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CP2D6_HUMAN_23_497_catalytic

Cytochrome P450 2D6 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2D6_HUMAN):106, 110, 112, 120, 121, 208, 209, 212, 213, 216, 220, 244, 247, 248, 297, 300, 301, 303:306, 308, 309, 370, 373, 374, 443, 483, 484106, 110, 112, 120, 121, 208, 209, 212, 213, 216, 220, 244, 247, 248, 297, 300, 301, 303:306, 308, 309, 370, 373, 374, 443, 483, 484
Cofactors (cF):hem
Metals (Me):Fe/Zn

Full PDB list

2f9q, 3qm4, 3tbg, 3tda, 4wnt, 4wnu, 4wnv, 4wnw, 4xry, 4xrz, 5tft, 5tfu (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
1
1
0
F
1
1
2
F
1
2
0
L
1
2
1
L
2
0
8
A
2
0
9
G
2
1
2
L
2
1
3
E
2
1
6
Q
2
4
4
F
2
4
7
L
2
4
8
I
2
9
7
A
3
0
0
D
3
0
1
S
3
0
4
A
3
0
5
V
3
0
8
T
3
0
9
V
3
7
0
V
3
7
4
F
4
8
3
L
4
8
4
[1]3tbg.a rtz25 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]3tda.d pn028 . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4wnt.a ajn26 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]4wnu.a qdn24 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]4wnv.a qi924 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]4xry.a si525 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]4xrz.a si624 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]5tft.a p6u25 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]5tfu.a p6m26 . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[2]2f9q.a none . . . . . . . . . . . . . . . . . . . . M . . 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
I
1
0
6
L
1
1
0
F
1
1
2
F
1
2
0
L
1
2
1
L
2
0
8
A
2
0
9
G
2
1
2
L
2
1
3
E
2
1
6
L
2
2
0
Q
2
4
4
F
2
4
7
L
2
4
8
I
2
9
7
A
3
0
0
D
3
0
1
F
3
0
3
S
3
0
4
A
3
0
5
G
3
0
6
V
3
0
8
T
3
0
9
V
3
7
0
G
3
7
3
V
3
7
4
C
4
4
3
F
4
8
3
L
4
8
4
[1]3tbg.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . hem Fe,Zn
[1]3tda.d . . . * . . . . . . . . . . . . . . . . . . . . . . . * . hem Fe
[1]4wnt.a . . . . . . . . * * . . . . . . . . . . . . . . . . . * . hem Fe,Zn
[1]4wnu.a . . . . . . . . . . . . . . . . . . * . . . . . . . . . . hem Fe,Zn
[1]4wnv.a . . . . . . . . . * . * . . . . . . * . . . . . . . . . . hem Fe,Zn
[1]4xry.a . . . . . . . . . . . . . . . . . . . . . . . . . . . * . hem Fe,Zn
[1]4xrz.a . . . . . . . . . * . . . . . . . . . . . . . . . . . * . hem Fe,Zn
[1]5tft.a . . . . . . . . . * . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[1]5tfu.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe,Zn
[2]2f9q.a . . . * . . . . * * . * . . . . . . . * . . . . . M . * . 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
3tbg.a:rtz
3tda.d:pn0
4wnt.a:ajn
4wnu.a:qdn
4wnv.a:qi9
4xry.a:si5
4xrz.a:si6
5tft.a:p6u
5tfu.a:p6m
2f9q.a is apo
[1] 3tbg.a
0.1
1.9 2.1 0.8 2.1 0.4 2.1 0.7 0.8 -
[1] 3tda.d 1.4
0
1.4 1.4 4.4 0.5 0.7 0.6 0.7 -
[1] 4wnt.a 4.1 1.9
0
3.1 4.7 2.8 2.4 3.0 4.0 -
[1] 4wnu.a 0.6 2.0 1.6
0
0.9 0.9 2.6 0.5 0.6 -
[1] 4wnv.a 0 1.3 1.3 0.9
0
0.6 1.8 1.0 0.7 -
[1] 4xry.a 1.1 0.6 1.0 1.3 4.0
0.1
1.1 0.2 0.7 -
[1] 4xrz.a 1.9 0.5 0.2 2.1 3.9 0.7
0
0.1 1.1 -
[1] 5tft.a 0.6 0.7 0.6 0.9 2.0 0.2 1.4
0
0.6 -
[1] 5tfu.a 0 0.5 1.0 0.4 1.1 0.1 0.8 0
0
-
[2] 2f9q.a 2.8 3.4 3.8 3.8 2.7 1.9 3.5 4.0 3.8
-
[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
3tbg.a
3tda.d
4wnt.a
4wnu.a
4wnv.a
4xry.a
4xrz.a
5tft.a
5tfu.a
2f9q.a
[1] 3tbg.a
0
.18 .25 .12 .12 .12 .22 .13 .13 .20
[1] 3tda.d .18
0
.19 .26 .27 .09 .12 .22 .18 .32
[1] 4wnt.a .25 .19
0
.32 .30 .18 .14 .26 .28 .29
[1] 4wnu.a .12 .26 .32
0
.13 .20 .24 .13 .15 .28
[1] 4wnv.a .12 .27 .30 .13
0
.20 .25 .11 .13 .25
[1] 4xry.a .12 .09 .18 .20 .20
0
.12 .14 .16 .29
[1] 4xrz.a .22 .12 .14 .24 .25 .12
0
.19 .21 .35
[1] 5tft.a .13 .22 .26 .13 .11 .14 .19
0
.08 .24
[1] 5tfu.a .13 .18 .28 .15 .13 .16 .21 .08
0
.29
[2] 2f9q.a .20 .32 .29 .28 .25 .29 .35 .24 .29
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
3tbg.a
3tda.d
4wnt.a
4wnu.a
4wnv.a
4xry.a
4xrz.a
5tft.a
5tfu.a
2f9q.a
[1] 3tbg.a
0
1.0 1.1 0.6 0.4 0.7 1.2 0.7 0.7 2.2
[1] 3tda.d 1.0
0
0.8 1.2 0.9 0.7 0.8 0.7 0.6 2.2
[1] 4wnt.a 1.1 0.8
0
1.2 1.1 0.9 0.7 0.9 0.9 2.1
[1] 4wnu.a 0.6 1.2 1.2
0
0.6 0.8 1.3 0.8 0.8 2.4
[1] 4wnv.a 0.4 0.9 1.1 0.6
0
0.6 1.1 0.6 0.5 2.2
[1] 4xry.a 0.7 0.7 0.9 0.8 0.6
0
1.0 0.4 0.3 2.2
[1] 4xrz.a 1.2 0.8 0.7 1.3 1.1 1.0
0
0.9 0.9 2.2
[1] 5tft.a 0.7 0.7 0.9 0.8 0.6 0.4 0.9
0
0.3 2.1
[1] 5tfu.a 0.7 0.6 0.9 0.8 0.5 0.3 0.9 0.3
0
2.2
[2] 2f9q.a 2.2 2.2 2.1 2.4 2.2 2.2 2.2 2.1 2.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
3tbg.a
3tda.d
4wnt.a
4wnu.a
4wnv.a
4xry.a
4xrz.a
5tft.a
5tfu.a
2f9q.a
[1] 3tbg.a
0
1.2 1.4 1.0 0.8 0.9 1.4 1.1 1.0 2.8
[1] 3tda.d 1.2
0
1.2 1.4 1.5 1.0 1.2 1.3 1.3 2.8
[1] 4wnt.a 1.4 1.2
0
1.5 1.5 1.2 0.9 1.4 1.5 2.8
[1] 4wnu.a 1.0 1.4 1.5
0
1.2 1.2 1.5 1.4 1.4 3.1
[1] 4wnv.a 0.8 1.5 1.5 1.2
0
1.2 1.6 0.9 0.9 2.8
[1] 4xry.a 0.9 1.0 1.2 1.2 1.2
0
1.2 0.9 0.9 2.8
[1] 4xrz.a 1.4 1.2 0.9 1.5 1.6 1.2
0
1.4 1.4 2.8
[1] 5tft.a 1.1 1.3 1.4 1.4 0.9 0.9 1.4
0
0.4 2.8
[1] 5tfu.a 1.0 1.3 1.5 1.4 0.9 0.9 1.4 0.4
0
2.8
[2] 2f9q.a 2.8 2.8 2.8 3.1 2.8 2.8 2.8 2.8 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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