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COMT_HUMAN_51_267

Catechol O-methyltransferase [Class I-like SAM-binding methyltransferase superfamily. Cation-dependent O- methyltransferase family]

Composition of the binding site

Protein chains monomer
A1 (COMT_HUMAN):88, 90, 118, 191:195, 219, 220, 223, 224, 248, 249, 251:25588, 90, 118, 191:195, 219, 220, 223, 224, 248, 249, 251:255
Cofactors (cF):sam
Metals (Me):Mg

Full PDB list

3a7e, 3bwm, 3bwy, 4pyi, 4pyj, 4pyk, 4xuc, 4xud, 4xue, 5lsa (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
W
8
8
M
9
0
D
1
9
1
H
1
9
2
W
1
9
3
K
1
9
4
D
1
9
5
D
2
1
9
N
2
2
0
C
2
2
3
P
2
2
4
L
2
4
8
E
2
4
9
R
2
5
1
[1]4xuc.a 43g20 . . . . . . . . . . . . . . sam Mg
[1]4xud.a 43h23 . . . . . . . . . . . . . . sam Mg
[1]4xue.b 43j21 . . . . . . . . . . . . . . sam Mg
[1]5lsa.a dnc14 . . . . . . . . . . . . . . sam Mg
[2]4pyj.a none - - . . . . . . . . . . . . Mg

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 cF Me
W
8
8
M
9
0
Y
1
1
8
D
1
9
1
H
1
9
2
W
1
9
3
K
1
9
4
D
1
9
5
D
2
1
9
N
2
2
0
C
2
2
3
P
2
2
4
L
2
4
8
E
2
4
9
R
2
5
1
E
2
5
2
V
2
5
3
V
2
5
4
D
2
5
5
[1]4xuc.a . . . . . . . . . . . . . . . . . . . sam Mg
[1]4xud.a . . . . . . . . . . . . . . . . . . . sam Mg
[1]4xue.b . . . . . . . . . . . . . . . . . . . sam Mg
[1]5lsa.a . . . . . . . . . . . . . . . . . . . sam Mg
[2]4pyj.a - - . . . . . . . . . . . . . . * . . Mg

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
4xuc.a:43g
4xud.a:43h
4xue.b:43j
5lsa.a:dnc
4pyj.a is apo
[1] 4xuc.a
0
0.1 0.1 0.1 -
[1] 4xud.a 0
0
0.1 0 -
[1] 4xue.b 0.8 0.8
0.1
0.2 -
[1] 5lsa.a 0.6 0.5 0.2
0.1
-
[2] 4pyj.a 2.4 2.5 1.9 1.4
-
[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
4xuc.a
4xud.a
4xue.b
5lsa.a
4pyj.a
[1] 4xuc.a
0
.01 .05 .04 .24
[1] 4xud.a .01
0
.05 .04 .24
[1] 4xue.b .05 .05
0
.02 .26
[1] 5lsa.a .04 .04 .02
0
.26
[2] 4pyj.a .24 .24 .26 .26
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
4xuc.a
4xud.a
4xue.b
5lsa.a
4pyj.a
[1] 4xuc.a
0
0.1 0.5 0.4 6.9
[1] 4xud.a 0.1
0
0.5 0.4 6.8
[1] 4xue.b 0.5 0.5
0
0.2 6.9
[1] 5lsa.a 0.4 0.4 0.2
0
6.9
[2] 4pyj.a 6.9 6.8 6.9 6.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
4xuc.a
4xud.a
4xue.b
5lsa.a
4pyj.a
[1] 4xuc.a
0
0.2 0.5 0.6 7.3
[1] 4xud.a 0.2
0
0.6 0.6 7.2
[1] 4xue.b 0.5 0.6
0
0.6 7.3
[1] 5lsa.a 0.6 0.6 0.6
0
7.2
[2] 4pyj.a 7.3 7.2 7.3 7.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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