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CP119_SULAC_1_368

Cytochrome P450 119 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP119_SULAC):151:156, 161, 209, 210, 213, 254, 317, 353, 354151:156, 161, 209, 210, 213, 254, 317, 353, 354
Cofactors (cF):hem/hem.res
Metals (Me):Fe

Full PDB list

1f4t, 1f4u, 1io7, 1io8, 1io9, 4tt5, 4tuv, 4wpd, 4wqj, 5bv5 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
V
1
5
1
A
1
5
2
F
1
5
3
L
1
5
5
G
1
5
6
I
1
6
1
A
2
0
9
G
2
1
0
T
2
1
3
V
2
5
4
V
3
5
3
L
3
5
4
[1]1f4t.a pim11 . . . . . . . . . . . . hem Fe
[1]4tuv.a cpz12 . . . . . . . . . . . . hem.res Fe
[1]4wpd.a 3sq12 . . . . . . . . . . . . hem Fe
[1]4wqj.a 36y12 . . . . . . . . . . . . hem Fe
[1]5bv5.a none - - - - - . . . A . . . hem Fe
[1]5bv5.b pim11 - - - - - - . . A . . . hem Fe
[2]1io8.a none . . . . . . . . . . . . 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
V
1
5
1
A
1
5
2
F
1
5
3
R
1
5
4
L
1
5
5
G
1
5
6
I
1
6
1
A
2
0
9
G
2
1
0
T
2
1
3
V
2
5
4
C
3
1
7
V
3
5
3
L
3
5
4
[1]1f4t.a . . . . . . . . . . . . . . hem Fe
[1]4tuv.a . . . . . . . . . . . . . . hem.res Fe
[1]4wpd.a . . . . . . . . . . . . . . hem Fe
[1]4wqj.a . . . . . . . . . . . . . . hem Fe
[1]5bv5.a - - - - - - . . . A . H . . hem Fe
[1]5bv5.b - - - - - - - . . A . H . . hem Fe
[2]1io8.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
1f4t.a:pim
4tuv.a:cpz
4wpd.a:3sq
4wqj.a:36y
5bv5.a is apo
5bv5.b:pim
1io8.a is apo
[1] 1f4t.a
0
0.4 0 0.7 - 0.1 -
[1] 4tuv.a 0.1
0
0.1 0 - 0.1 -
[1] 4wpd.a 0 0.4
0
0.7 - 0.1 -
[1] 4wqj.a 0.1 0.1 0.1
0
- 0.1 -
[1] 5bv5.a 0.1 0 0.1 0
-
0 -
[1] 5bv5.b 0 0 0 0 -
0
-
[2] 1io8.a 5.5 7.1 6.3 7.3 - 5.4
-
[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
1f4t.a
4tuv.a
4wpd.a
4wqj.a
5bv5.a
5bv5.b
1io8.a
[1] 1f4t.a
0
.06 0 .06 .06 .06 .58
[1] 4tuv.a .06
0
.06 0 .02 .01 .52
[1] 4wpd.a 0 .06
0
.06 .06 .06 .58
[1] 4wqj.a .06 0 .06
0
.02 .01 .52
[1] 5bv5.a .06 .02 .06 .02
0
.01 .54
[1] 5bv5.b .06 .01 .06 .01 .01
0
.54
[2] 1io8.a .58 .52 .58 .52 .54 .54
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 6.0 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
1f4t.a
4tuv.a
4wpd.a
4wqj.a
5bv5.a
5bv5.b
1io8.a
[1] 1f4t.a
0
5.1 0.3 5.1 6.8 0.9 4.4
[1] 4tuv.a 5.1
0
5.1 0.4 7.1 1.0 5.0
[1] 4wpd.a 0.3 5.1
0
5.2 6.8 0.9 4.3
[1] 4wqj.a 5.1 0.4 5.2
0
7.1 1.0 5.1
[1] 5bv5.a 6.8 7.1 6.8 7.1
0
0.5 5.2
[1] 5bv5.b 0.9 1.0 0.9 1.0 0.5
0
1.2
[2] 1io8.a 4.4 5.0 4.3 5.1 5.2 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 4.3 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
1f4t.a
4tuv.a
4wpd.a
4wqj.a
5bv5.a
5bv5.b
1io8.a
[1] 1f4t.a
0
6.3 0.6 6.4 7.4 1.1 6.1
[1] 4tuv.a 6.3
0
6.3 0.7 8.3 1.0 6.4
[1] 4wpd.a 0.6 6.3
0
6.4 7.6 0.9 6.0
[1] 4wqj.a 6.4 0.7 6.4
0
8.3 1.0 6.5
[1] 5bv5.a 7.4 8.3 7.6 8.3
0
0.5 6.0
[1] 5bv5.b 1.1 1.0 0.9 1.0 0.5
0
1.2
[2] 1io8.a 6.1 6.4 6.0 6.5 6.0 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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