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BPHB_COMTE_1_281

Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase [Short-chain dehydrogenases/reductases (SDR) family]

Composition of the binding site

Protein chains monomer
A1 (BPHB_COMTE):90, 142, 143, 149, 150, 155, 191, 204, 206, 207, 209, 212, 213, 25590, 142, 143, 149, 150, 155, 191, 204, 206, 207, 209, 212, 213, 255
Cofactors (cF):nad

Full PDB list

2y93, 2y99, 3zv3, 3zv4, 3zv5, 3zv6 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
W
9
0
S
1
4
2
N
1
4
3
N
1
4
9
G
1
5
0
Y
1
5
5
L
1
9
1
I
2
0
4
L
2
0
9
M
2
1
2
L
2
1
3
M
2
5
5
[1]2y93.a none . . . . . . . - . . . .
[1]3zv5.a bpy14 . . . . . . . . . . . . nad
[1]3zv6.a 4hb14 . . . . . . . . . . . . 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
W
9
0
S
1
4
2
N
1
4
3
N
1
4
9
G
1
5
0
Y
1
5
5
L
1
9
1
I
2
0
4
S
2
0
6
V
2
0
7
L
2
0
9
M
2
1
2
L
2
1
3
M
2
5
5
[1]2y93.a . . . . . . . - . . . . . .
[1]3zv5.a . . . . . . . . . . . . . . nad
[1]3zv6.a . . . . . . . . . . . . . . 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
2y93.a is apo
3zv5.a:bpy
3zv6.a:4hb
[1] 2y93.a
-
0.5 0.4
[1] 3zv5.a -
0.1
0.4
[1] 3zv6.a - 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
2y93.a
3zv5.a
3zv6.a
[1] 2y93.a
0
.06 .04
[1] 3zv5.a .06
0
.02
[1] 3zv6.a .04 .02
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
2y93.a
3zv5.a
3zv6.a
[1] 2y93.a
0
3.9 4.1
[1] 3zv5.a 3.9
0
0.5
[1] 3zv6.a 4.1 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
2y93.a
3zv5.a
3zv6.a
[1] 2y93.a
0
4.2 4.4
[1] 3zv5.a 4.2
0
0.7
[1] 3zv6.a 4.4 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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