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EZH2_HUMAN_519_746

Histone-lysine N-methyltransferase EZH2 [Class V-like SAM-binding methyltransferase superfamily. Histone-lysine methyltransferase family. EZ subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EZH2_HUMAN):R: Interaction with DNMT1, DNMT3A and DNMT3B (109:111, 130, 132)
D: SET (621:624, 657, 658, 660:665, 678, 685:689, 726)
733, 734, 736
109:111, 130, 132, 621:624, 657, 658, 660:665, 678, 685:689, 726, 733, 734, 736

Full PDB list

4mi0, 4mi5, 5hyn, 5ij7, 5ij8, 5ls6 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
1
0
9
M
1
1
0
Y
1
1
1
V
6
2
1
A
6
2
2
G
6
2
3
W
6
2
4
V
6
5
7
Y
6
5
8
Y
6
6
1
M
6
6
2
C
6
6
3
S
6
6
4
F
6
6
5
T
6
7
8
R
6
8
5
F
6
8
6
A
6
8
7
N
6
8
8
H
6
8
9
Y
7
2
6
L
7
3
4
Y
7
3
6
[1]5hyn.a sah26 . . . . . . . . . . . . . . . . . . . . . . .
[1]5ij8.b 6bn36 . . . . . . . . . . . . . . . . . . . . . - -
[1]5ls6.d 74d37 . . . . . . . . . . . . . . . . . . . . . - -
[2]4mi0.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
I
1
0
9
M
1
1
0
Y
1
1
1
N
1
3
0
P
1
3
2
V
6
2
1
A
6
2
2
G
6
2
3
W
6
2
4
V
6
5
7
Y
6
5
8
K
6
6
0
Y
6
6
1
M
6
6
2
C
6
6
3
S
6
6
4
F
6
6
5
T
6
7
8
R
6
8
5
F
6
8
6
A
6
8
7
N
6
8
8
H
6
8
9
Y
7
2
6
A
7
3
3
L
7
3
4
Y
7
3
6
[1]5hyn.a . . . . . . . . . . . . . . . . * . . . . . . . . . .
[1]5ij8.b . . . - - . . . . . . . . . * . . . . . . . . . . - -
[1]5ls6.d . . . . . . . . . . . . . . . . * . . . . . . . - - -
[2]4mi0.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
5hyn.a:sah
5ij8.b:6bn
5ls6.d:74d
4mi0.a is apo
[1] 5hyn.a
0.2
2.2 1.8 -
[1] 5ij8.b 1.0
0
1.4 -
[1] 5ls6.d 2.4 0.3
0
-
[2] 4mi0.a 0.6 10 9.3
-
[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
5hyn.a
5ij8.b
5ls6.d
4mi0.a
[1] 5hyn.a
0
.11 .04 .33
[1] 5ij8.b .11
0
.09 .37
[1] 5ls6.d .04 .09
0
.34
[2] 4mi0.a .33 .37 .34
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.7 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
5hyn.a
5ij8.b
5ls6.d
4mi0.a
[1] 5hyn.a
0
4.6 0.8 5.1
[1] 5ij8.b 4.6
0
1.2 4.8
[1] 5ls6.d 0.8 1.2
0
5.4
[2] 4mi0.a 5.1 4.8 5.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.9 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
5hyn.a
5ij8.b
5ls6.d
4mi0.a
[1] 5hyn.a
0
3.8 1.0 5.4
[1] 5ij8.b 3.8
0
1.7 5.2
[1] 5ls6.d 1.0 1.7
0
5.7
[2] 4mi0.a 5.4 5.2 5.7
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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