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DNMT1_MOUSE_730_1609

DNA (cytosine-5)-methyltransferase 1 [Class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DNMT1_MOUSE):D: SAM-dependent MTase C5-type (1148:1150, 1152:1154, 1170:1173, 1192:1194, 1226:1229, 1233, 1235, 1247, 1250, 1269:1271, 1313, 1315, 1528, 1530, 1579:1582)
R: Catalytic (1148:1150, 1152, 1170, 1173, 1192, 1226:1229, 1233, 1235, 1247, 1250, 1269:1271, 1313, 1315, 1528, 1530, 1579:1582)
R: S-adenosyl-L-methionine binding (1153, 1154)
R: S-adenosyl-L-methionine binding (1171, 1172)
R: S-adenosyl-L-methionine binding (1193, 1194)
651
651, 702:705, 1148:1150, 1152:1154, 1170:1173, 1192:1194, 1226:1229, 1233, 1235, 1247, 1250, 1269:1271, 1313, 1315, 1528, 1530, 1579:1582

Full PDB list

3av4, 3av5, 3av6, 3pt6, 3pt9, 4da4, 5gut, 5guv, 5wy1 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
1
4
8
S
1
1
4
9
G
1
1
5
0
G
1
1
5
2
G
1
1
5
3
L
1
1
5
4
E
1
1
7
1
M
1
1
7
2
W
1
1
7
3
E
1
1
9
2
D
1
1
9
3
C
1
1
9
4
G
1
2
2
6
P
1
2
2
7
P
1
2
2
8
C
1
2
2
9
S
1
2
3
3
M
1
2
3
5
K
1
2
4
7
L
1
2
5
0
E
1
2
6
9
N
1
2
7
0
V
1
2
7
1
R
1
3
1
3
R
1
3
1
5
T
1
5
3
0
G
1
5
7
9
N
1
5
8
0
A
1
5
8
1
V
1
5
8
2
[1]3av6.a sam27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pt6.a sah26 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4da4.a c49,sah47 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5guv.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
M
6
5
1
A
7
0
2
D
7
0
3
D
7
0
4
D
7
0
5
F
1
1
4
8
S
1
1
4
9
G
1
1
5
0
G
1
1
5
2
G
1
1
5
3
L
1
1
5
4
I
1
1
7
0
E
1
1
7
1
M
1
1
7
2
W
1
1
7
3
E
1
1
9
2
D
1
1
9
3
C
1
1
9
4
G
1
2
2
6
P
1
2
2
7
P
1
2
2
8
C
1
2
2
9
S
1
2
3
3
M
1
2
3
5
K
1
2
4
7
L
1
2
5
0
E
1
2
6
9
N
1
2
7
0
V
1
2
7
1
R
1
3
1
3
R
1
3
1
5
T
1
5
2
8
T
1
5
3
0
G
1
5
7
9
N
1
5
8
0
A
1
5
8
1
V
1
5
8
2
[1]3av6.a - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pt6.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4da4.a - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5guv.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
3av6.a:sam
3pt6.a:sah
4da4.a:c49,sah
5guv.a is apo
[1] 3av6.a
0
0.1 0.2 -
[1] 3pt6.a 0.1
0
0.6 -
[1] 4da4.a 0 0.1
0.5
-
[1] 5guv.a 0 0 0.3
-
[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
3av6.a
3pt6.a
4da4.a
5guv.a
[1] 3av6.a
0
.02 .02 .02
[1] 3pt6.a .02
0
.03 .01
[1] 4da4.a .02 .03
0
.02
[1] 5guv.a .02 .01 .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.4 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
3av6.a
3pt6.a
4da4.a
5guv.a
[1] 3av6.a
0
4.2 3.2 1.0
[1] 3pt6.a 4.2
0
3.2 0.7
[1] 4da4.a 3.2 3.2
0
3.4
[1] 5guv.a 1.0 0.7 3.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.1 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
3av6.a
3pt6.a
4da4.a
5guv.a
[1] 3av6.a
0
3.8 4.2 1.6
[1] 3pt6.a 3.8
0
3.2 0.8
[1] 4da4.a 4.2 3.2
0
4.4
[1] 5guv.a 1.6 0.8 4.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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