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HCD2_RAT_1_261

3-hydroxyacyl-CoA dehydrogenase type-2 [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (HCD2_RAT):95, 165, 168, 205, 206, 208:210, 213, 21495, 165, 168, 205, 206, 208:210, 213, 214
Cofactors (cF):nad

Full PDB list

1e3s, 1e3w, 1e6w (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
A
9
5
Q
1
6
5
Y
1
6
8
L
2
0
5
L
2
0
6
T
2
0
8
[1]1e3w.d aae7 . . . . . . nad
[1]1e6w.c est20 . . . . . - nad
[1]1e6w.d none . . . . . . 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
5
Q
1
6
5
Y
1
6
8
L
2
0
5
L
2
0
6
T
2
0
8
L
2
0
9
P
2
1
0
V
2
1
3
R
2
1
4
[1]1e3w.d . . . . . . * * . . nad
[1]1e6w.c . . . . . - - - - - nad
[1]1e6w.d . . . . . . * * . . 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
1e3w.d:aae
1e6w.c:est
1e6w.d is apo
[1] 1e3w.d
0.1
2.6 -
[1] 1e6w.c 0
0
-
[1] 1e6w.d 0.1 2.6
-
[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
1e3w.d
1e6w.c
1e6w.d
[1] 1e3w.d
0
.23 0
[1] 1e6w.c .23
0
.23
[1] 1e6w.d 0 .23
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1e3w.d
1e6w.c
1e6w.d
[1] 1e3w.d
0
0.6 0.3
[1] 1e6w.c 0.6
0
0.5
[1] 1e6w.d 0.3 0.5
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

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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
1e3w.d
1e6w.c
1e6w.d
[1] 1e3w.d
0
0.4 0.3
[1] 1e6w.c 0.4
0
0.4
[1] 1e6w.d 0.3 0.4
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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