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CP2C9_HUMAN_20_490_peripheralWarfarin

Cytochrome P450 2C9 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2C9_HUMAN):45, 47, 50, 69, 74, 97:108, 113, 114, 200, 201, 204, 205, 208, 209, 212:215, 217, 218, 233, 236, 237, 240, 292, 293, 296, 297, 300, 301, 304, 361:367, 388, 474, 476, 477, 47945, 47, 50, 69, 74, 97:108, 113, 114, 200, 201, 204, 205, 208, 209, 212:215, 217, 218, 233, 236, 237, 240, 292, 293, 296, 297, 300, 301, 304, 361:367, 388, 474, 476, 477, 479
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1og2, 1og5, 1r9o, 4nz2, 5a5i, 5a5j, 5k7k, 5w0c, 5x23, 5x24, 5xxi

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
I
4
5
F
6
9
I
7
4
R
9
7
G
9
8
F
1
0
0
L
1
0
2
A
1
0
3
A
1
0
6
N
1
0
7
R
1
0
8
V
1
1
3
F
1
1
4
L
2
0
1
N
2
0
4
I
2
0
5
L
2
0
8
S
2
0
9
Q
2
1
4
I
2
1
5
N
2
1
7
N
2
1
8
L
2
3
3
N
2
3
6
V
2
3
7
M
2
4
0
V
2
9
2
D
2
9
3
G
2
9
6
A
2
9
7
E
3
0
0
T
3
0
1
T
3
0
4
L
3
6
1
L
3
6
2
P
3
6
3
T
3
6
4
S
3
6
5
L
3
6
6
P
3
6
7
L
3
8
8
N
4
7
4
F
4
7
6
A
4
7
7
V
4
7
9
[1]1r9o.a flp18 . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5a5i.a xi124 . . . . . - . . . . . . . . . . . . - - - - . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5a5j.a 6yf28 . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5k7k.a 6rj30 . . . . . . . . . . . . . . . . . . - - - - . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[1]5w0c.a 9w625 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[2]1og2.a none . . . . . . . . . . . . . . . . . . . V . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[2]1og5.a swf23 . . . . . . . . . . . . . . . . . . . V . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[2]4nz2.b 2qj27 . . . . . . . . . . . . . . . . . . . V . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[3]5x23.a lsn,lsn60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . hem Fe
[3]5x24.a lsn30 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . hem Fe
[3]5xxi.a lsn,lsn60 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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
I
4
5
I
4
7
I
5
0
F
6
9
I
7
4
R
9
7
G
9
8
I
9
9
F
1
0
0
P
1
0
1
L
1
0
2
A
1
0
3
E
1
0
4
R
1
0
5
A
1
0
6
N
1
0
7
R
1
0
8
V
1
1
3
F
1
1
4
K
2
0
0
L
2
0
1
N
2
0
4
I
2
0
5
L
2
0
8
S
2
0
9
W
2
1
2
I
2
1
3
Q
2
1
4
I
2
1
5
N
2
1
7
N
2
1
8
L
2
3
3
N
2
3
6
V
2
3
7
M
2
4
0
V
2
9
2
D
2
9
3
G
2
9
6
A
2
9
7
E
3
0
0
T
3
0
1
T
3
0
4
L
3
6
1
L
3
6
2
P
3
6
3
T
3
6
4
S
3
6
5
L
3
6
6
P
3
6
7
L
3
8
8
N
4
7
4
F
4
7
6
A
4
7
7
V
4
7
9
[1]1r9o.a . . . . . . . . * * . . . . . . . . . . . . * . . . . - - - - . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[1]5a5i.a . . . . . . . . - - . . . . . . . . . . . . * . . . . - - - - . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[1]5a5j.a . . . . . . . . * * . . . . . . * . * . . . . . . . . - - - - . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[1]5k7k.a . . . . . . . . * * . . * . . . * . . . . . . * . . . - - - - . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[1]5w0c.a . . . . . . . . * . . . . . . . . . . . . . * . . . . . . . . . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[2]1og2.a . . . * . . . . * . . . . . * . . . * . . . . . . . . . V * . . . . * . . . . . . . . . . . . . . . . * . . Fe
[2]1og5.a . . . * . . . . . . . * . . * . . . . . . . . . . . . . V * . . . . * . . . . . . . . . . . . . . . . * . . Fe
[2]4nz2.b . . . * . . . . . . . . . . * . . . * . . . * . . . . . V * . . . . * . . . . . . . . . . . . . . . . * . . hem Fe
[3]5x23.a . . . . . . . . . . . . . . * . * . * . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . T . hem Fe
[3]5x24.a . . . . . . . . . . * . . . * . * . * . . . . * . . . * . . * . . . . . . . . . . . . . . . . . . . . * . . hem Fe
[3]5xxi.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
1r9o.a:flp
5a5i.a:xi1
5a5j.a:6yf
5k7k.a:6rj
5w0c.a:9w6
1og2.a is apo
1og5.a:swf
4nz2.b:2qj
5x23.a:lsn
5x24.a:lsn
5xxi.a:lsn
[1] 1r9o.a
0
0.7 1.1 1.0 2.3 - 6.6 0.4 11 2.3 12
[1] 5a5i.a 0
0.2
1.2 0.7 0.4 - 2.7 0.3 7.8 1.8 7.9
[1] 5a5j.a 0.8 1.4
0.1
1.4 3.1 - 5.9 2.0 12 4.3 13
[1] 5k7k.a 0.5 0.9 1.9
0.1
4.7 - 7.2 4.0 10 4.0 13
[1] 5w0c.a 0 0.3 0.8 1.6
0
- 1.8 0.3 7.3 2.5 8.9
[2] 1og2.a 0 0.6 0.6 0.5 2.8
-
1.8 0.5 9.1 2.0 7.9
[2] 1og5.a 0 0.6 0.5 0.5 2.7 -
0
0.4 8.9 1.8 6.8
[2] 4nz2.b 0.1 0.5 0.9 0.9 2.3 - 1.8
0
7.8 1.9 7.2
[3] 5x23.a 0 0.5 2.1 1.0 6.0 - 2.5 1.4
1.0
0.4 1.4
[3] 5x24.a 0 0.4 1.9 1.2 5.8 - 3.8 1.6 5.0
0.2
5.2
[3] 5xxi.a 0 0.2 1.7 1.0 5.7 - 4.4 1.1 1.7 0.2
1.9
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (3 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
1r9o.a
5a5i.a
5a5j.a
5k7k.a
5w0c.a
1og2.a
1og5.a
4nz2.b
5x23.a
5x24.a
5xxi.a
[1] 1r9o.a
0
.18 .09 .17 .14 .33 .35 .35 .44 .41 .45
[1] 5a5i.a .18
0
.23 .27 .12 .29 .28 .27 .32 .29 .34
[1] 5a5j.a .09 .23
0
.17 .18 .33 .37 .36 .40 .37 .43
[1] 5k7k.a .17 .27 .17
0
.20 .35 .37 .38 .42 .41 .44
[1] 5w0c.a .14 .12 .18 .20
0
.26 .25 .25 .35 .33 .37
[2] 1og2.a .33 .29 .33 .35 .26
0
.08 .11 .33 .37 .38
[2] 1og5.a .35 .28 .37 .37 .25 .08
0
.11 .36 .41 .40
[2] 4nz2.b .35 .27 .36 .38 .25 .11 .11
0
.31 .39 .33
[3] 5x23.a .44 .32 .40 .42 .35 .33 .36 .31
0
.13 .07
[3] 5x24.a .41 .29 .37 .41 .33 .37 .41 .39 .13
0
.10
[3] 5xxi.a .45 .34 .43 .44 .37 .38 .40 .33 .07 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 3.1 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
1r9o.a
5a5i.a
5a5j.a
5k7k.a
5w0c.a
1og2.a
1og5.a
4nz2.b
5x23.a
5x24.a
5xxi.a
[1] 1r9o.a
0
0.5 0.7 1.0 1.5 2.9 2.9 2.7 2.9 2.9 2.9
[1] 5a5i.a 0.5
0
0.8 0.9 1.2 2.9 2.9 2.7 2.9 2.8 2.9
[1] 5a5j.a 0.7 0.8
0
0.8 1.8 2.9 2.8 2.8 3.0 3.0 3.0
[1] 5k7k.a 1.0 0.9 0.8
0
1.8 2.9 2.8 2.8 3.0 2.9 3.0
[1] 5w0c.a 1.5 1.2 1.8 1.8
0
3.7 3.7 3.6 4.1 4.1 4.2
[2] 1og2.a 2.9 2.9 2.9 2.9 3.7
0
0.4 0.6 1.9 2.0 1.9
[2] 1og5.a 2.9 2.9 2.8 2.8 3.7 0.4
0
0.6 2.0 2.0 2.0
[2] 4nz2.b 2.7 2.7 2.8 2.8 3.6 0.6 0.6
0
1.8 1.8 1.8
[3] 5x23.a 2.9 2.9 3.0 3.0 4.1 1.9 2.0 1.8
0
0.5 0.3
[3] 5x24.a 2.9 2.8 3.0 2.9 4.1 2.0 2.0 1.8 0.5
0
0.5
[3] 5xxi.a 2.9 2.9 3.0 3.0 4.2 1.9 2.0 1.8 0.3 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 2.0 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
1r9o.a
5a5i.a
5a5j.a
5k7k.a
5w0c.a
1og2.a
1og5.a
4nz2.b
5x23.a
5x24.a
5xxi.a
[1] 1r9o.a
0
0.7 1.1 1.5 2.1 4.2 4.1 4.0 3.9 3.9 4.0
[1] 5a5i.a 0.7
0
1.1 1.4 1.9 4.2 4.1 4.1 3.8 3.9 4.0
[1] 5a5j.a 1.1 1.1
0
1.1 2.4 4.3 4.2 4.2 4.0 3.9 4.1
[1] 5k7k.a 1.5 1.4 1.1
0
2.5 4.4 4.3 4.3 4.1 4.0 4.2
[1] 5w0c.a 2.1 1.9 2.4 2.5
0
4.8 4.7 4.5 4.9 5.0 5.0
[2] 1og2.a 4.2 4.2 4.3 4.4 4.8
0
0.8 1.1 2.9 3.0 3.0
[2] 1og5.a 4.1 4.1 4.2 4.3 4.7 0.8
0
1.0 2.9 3.1 3.0
[2] 4nz2.b 4.0 4.1 4.2 4.3 4.5 1.1 1.0
0
2.9 3.1 3.0
[3] 5x23.a 3.9 3.8 4.0 4.1 4.9 2.9 2.9 2.9
0
1.1 0.8
[3] 5x24.a 3.9 3.9 3.9 4.0 5.0 3.0 3.1 3.1 1.1
0
1.0
[3] 5xxi.a 4.0 4.0 4.1 4.2 5.0 3.0 3.0 3.0 0.8 1.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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