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CP2B6_HUMAN_20_491_peripheralAmlodipine

Cytochrome P450 2B6 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2B6_HUMAN):49, 51, 70, 73, 100:103, 212, 214:216, 218, 219, 365, 368, 387, 389, 476, 47749, 51, 70, 73, 100:103, 212, 214:216, 218, 219, 365, 368, 387, 389, 476, 477
Cofactors (cF):82s/cm5
Metals (Me):Fe

Full PDB list

3ibd, 3qoa, 3qu8, 3ua5, 4i91, 4rql, 4rrt, 4zv8, 5uap, 5uda, 5uec, 5ufg (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
4
9
L
5
1
R
7
3
Q
2
1
5
E
2
1
8
L
2
1
9
M
3
6
5
P
3
6
8
F
3
8
9
G
4
7
6
V
4
7
7
[1]3ua5.a 06x28 . . . . . . . . . . . Fe
[2]5uap.a none . . . . . . . . . . . 82s,cm5 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

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PDB.ch
A1 cF Me
R
4
9
L
5
1
L
7
0
R
7
3
K
1
0
0
I
1
0
1
A
1
0
2
M
1
0
3
V
2
1
2
G
2
1
4
Q
2
1
5
L
2
1
6
E
2
1
8
L
2
1
9
M
3
6
5
P
3
6
8
E
3
8
7
F
3
8
9
G
4
7
6
V
4
7
7
[1]3ua5.a . . . . . . . . . . . . . . . . . . . . Fe
[2]5uap.a . . . . . . . . . . * . * . . . . . . . 82s,cm5 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
3ua5.a:06x
5uap.a is apo
[1] 3ua5.a
0
-
[2] 5uap.a 7.0
-
[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
3ua5.a
5uap.a
[1] 3ua5.a
0
.35
[2] 5uap.a .35
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.7 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
3ua5.a
5uap.a
[1] 3ua5.a
0
2.6
[2] 5uap.a 2.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.3 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
3ua5.a
5uap.a
[1] 3ua5.a
0
3.4
[2] 5uap.a 3.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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