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FABI_HELPY_1_275

Enoyl-[acyl-carrier-protein] reductase [NADH] FabI [Short-chain dehydrogenases/reductases (SDR) family. FabI subfamily]

Composition of the binding site

Protein chains monomer
A1 (FABI_HELPY):93:95, 100, 145, 155, 158, 162, 190, 195, 196, 199, 20293:95, 100, 145, 155, 158, 162, 190, 195, 196, 199, 202
Cofactors (cF):nad

Full PDB list

2pd3, 2pd4

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
A
9
3
F
9
4
A
9
5
L
1
0
0
Y
1
4
5
Y
1
5
5
M
1
5
8
P
1
9
0
A
1
9
5
S
1
9
6
I
1
9
9
F
2
0
2
[1]2pd3.b tcl17 . . . . . . . . . . . . nad
[1]2pd4.b dcn16 . . . . . . . . . . . . nad

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
A
9
3
F
9
4
A
9
5
L
1
0
0
Y
1
4
5
Y
1
5
5
M
1
5
8
K
1
6
2
P
1
9
0
A
1
9
5
S
1
9
6
I
1
9
9
F
2
0
2
[1]2pd3.b . . . . . . . . . . . . . nad
[1]2pd4.b . . . . . . . . . . . . . nad

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
2pd3.b:tcl
2pd4.b:dcn
[1] 2pd3.b
0.1
0.3
[1] 2pd4.b 0.2
0.1
[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
2pd3.b
2pd4.b
[1] 2pd3.b
0
.02
[1] 2pd4.b .02
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.1 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
2pd3.b
2pd4.b
[1] 2pd3.b
0
0.2
[1] 2pd4.b 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
2pd3.b
2pd4.b
[1] 2pd3.b
0
0.3
[1] 2pd4.b 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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