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CP2AD_HUMAN_24_494_catalytic

Cytochrome P450 2A13 [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CP2AD_HUMAN):107, 111, 117, 118, 209, 241, 296, 297, 300, 301, 305, 365, 366, 370, 480107, 111, 117, 118, 209, 241, 296, 297, 300, 301, 305, 365, 366, 370, 480
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

2p85, 3t3s, 4ejg, 4ejh, 4eji (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
F
1
0
7
F
1
1
1
A
1
1
7
F
1
1
8
F
2
0
9
N
2
9
7
F
3
0
0
A
3
0
1
T
3
0
5
L
3
6
6
L
3
7
0
F
4
8
0
[1]2p85.a ind,ind18 . . . . . . . . . . . . hem Fe
[1]3t3s.b 9pl15 . . . . . . . . . . . . hem Fe
[1]4ejg.b nct12 . . . . . . . . . . . . hem Fe
[1]4ejh.a 0qa15 . . . . . . . . . . . . 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
F
1
0
7
F
1
1
1
A
1
1
7
F
1
1
8
F
2
0
9
L
2
4
1
L
2
9
6
N
2
9
7
F
3
0
0
A
3
0
1
T
3
0
5
M
3
6
5
L
3
6
6
L
3
7
0
F
4
8
0
[1]2p85.a . . . . . . . . . . . . . . . hem Fe
[1]3t3s.b . . . . . . . . . . . . . . . hem Fe
[1]4ejg.b . . . . . . . . . . . . . . . hem Fe
[1]4ejh.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
2p85.a:ind
3t3s.b:9pl
4ejg.b:nct
4ejh.a:0qa
[1] 2p85.a
0
0.5 0.2 0.4
[1] 3t3s.b 0
0.3
0.1 0
[1] 4ejg.b 0 0.5
0
0.1
[1] 4ejh.a 0 0.2 0
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
2p85.a
3t3s.b
4ejg.b
4ejh.a
[1] 2p85.a
0
.03 .03 .03
[1] 3t3s.b .03
0
.03 .01
[1] 4ejg.b .03 .03
0
.03
[1] 4ejh.a .03 .01 .03
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2p85.a
3t3s.b
4ejg.b
4ejh.a
[1] 2p85.a
0
0.4 0.3 0.3
[1] 3t3s.b 0.4
0
0.3 0.3
[1] 4ejg.b 0.3 0.3
0
0.2
[1] 4ejh.a 0.3 0.3 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2p85.a
3t3s.b
4ejg.b
4ejh.a
[1] 2p85.a
0
0.7 1.0 0.6
[1] 3t3s.b 0.7
0
1.0 0.5
[1] 4ejg.b 1.0 1.0
0
0.9
[1] 4ejh.a 0.6 0.5 0.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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