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CP2C8_HUMAN_20_490

Cytochrome P450 2C8 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2C8_HUMAN):97:100, 102, 103, 106, 107, 113, 114, 200, 201, 204, 205, 208, 209, 213, 214, 217, 236, 237, 240, 241, 292, 296, 297, 300, 301, 362, 365:367, 476, 47797:100, 102, 103, 106, 107, 113, 114, 200, 201, 204, 205, 208, 209, 213, 214, 217, 236, 237, 240, 241, 292, 296, 297, 300, 301, 362, 365:367, 476, 477
Cofactors (cF):hem/plm
Metals (Me):Fe

Full PDB list

1pq2, 2nnh, 2nni, 2nnj, 2vn0

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
9
7
G
9
8
N
9
9
S
1
0
0
I
1
0
2
S
1
0
3
I
1
0
6
T
1
0
7
I
1
1
3
S
1
1
4
R
2
0
0
F
2
0
1
N
2
0
4
F
2
0
5
L
2
0
8
N
2
0
9
I
2
1
3
N
2
1
7
N
2
3
6
V
2
3
7
T
2
4
0
R
2
4
1
A
2
9
2
V
2
9
6
A
2
9
7
E
3
0
0
T
3
0
1
V
3
6
2
G
3
6
5
V
3
6
6
P
3
6
7
I
4
7
6
V
4
7
7
[1]1pq2.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2nnh.a rea,rea44 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2nni.a mtk41 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2nnj.a 22525 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2vn0.a tdz31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm 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
R
9
7
G
9
8
N
9
9
S
1
0
0
I
1
0
2
S
1
0
3
I
1
0
6
T
1
0
7
I
1
1
3
S
1
1
4
R
2
0
0
F
2
0
1
N
2
0
4
F
2
0
5
L
2
0
8
N
2
0
9
I
2
1
3
Q
2
1
4
N
2
1
7
N
2
3
6
V
2
3
7
T
2
4
0
R
2
4
1
A
2
9
2
V
2
9
6
A
2
9
7
E
3
0
0
T
3
0
1
V
3
6
2
G
3
6
5
V
3
6
6
P
3
6
7
I
4
7
6
V
4
7
7
[1]1pq2.a . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2nnh.a . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . hem,plm Fe
[1]2nni.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2nnj.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem,plm Fe
[1]2vn0.a . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . hem,plm 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
1pq2.a is apo
2nnh.a:rea
2nni.a:mtk
2nnj.a:225
2vn0.a:tdz
[1] 1pq2.a
-
4.5 0.4 0.2 0.6
[1] 2nnh.a -
0
1.8 0.8 0.5
[1] 2nni.a - 2.6
0
0.4 0
[1] 2nnj.a - 3.2 0.6
0
0.3
[1] 2vn0.a - 2.6 1.3 0.8
0.1
[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
1pq2.a
2nnh.a
2nni.a
2nnj.a
2vn0.a
[1] 1pq2.a
0
.22 .09 .10 .14
[1] 2nnh.a .22
0
.15 .16 .14
[1] 2nni.a .09 .15
0
.05 .06
[1] 2nnj.a .10 .16 .05
0
.09
[1] 2vn0.a .14 .14 .06 .09
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1pq2.a
2nnh.a
2nni.a
2nnj.a
2vn0.a
[1] 1pq2.a
0
1.0 0.5 0.5 0.6
[1] 2nnh.a 1.0
0
0.9 0.9 0.9
[1] 2nni.a 0.5 0.9
0
0.4 0.5
[1] 2nnj.a 0.5 0.9 0.4
0
0.4
[1] 2vn0.a 0.6 0.9 0.5 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1pq2.a
2nnh.a
2nni.a
2nnj.a
2vn0.a
[1] 1pq2.a
0
1.4 0.9 0.9 1.2
[1] 2nnh.a 1.4
0
1.2 1.3 1.0
[1] 2nni.a 0.9 1.2
0
0.8 1.1
[1] 2nnj.a 0.9 1.3 0.8
0
1.0
[1] 2vn0.a 1.2 1.0 1.1 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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