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CP46A_HUMAN_50_500

Cholesterol 24-hydroxylase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP46A_HUMAN):79:82, 108:112, 121, 126, 127, 219, 222, 226:229, 298, 301, 302, 305, 306, 367:369, 371, 437, 472:47579:82, 108:112, 121, 126, 127, 219, 222, 226:229, 298, 301, 302, 305, 306, 367:369, 371, 437, 472:475
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2q9f, 2q9g, 3mdm, 3mdr, 3mdt, 3mdv, 4enh, 4fia, 4j14

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
V
7
9
F
8
0
H
8
1
M
1
0
8
Y
1
0
9
R
1
1
0
A
1
1
1
L
1
1
2
F
1
2
1
V
1
2
6
S
1
2
7
L
2
1
9
I
2
2
2
R
2
2
6
N
2
2
7
T
2
9
8
I
3
0
1
A
3
0
2
E
3
0
5
T
3
0
6
A
3
6
7
W
3
6
8
G
3
6
9
F
3
7
1
E
4
7
2
A
4
7
4
T
4
7
5
[1]2q9g.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3mdm.a fjz20 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3mdr.a gjz10 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3mdt.b vor25 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3mdv.a cl625 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4enh.a fvx22 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]4fia.a 0u9,19858 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]2q9f.a c3s32 . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]4j14.a x2n51 . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
V
7
9
F
8
0
H
8
1
K
8
2
M
1
0
8
Y
1
0
9
R
1
1
0
A
1
1
1
L
1
1
2
F
1
2
1
V
1
2
6
S
1
2
7
L
2
1
9
I
2
2
2
R
2
2
6
N
2
2
7
T
2
2
8
L
2
2
9
T
2
9
8
I
3
0
1
A
3
0
2
E
3
0
5
T
3
0
6
A
3
6
7
W
3
6
8
G
3
6
9
F
3
7
1
C
4
3
7
E
4
7
2
Q
4
7
3
A
4
7
4
T
4
7
5
[1]2q9g.a . * * * . . . . . . . . . . * . . . . . . . . . . . . . . . . . hem Fe
[1]3mdm.a . * * . . . . . * * . . . . * . . . . . . . . . * . . . . . . . hem Fe
[1]3mdr.a . * * . . . . . * * . . . . * . . - . . . . . . . . . . . . . . hem Fe
[1]3mdt.b . * * . . . . . . . . . . . * . . - . . . . . . . . . . . . . . hem Fe
[1]3mdv.a . * * . . . . . . . . . . . * . . - . . . . . . . . . . . . . . hem Fe
[1]4enh.a . * . * . . . . * . . . . . * . . . . . . . . . . . . . . . . . hem Fe
[1]4fia.a . * * . . . . . * * . . . . . . . - . . . . . . . . . . . . . . hem Fe
[2]2q9f.a . . * . . . . . * * . . . . . * . . . . . . . . . . . . . . . . hem Fe
[2]4j14.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
2q9g.a is apo
3mdm.a:fjz
3mdr.a:gjz
3mdt.b:vor
3mdv.a:cl6
4enh.a:fvx
4fia.a:0u9,198
2q9f.a:c3s
4j14.a:x2n
[1] 2q9g.a
-
0.2 0 0.6 0.2 0 2.0 6.0 9.9
[1] 3mdm.a -
0
0 1.7 2.7 0.3 3.9 7.6 9.0
[1] 3mdr.a - 1.0
0
1.1 1.8 0.1 4.4 8.2 10
[1] 3mdt.b - 0.6 0
0
0.2 0 2.5 6.9 11
[1] 3mdv.a - 0.5 0 0.4
0
0 2.1 7.4 11
[1] 4enh.a - 0.7 0 1.3 0.8
0
4.0 6.9 8.6
[1] 4fia.a - 0.4 0 1.5 2.1 0.1
0
4.8 11
[2] 2q9f.a - 0.1 0 1.6 2.1 0.6 1.0
0.2
4.5
[2] 4j14.a - 0.5 0 1.5 0.8 0.4 0.1 0.1
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
2q9g.a
3mdm.a
3mdr.a
3mdt.b
3mdv.a
4enh.a
4fia.a
2q9f.a
4j14.a
[1] 2q9g.a
0
.22 .18 .13 .16 .11 .16 .48 .37
[1] 3mdm.a .22
0
.22 .27 .29 .15 .19 .43 .43
[1] 3mdr.a .18 .22
0
.10 .10 .14 .20 .48 .42
[1] 3mdt.b .13 .27 .10
0
.07 .19 .23 .50 .40
[1] 3mdv.a .16 .29 .10 .07
0
.20 .27 .54 .44
[1] 4enh.a .11 .15 .14 .19 .20
0
.20 .47 .38
[1] 4fia.a .16 .19 .20 .23 .27 .20
0
.43 .38
[2] 2q9f.a .48 .43 .48 .50 .54 .47 .43
0
.23
[2] 4j14.a .37 .43 .42 .40 .44 .38 .38 .23
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
2q9g.a
3mdm.a
3mdr.a
3mdt.b
3mdv.a
4enh.a
4fia.a
2q9f.a
4j14.a
[1] 2q9g.a
0
1.2 0.7 0.5 0.5 0.7 0.7 2.1 1.7
[1] 3mdm.a 1.2
0
0.8 1.0 0.9 1.1 0.7 2.1 1.8
[1] 3mdr.a 0.7 0.8
0
0.8 0.6 0.7 0.7 2.1 1.7
[1] 3mdt.b 0.5 1.0 0.8
0
0.6 0.8 0.9 2.0 1.7
[1] 3mdv.a 0.5 0.9 0.6 0.6
0
0.7 0.8 1.9 1.6
[1] 4enh.a 0.7 1.1 0.7 0.8 0.7
0
0.7 2.2 1.8
[1] 4fia.a 0.7 0.7 0.7 0.9 0.8 0.7
0
1.9 1.5
[2] 2q9f.a 2.1 2.1 2.1 2.0 1.9 2.2 1.9
0
1.9
[2] 4j14.a 1.7 1.8 1.7 1.7 1.6 1.8 1.5 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
2q9g.a
3mdm.a
3mdr.a
3mdt.b
3mdv.a
4enh.a
4fia.a
2q9f.a
4j14.a
[1] 2q9g.a
0
1.7 1.3 1.1 1.1 1.0 1.4 3.5 3.0
[1] 3mdm.a 1.7
0
1.4 1.6 1.4 1.4 1.3 3.4 3.0
[1] 3mdr.a 1.3 1.4
0
1.1 0.9 1.4 1.4 3.2 2.9
[1] 3mdt.b 1.1 1.6 1.1
0
0.8 1.4 1.5 3.2 3.0
[1] 3mdv.a 1.1 1.4 0.9 0.8
0
1.3 1.4 3.1 2.9
[1] 4enh.a 1.0 1.4 1.4 1.4 1.3
0
1.1 3.5 3.0
[1] 4fia.a 1.4 1.3 1.4 1.5 1.4 1.1
0
3.2 2.8
[2] 2q9f.a 3.5 3.4 3.2 3.2 3.1 3.5 3.2
0
2.8
[2] 4j14.a 3.0 3.0 2.9 3.0 2.9 3.0 2.8 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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