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CP2B4_RABIT_22_491_catalytic

Cytochrome P450 2B4 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2B4_RABIT):42:48, 50, 51, 55, 57, 68:71, 73, 75, 100:104, 108, 110:115, 128, 132, 202, 206, 209:219, 238, 290:299, 301, 302, 363, 365:368, 387, 389, 436, 475:47842:48, 50, 51, 55, 57, 68:71, 73, 75, 100:104, 108, 110:115, 128, 132, 202, 206, 209:219, 238, 290:299, 301, 302, 363, 365:368, 387, 389, 436, 475:478
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1po5, 1suo, 2bdm, 2q6n, 3g5n, 3g93, 3kw4, 3me6, 3mvr, 3r1a, 3r1b, 3tk3, 3tmz, 3uas, 4h1n, 4jlt, 4mgj, 5em4, 5iut, 5iuz (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
N
4
2
L
4
3
L
4
4
Q
4
5
M
4
6
D
4
7
R
4
8
G
5
0
L
5
1
V
6
8
Y
6
9
L
7
0
R
7
3
I
1
0
1
V
1
0
4
F
1
0
8
I
1
1
4
F
1
1
5
S
1
2
8
M
1
3
2
F
2
0
2
F
2
0
6
I
2
0
9
S
2
1
0
F
2
1
2
Q
2
1
5
V
2
1
6
E
2
1
8
L
2
1
9
L
2
3
8
L
2
9
5
F
2
9
6
F
2
9
7
A
2
9
8
G
2
9
9
E
3
0
1
T
3
0
2
I
3
6
3
F
3
6
5
G
3
6
6
V
3
6
7
P
3
6
8
E
3
8
7
F
3
8
9
V
4
7
7
G
4
7
8
[1]1suo.a cpz12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2q6n.d 1ci12 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem
[1]3kw4.a cm5,tic51 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3me6.b cge21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3mvr.a cm534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]3r1a.a tb213 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . hem Fe
[1]3uas.a 0bv17 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . hem Fe
[1]4h1n.a cge,cm533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A . . . . . . . . . . . . . hem Fe
[1]4jlt.a 8pr,cm536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5iut.a 32m27 . . . . . . . . . . . . . . . . . . . . W . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5iuz.a cm534 . . . . . . . . . . . . . . . . . . . . W . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]1po5.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]3g5n.d pb2,pb2,pb248 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]3g93.a pb218 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . - . hem Fe
[3]2bdm.a tmi,tmi48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[4]3tmz.a 06x,06x56 . . . . . . - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
N
4
2
L
4
3
L
4
4
Q
4
5
M
4
6
D
4
7
R
4
8
G
5
0
L
5
1
F
5
5
R
5
7
V
6
8
Y
6
9
L
7
0
G
7
1
R
7
3
V
7
5
K
1
0
0
I
1
0
1
A
1
0
2
V
1
0
3
V
1
0
4
F
1
0
8
G
1
1
0
Y
1
1
1
G
1
1
2
V
1
1
3
I
1
1
4
F
1
1
5
S
1
2
8
M
1
3
2
F
2
0
2
F
2
0
6
I
2
0
9
S
2
1
0
S
2
1
1
F
2
1
2
S
2
1
3
S
2
1
4
Q
2
1
5
V
2
1
6
F
2
1
7
E
2
1
8
L
2
1
9
L
2
3
8
L
2
9
0
T
2
9
1
V
2
9
2
L
2
9
3
S
2
9
4
L
2
9
5
F
2
9
6
F
2
9
7
A
2
9
8
G
2
9
9
E
3
0
1
T
3
0
2
I
3
6
3
F
3
6
5
G
3
6
6
V
3
6
7
P
3
6
8
E
3
8
7
F
3
8
9
C
4
3
6
S
4
7
5
G
4
7
6
V
4
7
7
G
4
7
8
[1]1suo.a . . . . * . . . * . . . . * . * . . * . . . . . . . . * . . . . * . . . . . * * . . * * . . * . . * * . * * . * * . * . . . . . . . . * .
[1]2q6n.d . . . . . . . . * . . . . * . * . . * . . . . . . . . . * . . . * . . . . . * * * . * * . . * . . * * . * . . . * . * . . . . . . . . * . hem
[1]3kw4.a . . . . * . . . * . . . . * . * . . * . . . . . . . . . . . . . * . . . . . * * . . * * . . . . . * * . * * . . * . * . . . . . . . . * . hem Fe
[1]3me6.b . . . . . . . . * . . . . * . * . . * . . . . . . . . * . . . . * . . . . . * * . . * * . . * . . * * . * . . . * . * . . . . . . . . * . hem Fe
[1]3mvr.a . . . . * . . . * . . . . * . * . . * . . . . . . . . . . . . . * . . . . . * * . . * * . . . . . * * . * * . . * . . . . . . . . . . * . hem Fe
[1]3r1a.a . . . . . . . . * . . . . * . * . . . . . . . . . . . * . . . . * . . . . . * * * . * * . . * . . * * . * . . . * . . . . . . . . . . . . hem Fe
[1]3uas.a . . . . . . . . * . . . . * . * . . . . . . . . . . . * . . . . * . . . . . * * . . * * . . * . . * * . * * . . * . * . . . . . . . . * . hem Fe
[1]4h1n.a . . . . * . . . * . . . . * . * . . * . . . . . . . . * . . . . * . . . . . * * . . * . . . * . . * * . A * . . . . * . . . . . . . . . . hem Fe
[1]4jlt.a . . . . * . . . * . . . . * . * . . * . . . . . . . . . . . . . * . . . . . * * . . * * . . . . . * * . * * . . * . * . . . . . . . . . . hem Fe
[1]5iut.a . . . . * . . . . . . . . * . * . . * . . . . . . . . * . . . W * . . . . . . * . . . . . . . . . * * . * * . . * . . . . . . . . - . . . hem Fe
[1]5iuz.a . . . . * . . . * . . . . * . * . . * . . . . . . . . . . . . W * . . . . . * * . . * * . . * . . * * . * * . . * . . . . . . . . . . * . hem Fe
[2]1po5.a . . . . * . . . . . . . . * . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . . . . . . . . . . . . hem Fe
[2]3g5n.d . * . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . . * . . . . . . . . . . . . hem Fe
[2]3g93.a . * . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . * . . * . . . . . . . . - - - . hem Fe
[3]2bdm.a . . * * . . . . . . . . . . . * . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . . . . . . . . . . . . hem Fe
[4]3tmz.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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1suo.a:cpz
2q6n.d:1ci
3kw4.a:cm5,tic
3me6.b:cge
3mvr.a:cm5
3r1a.a:tb2
3uas.a:0bv
4h1n.a:cge,cm5
4jlt.a:8pr,cm5
5iut.a:32m
5iuz.a:cm5
1po5.a is apo
3g5n.d:pb2
3g93.a:pb2
2bdm.a:tmi
3tmz.a:06x
[1] 1suo.a
0
1.6 2.2 4.3 0 5.3 1.6 4.5 2.8 4.3 0 - 9.3 1.9 22 12
[1] 2q6n.d 0
0
3.0 1.6 0 1.8 1.0 3.1 2.9 3.1 0 - 9.1 1.4 19 13
[1] 3kw4.a 0.4 1.5
0
5.2 0 3.5 0.6 4.4 1.3 3.8 0 - 11 2.3 21 11
[1] 3me6.b 0 0.1 1.9
0
0 0.8 0.9 2.4 1.6 2.9 0 - 9.7 1.3 18 11
[1] 3mvr.a 0.2 1.6 0.1 5.1
0
3.7 1.3 4.3 1.0 3.2 0 - 10 2.0 21 10
[1] 3r1a.a 0 0 2.0 0.2 0.1
0.6
0.7 2.3 1.6 2.3 0 - 8.1 1.0 20 11
[1] 3uas.a 0.1 1.8 0.2 5.3 0 4.3
0.6
4.1 1.6 3.3 0 - 9.9 1.8 21 11
[1] 4h1n.a 0.4 0.3 2.2 0.9 0 1.3 1.0
0
1.3 2.6 0 - 10 1.7 18 11
[1] 4jlt.a 0.3 1.8 0.1 5.0 0 3.7 1.1 4.2
0.1
2.5 0 - 10 2.2 21 10
[1] 5iut.a 0.2 1.8 0.7 5.3 0.5 4.3 1.1 5.3 1.1
0
0.8 - 5.5 2.0 19 6.4
[1] 5iuz.a 0.4 1.8 0 5.4 0 4.2 1.0 4.5 1.6 3.4
0
- 10 2.8 21 11
[2] 1po5.a 0 0 2.3 0 1.8 1.1 0.7 2.9 2.4 1.1 2.4
-
4.8 0.1 4.3 1.2
[2] 3g5n.d 0 0.1 0.8 0.3 0.5 0.7 0.3 0.9 0.8 0.4 0.5 -
0.2
0.3 9.2 0.5
[2] 3g93.a 0 0 0.2 0.3 0.2 0.7 0.3 0.1 0.1 0 0.2 - 1.7
0.1
8.4 0.3
[3] 2bdm.a 0 0 3.8 0 3.9 0.8 0.6 3.9 4.1 4.6 3.8 - 4.8 0.3
0
0.8
[4] 3tmz.a 0.1 0.3 1.1 3.1 0.6 2.9 1.5 5.6 1.2 0.5 0.7 - 2.9 1.4 17
0.3
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1suo.a
2q6n.d
3kw4.a
3me6.b
3mvr.a
3r1a.a
3uas.a
4h1n.a
4jlt.a
5iut.a
5iuz.a
1po5.a
3g5n.d
3g93.a
2bdm.a
3tmz.a
[1] 1suo.a
0
.18 .17 .14 .17 .17 .14 .17 .18 .24 .15 .51 .46 .45 .54 .32
[1] 2q6n.d .18
0
.20 .10 .17 .09 .16 .13 .19 .27 .17 .52 .46 .46 .50 .33
[1] 3kw4.a .17 .20
0
.15 .04 .23 .08 .13 .04 .16 .05 .51 .43 .42 .53 .31
[1] 3me6.b .14 .10 .15
0
.14 .08 .11 .10 .15 .23 .15 .50 .43 .43 .49 .30
[1] 3mvr.a .17 .17 .04 .14
0
.19 .08 .12 .04 .13 .04 .49 .43 .42 .51 .29
[1] 3r1a.a .17 .09 .23 .08 .19
0
.17 .15 .21 .27 .19 .50 .43 .43 .49 .30
[1] 3uas.a .14 .16 .08 .11 .08 .17
0
.12 .09 .15 .06 .50 .44 .43 .51 .29
[1] 4h1n.a .17 .13 .13 .10 .12 .15 .12
0
.12 .19 .11 .45 .40 .39 .46 .26
[1] 4jlt.a .18 .19 .04 .15 .04 .21 .09 .12
0
.14 .05 .47 .42 .40 .49 .28
[1] 5iut.a .24 .27 .16 .23 .13 .27 .15 .19 .14
0
.13 .40 .37 .37 .44 .23
[1] 5iuz.a .15 .17 .05 .15 .04 .19 .06 .11 .05 .13
0
.49 .43 .42 .51 .28
[2] 1po5.a .51 .52 .51 .50 .49 .50 .50 .45 .47 .40 .49
0
.22 .20 .27 .31
[2] 3g5n.d .46 .46 .43 .43 .43 .43 .44 .40 .42 .37 .43 .22
0
.04 .25 .24
[2] 3g93.a .45 .46 .42 .43 .42 .43 .43 .39 .40 .37 .42 .20 .04
0
.25 .23
[3] 2bdm.a .54 .50 .53 .49 .51 .49 .51 .46 .49 .44 .51 .27 .25 .25
0
.39
[4] 3tmz.a .32 .33 .31 .30 .29 .30 .29 .26 .28 .23 .28 .31 .24 .23 .39
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.8 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
1suo.a
2q6n.d
3kw4.a
3me6.b
3mvr.a
3r1a.a
3uas.a
4h1n.a
4jlt.a
5iut.a
5iuz.a
1po5.a
3g5n.d
3g93.a
2bdm.a
3tmz.a
[1] 1suo.a
0
0.7 0.7 0.5 0.8 0.8 0.5 0.7 0.8 1.4 0.6 9.4 7.3 7.5 9.8 1.9
[1] 2q6n.d 0.7
0
1.1 0.7 1.1 0.5 0.9 1.0 1.2 1.6 1.0 9.3 7.5 7.7 9.8 2.1
[1] 3kw4.a 0.7 1.1
0
0.9 0.3 1.3 0.5 0.5 0.5 1.3 0.3 9.4 7.2 7.4 9.6 1.5
[1] 3me6.b 0.5 0.7 0.9
0
1.0 0.7 0.7 0.8 1.0 1.4 0.8 9.3 7.3 7.6 9.7 1.9
[1] 3mvr.a 0.8 1.1 0.3 1.0
0
1.3 0.5 0.5 0.5 1.3 0.4 9.4 7.2 7.4 9.7 1.4
[1] 3r1a.a 0.8 0.5 1.3 0.7 1.3
0
1.0 1.1 1.4 1.7 1.1 9.2 7.6 7.8 9.8 2.3
[1] 3uas.a 0.5 0.9 0.5 0.7 0.5 1.0
0
0.5 0.6 1.3 0.4 9.3 7.2 7.4 9.7 1.7
[1] 4h1n.a 0.7 1.0 0.5 0.8 0.5 1.1 0.5
0
0.6 1.2 0.5 9.3 7.2 7.5 9.7 1.6
[1] 4jlt.a 0.8 1.2 0.5 1.0 0.5 1.4 0.6 0.6
0
1.1 0.5 9.4 7.2 7.3 9.7 1.5
[1] 5iut.a 1.4 1.6 1.3 1.4 1.3 1.7 1.3 1.2 1.1
0
1.3 9.4 7.0 7.2 9.5 1.4
[1] 5iuz.a 0.6 1.0 0.3 0.8 0.4 1.1 0.4 0.5 0.5 1.3
0
9.3 7.2 7.4 9.7 1.6
[2] 1po5.a 9.4 9.3 9.4 9.3 9.4 9.2 9.3 9.3 9.4 9.4 9.3
0
12 12 10 9.7
[2] 3g5n.d 7.3 7.5 7.2 7.3 7.2 7.6 7.2 7.2 7.2 7.0 7.2 12
0
1.0 10 6.8
[2] 3g93.a 7.5 7.7 7.4 7.6 7.4 7.8 7.4 7.5 7.3 7.2 7.4 12 1.0
0
10 7.0
[3] 2bdm.a 9.8 9.8 9.6 9.7 9.7 9.8 9.7 9.7 9.7 9.5 9.7 10 10 10
0
9.3
[4] 3tmz.a 1.9 2.1 1.5 1.9 1.4 2.3 1.7 1.6 1.5 1.4 1.6 9.7 6.8 7.0 9.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.5 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
1suo.a
2q6n.d
3kw4.a
3me6.b
3mvr.a
3r1a.a
3uas.a
4h1n.a
4jlt.a
5iut.a
5iuz.a
1po5.a
3g5n.d
3g93.a
2bdm.a
3tmz.a
[1] 1suo.a
0
1.2 0.9 1.1 1.1 1.3 0.8 1.1 1.1 1.8 1.1 10 8.1 8.3 11 2.1
[1] 2q6n.d 1.2
0
1.4 1.0 1.5 0.8 1.3 1.1 1.5 2.0 1.4 9.9 8.3 8.5 11 2.4
[1] 3kw4.a 0.9 1.4
0
1.2 0.6 1.5 0.6 0.8 0.6 1.3 0.8 10 8.0 8.2 10 1.8
[1] 3me6.b 1.1 1.0 1.2
0
1.3 0.8 1.1 1.0 1.4 1.9 1.3 9.8 8.1 8.3 10 2.3
[1] 3mvr.a 1.1 1.5 0.6 1.3
0
1.6 0.8 0.8 0.5 1.5 0.8 10 8.0 8.2 10 1.8
[1] 3r1a.a 1.3 0.8 1.5 0.8 1.6
0
1.3 1.2 1.6 2.0 1.4 9.9 8.4 8.6 11 2.5
[1] 3uas.a 0.8 1.3 0.6 1.1 0.8 1.3
0
0.9 0.8 1.5 0.9 9.9 8.0 8.2 10 2.0
[1] 4h1n.a 1.1 1.1 0.8 1.0 0.8 1.2 0.9
0
0.8 1.4 0.9 10 8.1 8.2 10 1.9
[1] 4jlt.a 1.1 1.5 0.6 1.4 0.5 1.6 0.8 0.8
0
1.2 0.8 10 8.0 8.2 10 1.8
[1] 5iut.a 1.8 2.0 1.3 1.9 1.5 2.0 1.5 1.4 1.2
0
1.6 10 8.0 8.1 10 1.7
[1] 5iuz.a 1.1 1.4 0.8 1.3 0.8 1.4 0.9 0.9 0.8 1.6
0
9.9 8.0 8.2 10 1.8
[2] 1po5.a 10 9.9 10 9.8 10 9.9 9.9 10 10 10 9.9
0
12 12 11 10
[2] 3g5n.d 8.1 8.3 8.0 8.1 8.0 8.4 8.0 8.1 8.0 8.0 8.0 12
0
1.1 10 7.7
[2] 3g93.a 8.3 8.5 8.2 8.3 8.2 8.6 8.2 8.2 8.2 8.1 8.2 12 1.1
0
10 7.9
[3] 2bdm.a 11 11 10 10 10 11 10 10 10 10 10 11 10 10
0
10
[4] 3tmz.a 2.1 2.4 1.8 2.3 1.8 2.5 2.0 1.9 1.8 1.7 1.8 10 7.7 7.9 10
0
[Binding site full-atom RMSD matrix]







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