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DNMT1_HUMAN_1129_1600_catalytic

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_HUMAN):D: SAM-dependent MTase C5-type (1145:1151, 1167:1170, 1189:1191, 1223, 1225, 1247, 1266, 1578:1580)
R: Catalytic (1145:1149, 1167, 1170, 1189, 1223, 1225, 1247, 1266, 1578:1580)
R: S-adenosyl-L-methionine binding (1150, 1151)
R: S-adenosyl-L-methionine binding (1168, 1169)
1145:1151, 1167:1170, 1189:1191, 1223, 1225, 1247, 1266, 1578:1580

Full PDB list

3swr, 4wxx, 4yoc

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
F
1
1
4
5
S
1
1
4
6
G
1
1
4
7
G
1
1
4
9
G
1
1
5
0
L
1
1
5
1
I
1
1
6
7
E
1
1
6
8
M
1
1
6
9
W
1
1
7
0
E
1
1
8
9
D
1
1
9
0
C
1
1
9
1
G
1
2
2
3
P
1
2
2
5
L
1
2
4
7
E
1
2
6
6
N
1
5
7
8
A
1
5
7
9
V
1
5
8
0
[1]3swr.a sfg27 . . . . . . . . . . . . . . . . . . . .
[1]4wxx.a sah26 . . . . . . . . . . . . . . . . . . . .
[1]4yoc.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
F
1
1
4
5
S
1
1
4
6
G
1
1
4
7
C
1
1
4
8
G
1
1
4
9
G
1
1
5
0
L
1
1
5
1
I
1
1
6
7
E
1
1
6
8
M
1
1
6
9
W
1
1
7
0
E
1
1
8
9
D
1
1
9
0
C
1
1
9
1
G
1
2
2
3
P
1
2
2
5
L
1
2
4
7
E
1
2
6
6
N
1
5
7
8
A
1
5
7
9
V
1
5
8
0
[1]3swr.a . . . . . . . . . . . . . . . . . . . . .
[1]4wxx.a . . . . . . . . . . . . . . . . . . . . .
[1]4yoc.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
3swr.a:sfg
4wxx.a:sah
4yoc.a is apo
[1] 3swr.a
0
0.1 -
[1] 4wxx.a 0.1
0.2
-
[1] 4yoc.a 0.2 0.1
-
[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
3swr.a
4wxx.a
4yoc.a
[1] 3swr.a
0
0 0
[1] 4wxx.a 0
0
.01
[1] 4yoc.a 0 .01
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
3swr.a
4wxx.a
4yoc.a
[1] 3swr.a
0
0.4 0.5
[1] 4wxx.a 0.4
0
0.7
[1] 4yoc.a 0.5 0.7
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
3swr.a
4wxx.a
4yoc.a
[1] 3swr.a
0
0.6 0.7
[1] 4wxx.a 0.6
0
0.9
[1] 4yoc.a 0.7 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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