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CP2C5_RABIT_20_487

Cytochrome P450 2C5 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2C5_RABIT):102, 103, 106, 113, 114, 201, 204, 205, 208, 213, 237, 293, 294, 298, 359, 363, 473102, 103, 106, 113, 114, 201, 204, 205, 208, 213, 237, 293, 294, 298, 359, 363, 473
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1dt6, 1n6b, 1nr6

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
L
1
0
3
V
1
0
6
A
1
1
3
F
1
1
4
L
2
0
1
N
2
0
4
V
2
0
5
A
2
3
7
G
2
9
3
A
2
9
4
T
2
9
8
L
3
5
9
L
3
6
3
F
4
7
3
[1]1dt6.a none . . . . . . . . . . . . . . hem Fe
[1]1n6b.a dmz23 . . . . . . . . . . . . . . hem Fe
[1]1nr6.a dif19 . . . . . . . . . . . . . . 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

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PDB.ch
A1 cF Me
I
1
0
2
L
1
0
3
V
1
0
6
A
1
1
3
F
1
1
4
L
2
0
1
N
2
0
4
V
2
0
5
L
2
0
8
L
2
1
3
A
2
3
7
G
2
9
3
A
2
9
4
T
2
9
8
L
3
5
9
L
3
6
3
F
4
7
3
[1]1dt6.a . . . . . . . * . - . . . . . . . hem Fe
[1]1n6b.a . . . . . . . . . . . . . . . . . hem Fe
[1]1nr6.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
1dt6.a is apo
1n6b.a:dmz
1nr6.a:dif
[1] 1dt6.a
-
0.6 0
[1] 1n6b.a -
0
0.4
[1] 1nr6.a - 0.4
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
1dt6.a
1n6b.a
1nr6.a
[1] 1dt6.a
0
.06 .06
[1] 1n6b.a .06
0
.05
[1] 1nr6.a .06 .05
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 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
1dt6.a
1n6b.a
1nr6.a
[1] 1dt6.a
0
1.9 2.4
[1] 1n6b.a 1.9
0
1.0
[1] 1nr6.a 2.4 1.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1dt6.a
1n6b.a
1nr6.a
[1] 1dt6.a
0
2.6 3.1
[1] 1n6b.a 2.6
0
1.4
[1] 1nr6.a 3.1 1.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

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