06 .04 .11 .08
[1] 3k9b.b .11 .10 .08 .07 .11 .07 .11 .09 .10 .08 .06
0
.05 .16 .09
[1] 3k9b.c .08 .07 .06 .06 .09 .05 .08 .07 .09 .06 .04 .05
0
.14 .07
[1] 5a7f.a .10 .08 .09 .11 .12 .10 .15 .11 .10 .11 .11 .16 .14
0
.12
[1] 5a7g.a .07 .06 .06 .06 .07 .05 .09 .07 .05 .05 .08 .09 .07 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1mx1.c
1mx5.b
1ya4.c
1ya8.b
1yah.b
2dqz.b
2dr0.a
2h7c.b
2hrq.b
2hrr.b
3k9b.a
3k9b.b
3k9b.c
5a7f.a
5a7g.a
[1] 1mx1.c
0
0.3 0.4 1.2 0.5 0.5 0.7 0.2 0.3 0.3 0.4 2.6 1.5 0.4 0.7
[1] 1mx5.b 0.3
0
0.3 1.1 0.4 0.5 0.7 0.3 0.3 0.3 0.3 2.6 1.6 0.4 0.7
[1] 1ya4.c 0.4 0.3
0
1.1 0.5 0.5 0.6 0.4 0.4 0.4 0.4 2.7 1.6 0.5 0.8
[1] 1ya8.b 1.2 1.1 1.1
0
0.9 0.9 0.7 1.2 1.1 1.1 0.4 3.2 2.0 1.3 0.5
[1] 1yah.b 0.5 0.4 0.5 0.9
0
0.3 0.5 0.5 0.4 0.4 0.4 2.8 1.6 0.6 0.6
[1] 2dqz.b 0.5 0.5 0.5 0.9 0.3
0
0.5 0.5 0.5 0.5 0.4 2.8 1.7 0.6 0.5
[1] 2dr0.a 0.7 0.7 0.6 0.7 0.5 0.5
0
0.7 0.7 0.7 0.3 2.9 1.8 0.8 0.6
[1] 2h7c.b 0.2 0.3 0.4 1.2 0.5 0.5 0.7
0
0.3 0.3 0.4 2.6 1.5 0.4 0.7
[1] 2hrq.b 0.3 0.3 0.4 1.1 0.4 0.5 0.7 0.3
0
0.2 0.4 2.7 1.6 0.4 0.7
[1] 2hrr.b 0.3 0.3 0.4 1.1 0.4 0.5 0.7 0.3 0.2
0
0.3 2.6 1.5 0.4 0.7
[1] 3k9b.a 0.4 0.3 0.4 0.4 0.4 0.4 0.3 0.4 0.4 0.3
0
0 0 0.5 0.6
[1] 3k9b.b 2.6 2.6 2.7 3.2 2.8 2.8 2.9 2.6 2.7 2.6 0
0
1.2 2.6 2.2
[1] 3k9b.c 1.5 1.6 1.6 2.0 1.6 1.7 1.8 1.5 1.6 1.5 0 1.2
0
1.5 1.9
[1] 5a7f.a 0.4 0.4 0.5 1.3 0.6 0.6 0.8 0.4 0.4 0.4 0.5 2.6 1.5
0
0.8
[1] 5a7g.a 0.7 0.7 0.8 0.5 0.6 0.5 0.6 0.7 0.7 0.7 0.6 2.2 1.9 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

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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
1mx1.c
1mx5.b
1ya4.c
1ya8.b
1yah.b
2dqz.b
2dr0.a
2h7c.b
2hrq.b
2hrr.b
3k9b.a
3k9b.b
3k9b.c
5a7f.a
5a7g.a
[1] 1mx1.c
0
0.6 0.7 1.6 0.8 0.8 1.0 0.7 0.6 0.6 0.6 2.4 1.6 0.9 1.1
[1] 1mx5.b 0.6
0
0.7 1.6 0.8 0.8 1.0 0.8 0.6 0.6 0.6 2.4 1.6 0.8 1.0
[1] 1ya4.c 0.7 0.7
0
1.5 0.6 0.6 0.8 0.9 0.7 0.7 0.7 2.5 1.7 0.9 1.1
[1] 1ya8.b 1.6 1.6 1.5
0
1.4 1.2 1.3 1.7 1.5 1.5 0.7 2.9 2.0 1.7 0.9
[1] 1yah.b 0.8 0.8 0.6 1.4
0
0.6 0.7 1.0 0.7 0.7 0.6 2.5 1.7 1.0 1.1
[1] 2dqz.b 0.8 0.8 0.6 1.2 0.6
0
0.8 0.9 0.6 0.7 0.6 2.6 1.8 1.0 1.0
[1] 2dr0.a 1.0 1.0 0.8 1.3 0.7 0.8
0
1.1 1.0 1.0 0.6 2.6 1.8 1.1 1.1
[1] 2h7c.b 0.7 0.8 0.9 1.7 1.0 0.9 1.1
0
0.8 0.8 0.9 2.4 1.5 1.1 1.2
[1] 2hrq.b 0.6 0.6 0.7 1.5 0.7 0.6 1.0 0.8
0
0.5 0.6 2.5 1.7 0.8 1.0
[1] 2hrr.b 0.6 0.6 0.7 1.5 0.7 0.7 1.0 0.8 0.5
0
0.6 2.4 1.6 0.9 1.1
[1] 3k9b.a 0.6 0.6 0.7 0.7 0.6 0.6 0.6 0.9 0.6 0.6
0
0.2 0.6 0.9 0.9
[1] 3k9b.b 2.4 2.4 2.5 2.9 2.5 2.6 2.6 2.4 2.5 2.4 0.2
0
1.0 2.4 1.8
[1] 3k9b.c 1.6 1.6 1.7 2.0 1.7 1.8 1.8 1.5 1.7 1.6 0.6 1.0
0
1.7 2.0
[1] 5a7f.a 0.9 0.8 0.9 1.7 1.0 1.0 1.1 1.1 0.8 0.9 0.9 2.4 1.7
0
0.9
[1] 5a7g.a 1.1 1.0 1.1 0.9 1.1 1.0 1.1 1.2 1.0 1.1 0.9 1.8 2.0 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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