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CP2E1_HUMAN_22_493

Cytochrome P450 2E1 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CP2E1_HUMAN):R: Substrate binding (298, 299, 302, 303)
103, 106, 109, 115, 116, 203, 206, 207, 210, 239, 242, 243, 364, 368, 437, 478
103, 106, 109, 115, 116, 203, 206, 207, 210, 239, 242, 243, 298, 299, 302, 303, 364, 368, 437, 478
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3e4e, 3e6i, 3gph, 3koh, 3lc4, 3t3z

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
F
1
0
6
H
1
0
9
I
1
1
5
F
1
1
6
F
2
0
3
N
2
0
6
F
2
0
7
L
2
1
0
V
2
3
9
V
2
4
2
K
2
4
3
F
2
9
8
A
2
9
9
T
3
0
3
V
3
6
4
L
3
6
8
C
4
3
7
F
4
7
8
[1]3e4e.a 4pz6 . . . . . . . . . . . . . . . . . . hem Fe
[1]3e6i.a lz19 . . . . . . . . . . . . . . . . . . hem Fe
[1]3gph.b oid17 . . . . . . . . . . . . . . . . . . hem Fe
[1]3koh.b oio15 . . . . . . . . . . . . . . . . . . Fe
[1]3lc4.a lc419 . . . . . . . . . . . . . . . . . . hem Fe
[1]3t3z.c 9pl15 . . . . . . . . . . . . . . . . . . hem Fe

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
L
1
0
3
F
1
0
6
H
1
0
9
I
1
1
5
F
1
1
6
F
2
0
3
N
2
0
6
F
2
0
7
L
2
1
0
V
2
3
9
V
2
4
2
K
2
4
3
F
2
9
8
A
2
9
9
E
3
0
2
T
3
0
3
V
3
6
4
L
3
6
8
C
4
3
7
F
4
7
8
[1]3e4e.a . . . . . . . . . . . . * . . . . . . * hem Fe
[1]3e6i.a . . . . . . . . . . . . * . . . . . . * hem Fe
[1]3gph.b . . . . . . . . . . . . . . . . . . . * hem Fe
[1]3koh.b . . . . . . . . . . . . . . . . . . . * Fe
[1]3lc4.a . . . . . . . . . . . . . . . . . . . * hem Fe
[1]3t3z.c . . . . . . . . . . . . * . . . . . . . hem Fe

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
3e4e.a:4pz
3e6i.a:lz1
3gph.b:oid
3koh.b:oio
3lc4.a:lc4
3t3z.c:9pl
[1] 3e4e.a
0
0.1 2.2 3.0 3.0 1.9
[1] 3e6i.a 0
0
2.9 2.8 3.0 1.9
[1] 3gph.b 0.1 0.2
0
0.4 0.4 1.5
[1] 3koh.b 0.1 0.2 0
0.6
0.3 1.5
[1] 3lc4.a 0.3 0.4 0 0.6
0.2
1.7
[1] 3t3z.c 0 0 2.1 2.2 1.8
0
[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
3e4e.a
3e6i.a
3gph.b
3koh.b
3lc4.a
3t3z.c
[1] 3e4e.a
0
.01 .17 .16 .17 .15
[1] 3e6i.a .01
0
.18 .17 .18 .14
[1] 3gph.b .17 .18
0
.01 .03 .18
[1] 3koh.b .16 .17 .01
0
.04 .17
[1] 3lc4.a .17 .18 .03 .04
0
.20
[1] 3t3z.c .15 .14 .18 .17 .20
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
3e4e.a
3e6i.a
3gph.b
3koh.b
3lc4.a
3t3z.c
[1] 3e4e.a
0
0.2 0.3 0.4 0.4 0.3
[1] 3e6i.a 0.2
0
0.4 0.4 0.4 0.2
[1] 3gph.b 0.3 0.4
0
0.3 0.2 0.3
[1] 3koh.b 0.4 0.4 0.3
0
0.3 0.4
[1] 3lc4.a 0.4 0.4 0.2 0.3
0
0.3
[1] 3t3z.c 0.3 0.2 0.3 0.4 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
3e4e.a
3e6i.a
3gph.b
3koh.b
3lc4.a
3t3z.c
[1] 3e4e.a
0
0.4 1.0 0.8 0.9 0.9
[1] 3e6i.a 0.4
0
1.0 0.8 0.9 0.9
[1] 3gph.b 1.0 1.0
0
0.7 0.7 1.1
[1] 3koh.b 0.8 0.8 0.7
0
0.6 1.1
[1] 3lc4.a 0.9 0.9 0.7 0.6
0
1.0
[1] 3t3z.c 0.9 0.9 1.1 1.1 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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