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CP2B6_HUMAN_20_491_catalytic

Cytochrome P450 2B6 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2B6_HUMAN):101, 104, 108, 114, 115, 206, 209, 210, 297:302, 362, 363, 366, 367, 436, 477:480101, 104, 108, 114, 115, 206, 209, 210, 297:302, 362, 363, 366, 367, 436, 477:480
Cofactors (cF):hem
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
I
1
0
1
V
1
0
4
I
1
1
4
F
1
1
5
F
2
0
6
I
2
0
9
S
2
1
0
F
2
9
7
A
2
9
8
T
3
0
0
E
3
0
1
T
3
0
2
L
3
6
3
V
3
6
7
V
4
7
7
[1]3qoa.a 3qo13 . . . . . . . . . . . . . . . hem Fe
[1]3qu8.a 3qu7 . . . . . . . . . . . . . . . hem Fe
[1]4i91.a tmh10 . . . . . . . . . . . . . . . hem Fe
[1]4rql.b sne10 . . . . . . . . . . . . . . . hem Fe
[1]4rrt.a 3v410 . . . . . . . . . . . . . . . hem Fe
[1]5uap.a 82s11 . . . . . . . . . . . . . . . hem Fe
[1]5uda.a cae10 . . . . . . . . . . . . . . . Fe
[1]5uec.a 85d11 . . . . . . . . . . . . . . . hem Fe
[1]5ufg.a 85d11 . . V . . . . . . . . . . . . Fe
[2]3ibd.a cpz12 . . . . . . . . . . . . . . . hem Fe
[2]3ua5.a 06x28 . . . . . . . . . . . . . . . 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
1
V
1
0
4
F
1
0
8
I
1
1
4
F
1
1
5
F
2
0
6
I
2
0
9
S
2
1
0
F
2
9
7
A
2
9
8
G
2
9
9
T
3
0
0
E
3
0
1
T
3
0
2
L
3
6
2
L
3
6
3
G
3
6
6
V
3
6
7
C
4
3
6
V
4
7
7
G
4
7
8
K
4
7
9
I
4
8
0
[1]3qoa.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]3qu8.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]4i91.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]4rql.b . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]4rrt.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]5uap.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]5uda.a . . . . . * . * . . . . . * . . . . . * . . . Fe
[1]5uec.a . . . . . * . * . . . . . . . . . . . * . . . hem Fe
[1]5ufg.a . . . V . * . * . . . . . . . . . . . * . . . Fe
[2]3ibd.a . . . . . . . . * . . . . . . . . . . * . . . hem Fe
[2]3ua5.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
3qoa.a:3qo
3qu8.a:3qu
4i91.a:tmh
4rql.b:sne
4rrt.a:3v4
5uap.a:82s
5uda.a:cae
5uec.a:85d
5ufg.a:85d
3ibd.a:cpz
3ua5.a:06x
[1] 3qoa.a
0.1
0.3 0 0 0 0.1 0 0.1 0.3 0.4 4.3
[1] 3qu8.a 0.1
0
0 0 0 0.1 0 0 0.3 0.1 3.7
[1] 4i91.a 0.5 0.4
0
0 0 0 0 0.1 0.2 0.4 4.1
[1] 4rql.b 0.3 0.3 0
0
0 0 0 0 0.2 0.4 3.8
[1] 4rrt.a 0.7 0.3 0.1 0.1
0
0.4 0.2 0.1 0.2 0.4 4.5
[1] 5uap.a 0.7 0.4 0 0.1 0
0
0 0 0.2 0.4 4.1
[1] 5uda.a 0.2 0.5 0 0.1 0 0
0
0.1 0.2 0.4 3.7
[1] 5uec.a 0.5 0.3 0 0.1 0 0 0
0
0.2 0.4 3.9
[1] 5ufg.a 0.5 0.5 0 0 0 0 0 0
0.2
0.4 3.8
[2] 3ibd.a 2.3 0.2 1.8 1.8 1.1 1.3 1.2 1.3 1.7
0
1.9
[2] 3ua5.a 2.8 0.8 1.8 2.2 1.5 2.0 1.1 2.3 1.7 0.5
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
3qoa.a
3qu8.a
4i91.a
4rql.b
4rrt.a
5uap.a
5uda.a
5uec.a
5ufg.a
3ibd.a
3ua5.a
[1] 3qoa.a
0
.04 .04 .06 .05 .04 .04 .05 .05 .22 .34
[1] 3qu8.a .04
0
.03 .03 .07 .03 .03 .03 .03 .19 .30
[1] 4i91.a .04 .03
0
.03 .06 .01 .03 .03 .01 .20 .31
[1] 4rql.b .06 .03 .03
0
.05 .04 .03 .01 .03 .20 .31
[1] 4rrt.a .05 .07 .06 .05
0
.07 .07 .04 .06 .20 .32
[1] 5uap.a .04 .03 .01 .04 .07
0
.03 .03 .01 .20 .31
[1] 5uda.a .04 .03 .03 .03 .07 .03
0
.03 .03 .21 .32
[1] 5uec.a .05 .03 .03 .01 .04 .03 .03
0
.02 .20 .31
[1] 5ufg.a .05 .03 .01 .03 .06 .01 .03 .02
0
.18 .30
[2] 3ibd.a .22 .19 .20 .20 .20 .20 .21 .20 .18
0
.16
[2] 3ua5.a .34 .30 .31 .31 .32 .31 .32 .31 .30 .16
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
3qoa.a
3qu8.a
4i91.a
4rql.b
4rrt.a
5uap.a
5uda.a
5uec.a
5ufg.a
3ibd.a
3ua5.a
[1] 3qoa.a
0
0.5 0.4 0.3 0.4 0.5 0.4 0.4 0.5 0.8 2.1
[1] 3qu8.a 0.5
0
0.4 0.4 0.4 0.4 0.3 0.4 0.5 0.8 2.0
[1] 4i91.a 0.4 0.4
0
0.2 0.2 0.1 0.2 0.1 0.2 0.6 1.9
[1] 4rql.b 0.3 0.4 0.2
0
0.1 0.2 0.2 0.2 0.3 0.6 1.9
[1] 4rrt.a 0.4 0.4 0.2 0.1
0
0.2 0.2 0.2 0.3 0.6 2.0
[1] 5uap.a 0.5 0.4 0.1 0.2 0.2
0
0.2 0.1 0.2 0.6 1.9
[1] 5uda.a 0.4 0.3 0.2 0.2 0.2 0.2
0
0.2 0.3 0.7 2.0
[1] 5uec.a 0.4 0.4 0.1 0.2 0.2 0.1 0.2
0
0.2 0.6 1.9
[1] 5ufg.a 0.5 0.5 0.2 0.3 0.3 0.2 0.3 0.2
0
0.5 1.9
[2] 3ibd.a 0.8 0.8 0.6 0.6 0.6 0.6 0.7 0.6 0.5
0
1.7
[2] 3ua5.a 2.1 2.0 1.9 1.9 2.0 1.9 2.0 1.9 1.9 1.7
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
3qoa.a
3qu8.a
4i91.a
4rql.b
4rrt.a
5uap.a
5uda.a
5uec.a
5ufg.a
3ibd.a
3ua5.a
[1] 3qoa.a
0
0.8 0.5 0.5 0.6 0.7 0.5 0.6 0.7 1.6 2.4
[1] 3qu8.a 0.8
0
0.8 0.8 0.9 0.9 0.8 0.8 0.9 1.5 2.3
[1] 4i91.a 0.5 0.8
0
0.2 0.5 0.4 0.3 0.2 0.4 1.5 2.3
[1] 4rql.b 0.5 0.8 0.2
0
0.5 0.5 0.3 0.2 0.5 1.5 2.3
[1] 4rrt.a 0.6 0.9 0.5 0.5
0
0.4 0.6 0.5 0.7 1.5 2.3
[1] 5uap.a 0.7 0.9 0.4 0.5 0.4
0
0.4 0.4 0.6 1.5 2.3
[1] 5uda.a 0.5 0.8 0.3 0.3 0.6 0.4
0
0.3 0.5 1.6 2.4
[1] 5uec.a 0.6 0.8 0.2 0.2 0.5 0.4 0.3
0
0.4 1.5 2.3
[1] 5ufg.a 0.7 0.9 0.4 0.5 0.7 0.6 0.5 0.4
0
1.5 2.2
[2] 3ibd.a 1.6 1.5 1.5 1.5 1.5 1.5 1.6 1.5 1.5
0
2.0
[2] 3ua5.a 2.4 2.3 2.3 2.3 2.3 2.3 2.4 2.3 2.2 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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