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DFRA_VITVI_1_337

Dihydroflavonol 4-reductase [NAD(P)-dependent epimerase/dehydratase family. Dihydroflavonol-4-reductase subfamily]

Composition of the binding site

Protein chains monomer
A1 (DFRA_VITVI):88, 90, 128:130, 133, 134, 163, 164, 190:192, 204, 205, 208, 222, 227, 29288, 90, 128:130, 133, 134, 163, 164, 190:192, 204, 205, 208, 222, 227, 292
Cofactors (cF):nap

Full PDB list

2c29, 2iod, 2nnl, 3bxx, 3c1t (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
M
8
8
F
9
0
S
1
2
8
A
1
2
9
G
1
3
0
N
1
3
3
I
1
3
4
Y
1
6
3
F
1
6
4
P
1
9
0
T
1
9
1
L
1
9
2
P
2
0
4
S
2
0
5
T
2
0
8
I
2
2
2
Q
2
2
7
[1]2c29.d dqh22 . . . . . . . . . . . . . . . . . nap
[1]2iod.b myc23 . - . . . . . . . . . . . . . . . nap
[1]2nnl.d erd21 . . . . . . . . . . . . . . . . . nap
[1]3bxx.a none . . . . . . . . . . . . . . . . . nap
[1]3bxx.c que22 . . . . . . . . . . . . . . . . . nap

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
M
8
8
F
9
0
S
1
2
8
A
1
2
9
G
1
3
0
N
1
3
3
I
1
3
4
Y
1
6
3
F
1
6
4
P
1
9
0
T
1
9
1
L
1
9
2
P
2
0
4
S
2
0
5
T
2
0
8
I
2
2
2
Q
2
2
7
F
2
9
2
[1]2c29.d . . . . . . . . . . . . . . . . . . nap
[1]2iod.b . - . . . . . . . . . . . . . . . . nap
[1]2nnl.d . . . . . . . . . . . . . . . . . . nap
[1]3bxx.a . . . . . . . . . . . . . . . . . . nap
[1]3bxx.c . . . . . . . . . . . . . . . . . . nap

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
2c29.d:dqh
2iod.b:myc
2nnl.d:erd
3bxx.a is apo
3bxx.c:que
[1] 2c29.d
0
0.3 0.1 - 0.5
[1] 2iod.b 0.1
0.1
0.1 - 0.1
[1] 2nnl.d 0.2 0.3
0.3
- 0.3
[1] 3bxx.a 0.1 0.2 0.1
-
0.2
[1] 3bxx.c 0.2 0.1 0.1 -
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
2c29.d
2iod.b
2nnl.d
3bxx.a
3bxx.c
[1] 2c29.d
0
.02 .02 .03 .03
[1] 2iod.b .02
0
.01 .01 .01
[1] 2nnl.d .02 .01
0
.02 .02
[1] 3bxx.a .03 .01 .02
0
.01
[1] 3bxx.c .03 .01 .02 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
2c29.d
2iod.b
2nnl.d
3bxx.a
3bxx.c
[1] 2c29.d
0
0.7 0.2 2.0 2.0
[1] 2iod.b 0.7
0
0.6 0.9 0.8
[1] 2nnl.d 0.2 0.6
0
2.0 1.9
[1] 3bxx.a 2.0 0.9 2.0
0
0.3
[1] 3bxx.c 2.0 0.8 1.9 0.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 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
2c29.d
2iod.b
2nnl.d
3bxx.a
3bxx.c
[1] 2c29.d
0
1.5 0.2 3.5 3.4
[1] 2iod.b 1.5
0
1.4 0.8 0.7
[1] 2nnl.d 0.2 1.4
0
3.4 3.4
[1] 3bxx.a 3.5 0.8 3.4
0
0.3
[1] 3bxx.c 3.4 0.7 3.4 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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