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CP2A6_HUMAN_24_494

Cytochrome P450 2A6 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2A6_HUMAN):107, 111, 117, 118, 209, 296, 297, 300, 301, 304, 305, 366, 370, 480107, 111, 117, 118, 209, 296, 297, 300, 301, 304, 305, 366, 370, 480
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1z10, 1z11, 2fdu, 2fdv, 2fdw, 2fdy, 2pg5, 2pg6, 2pg7, 3ebs, 3t3q, 3t3r, 4ejj, 4rui (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
F
1
0
7
F
1
1
1
V
1
1
7
F
1
1
8
F
2
0
9
N
2
9
7
I
3
0
0
G
3
0
1
T
3
0
5
I
3
6
6
L
3
7
0
F
4
8
0
[1]1z10.a cou11 . . . . . . . . . . . . hem Fe
[1]1z11.a 8mo16 . . . . . . . . . . . . hem Fe
[1]2fdu.a d1g15 . . . . . . . . . . . . hem Fe
[1]2fdv.a d2g14 . . . . . . . . . . . . hem Fe
[1]2fdw.d d3g13 . . . . . . . . . . . . hem Fe
[1]2fdy.b d4g14 . . . . . . . . . . . . hem Fe
[1]2pg5.a none . . . . . Q . . . . . . hem Fe
[1]2pg7.a none . . . . . Q V . . . . . hem Fe
[1]3ebs.a n4e13 . . . . . . F A . . . . hem Fe
[1]3ebs.c none . . . . . . F A . . . . hem Fe
[1]3t3q.a 9pl15 . . . . . . F A . . . . hem Fe
[1]3t3r.b 9pl15 . . . . . . . . . . . . hem Fe
[1]4ejj.a nct12 . . . . . . . . . . . . hem Fe
[1]4rui.a sne10 . . . . . . . . . . . . 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
F
1
0
7
F
1
1
1
V
1
1
7
F
1
1
8
F
2
0
9
L
2
9
6
N
2
9
7
I
3
0
0
G
3
0
1
E
3
0
4
T
3
0
5
I
3
6
6
L
3
7
0
F
4
8
0
[1]1z10.a . . . . . . . . . . . . . . hem Fe
[1]1z11.a . . . . . . . . . . . . . . hem Fe
[1]2fdu.a . . . . . . . . . . . . * . hem Fe
[1]2fdv.a . . . . . . . . . . . . * . hem Fe
[1]2fdw.d . . . . . . . . . . . . * . hem Fe
[1]2fdy.b . . . . . . . . . . . . * . hem Fe
[1]2pg5.a . . . . . . Q . . . . . . . hem Fe
[1]2pg7.a . . . . . . Q V . . . . . . hem Fe
[1]3ebs.a . . . . . . . F A . . . . . hem Fe
[1]3ebs.c . . . . . . . F A . . . . . hem Fe
[1]3t3q.a . . . . . . . F A . . . . . hem Fe
[1]3t3r.b . . . . . . . . . . . . * . hem Fe
[1]4ejj.a . . . . . . . . . . . . * . hem Fe
[1]4rui.a . . . . . . . . . . . . . . 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
1z10.a:cou
1z11.a:8mo
2fdu.a:d1g
2fdv.a:d2g
2fdw.d:d3g
2fdy.b:d4g
2pg5.a is apo
2pg7.a is apo
3ebs.a:n4e
3ebs.c is apo
3t3q.a:9pl
3t3r.b:9pl
4ejj.a:nct
4rui.a:sne
[1] 1z10.a
0
0.2 0.7 0.3 0.5 1.0 - - 0.3 - 0.5 0.8 0.1 0
[1] 1z11.a 0
0.1
0.4 0.2 0.3 1.0 - - 0.5 - 0.7 0.6 0.2 0
[1] 2fdu.a 0 0.1
0
0 0.3 0.6 - - 0.8 - 0.9 1.0 0.2 0.1
[1] 2fdv.a 0 0.1 0.1
0
0.1 0.7 - - 0.8 - 1.0 1.0 0.4 0.1
[1] 2fdw.d 0 0.3 0.3 0.2
0
0.8 - - 1.1 - 0.4 0.4 0.2 0.1
[1] 2fdy.b 0 0.1 0 0 0
0
- - 0.8 - 0.3 0.2 0 0
[1] 2pg5.a 0 0.4 0.7 0.3 0.7 1.1
-
- 0.4 - 0.6 0.6 0.1 0
[1] 2pg7.a 0 0.2 0.8 0.4 0.6 1.2 -
-
0.1 - 0.7 0.6 0.1 0
[1] 3ebs.a 0.1 0.4 0.6 0 0.3 0.2 - -
0
- 0.8 0.5 0.2 0.1
[1] 3ebs.c 0.1 0.4 0.5 0 0 0.1 - - 0
-
0.5 0.6 0.2 0.1
[1] 3t3q.a 0.1 0.4 0.4 0.2 0.3 0.2 - - 0.2 -
0
0.4 0.1 0.1
[1] 3t3r.b 0 0.1 0.3 0.3 0.5 0.6 - - 1.1 - 0.2
0
0 0
[1] 4ejj.a 0 0 0.4 0.2 0.5 0.8 - - 1.0 - 0.2 0.3
0
0
[1] 4rui.a 0 0.1 0.8 0.4 0.5 0.9 - - 0.5 - 0.4 0.4 0.1
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
1z10.a
1z11.a
2fdu.a
2fdv.a
2fdw.d
2fdy.b
2pg5.a
2pg7.a
3ebs.a
3ebs.c
3t3q.a
3t3r.b
4ejj.a
4rui.a
[1] 1z10.a
0
.06 .12 .14 .11 .14 .04 .04 .11 .09 .09 .11 .09 .04
[1] 1z11.a .06
0
.08 .10 .10 .09 .08 .06 .12 .11 .11 .09 .07 .08
[1] 2fdu.a .12 .08
0
.02 .14 .09 .16 .14 .10 .15 .16 .09 .09 .16
[1] 2fdv.a .14 .10 .02
0
.13 .08 .18 .16 .12 .16 .18 .11 .11 .18
[1] 2fdw.d .11 .10 .14 .13
0
.09 .14 .14 .16 .13 .15 .11 .10 .14
[1] 2fdy.b .14 .09 .09 .08 .09
0
.17 .15 .13 .09 .11 .09 .11 .17
[1] 2pg5.a .04 .08 .16 .18 .14 .17
0
.04 .14 .12 .11 .11 .09 .04
[1] 2pg7.a .04 .06 .14 .16 .14 .15 .04
0
.12 .11 .09 .13 .10 .05
[1] 3ebs.a .11 .12 .10 .12 .16 .13 .14 .12
0
.05 .07 .18 .16 .14
[1] 3ebs.c .09 .11 .15 .16 .13 .09 .12 .11 .05
0
.05 .16 .14 .12
[1] 3t3q.a .09 .11 .16 .18 .15 .11 .11 .09 .07 .05
0
.14 .11 .09
[1] 3t3r.b .11 .09 .09 .11 .11 .09 .11 .13 .18 .16 .14
0
.03 .09
[1] 4ejj.a .09 .07 .09 .11 .10 .11 .09 .10 .16 .14 .11 .03
0
.06
[1] 4rui.a .04 .08 .16 .18 .14 .17 .04 .05 .14 .12 .09 .09 .06
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
1z10.a
1z11.a
2fdu.a
2fdv.a
2fdw.d
2fdy.b
2pg5.a
2pg7.a
3ebs.a
3ebs.c
3t3q.a
3t3r.b
4ejj.a
4rui.a
[1] 1z10.a
0
0.1 0.3 0.3 0.3 0.5 0.2 0.3 0.4 0.3 0.4 0.3 0.2 0.2
[1] 1z11.a 0.1
0
0.2 0.3 0.4 0.4 0.2 0.3 0.3 0.3 0.4 0.3 0.2 0.3
[1] 2fdu.a 0.3 0.2
0
0.1 0.5 0.5 0.4 0.4 0.3 0.4 0.5 0.5 0.4 0.4
[1] 2fdv.a 0.3 0.3 0.1
0
0.5 0.5 0.4 0.5 0.3 0.4 0.5 0.5 0.4 0.4
[1] 2fdw.d 0.3 0.4 0.5 0.5
0
0.6 0.3 0.4 0.6 0.5 0.5 0.5 0.4 0.4
[1] 2fdy.b 0.5 0.4 0.5 0.5 0.6
0
0.5 0.6 0.5 0.5 0.5 0.4 0.4 0.5
[1] 2pg5.a 0.2 0.2 0.4 0.4 0.3 0.5
0
0.2 0.4 0.3 0.4 0.4 0.3 0.3
[1] 2pg7.a 0.3 0.3 0.4 0.5 0.4 0.6 0.2
0
0.5 0.4 0.5 0.5 0.4 0.3
[1] 3ebs.a 0.4 0.3 0.3 0.3 0.6 0.5 0.4 0.5
0
0.3 0.4 0.4 0.4 0.4
[1] 3ebs.c 0.3 0.3 0.4 0.4 0.5 0.5 0.3 0.4 0.3
0
0.3 0.4 0.3 0.4
[1] 3t3q.a 0.4 0.4 0.5 0.5 0.5 0.5 0.4 0.5 0.4 0.3
0
0.4 0.3 0.4
[1] 3t3r.b 0.3 0.3 0.5 0.5 0.5 0.4 0.4 0.5 0.4 0.4 0.4
0
0.2 0.3
[1] 4ejj.a 0.2 0.2 0.4 0.4 0.4 0.4 0.3 0.4 0.4 0.3 0.3 0.2
0
0.3
[1] 4rui.a 0.2 0.3 0.4 0.4 0.4 0.5 0.3 0.3 0.4 0.4 0.4 0.3 0.3
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
1z10.a
1z11.a
2fdu.a
2fdv.a
2fdw.d
2fdy.b
2pg5.a
2pg7.a
3ebs.a
3ebs.c
3t3q.a
3t3r.b
4ejj.a
4rui.a
[1] 1z10.a
0
0.3 0.5 0.5 0.5 0.8 0.3 0.5 0.6 0.6 0.6 0.6 0.4 0.4
[1] 1z11.a 0.3
0
0.3 0.4 0.5 0.8 0.4 0.6 0.6 0.7 0.7 0.6 0.3 0.5
[1] 2fdu.a 0.5 0.3
0
0.1 0.6 0.8 0.6 0.7 0.8 0.8 0.8 0.7 0.5 0.7
[1] 2fdv.a 0.5 0.4 0.1
0
0.6 0.8 0.6 0.8 0.8 0.8 0.9 0.7 0.6 0.7
[1] 2fdw.d 0.5 0.5 0.6 0.6
0
0.9 0.6 0.7 0.8 0.7 0.7 0.8 0.5 0.7
[1] 2fdy.b 0.8 0.8 0.8 0.8 0.9
0
0.9 1.0 1.1 1.1 1.1 0.6 0.8 0.9
[1] 2pg5.a 0.3 0.4 0.6 0.6 0.6 0.9
0
0.4 0.7 0.7 0.6 0.7 0.5 0.5
[1] 2pg7.a 0.5 0.6 0.7 0.8 0.7 1.0 0.4
0
0.7 0.7 0.7 0.8 0.6 0.7
[1] 3ebs.a 0.6 0.6 0.8 0.8 0.8 1.1 0.7 0.7
0
0.3 0.6 0.9 0.7 0.7
[1] 3ebs.c 0.6 0.7 0.8 0.8 0.7 1.1 0.7 0.7 0.3
0
0.6 0.9 0.7 0.7
[1] 3t3q.a 0.6 0.7 0.8 0.9 0.7 1.1 0.6 0.7 0.6 0.6
0
0.8 0.6 0.7
[1] 3t3r.b 0.6 0.6 0.7 0.7 0.8 0.6 0.7 0.8 0.9 0.9 0.8
0
0.5 0.7
[1] 4ejj.a 0.4 0.3 0.5 0.6 0.5 0.8 0.5 0.6 0.7 0.7 0.6 0.5
0
0.5
[1] 4rui.a 0.4 0.5 0.7 0.7 0.7 0.9 0.5 0.7 0.7 0.7 0.7 0.7 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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