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DYR_CHICK_1_189

Dihydrofolate reductase [Dihydrofolate reductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (DYR_CHICK):D: DHFR (7:9, 22, 30, 31, 34, 56, 115)
R: Substrate binding (30, 31, 34)
7:9, 22, 30, 31, 34, 56, 115
Cofactors (cF):nap/tap
Metals (Me):Ca

Full PDB list

1dr1, 1dr2, 1dr3, 1dr4, 1dr5, 1dr6, 1dr7, 8dfr (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
I
7
V
8
A
9
L
2
2
E
3
0
Y
3
1
F
3
4
T
5
6
V
1
1
5
[1]1dr2.a none . . . . . . . . . tap Ca
[1]1dr6.a hbi17 . . . . . . . . . nap Ca

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
I
7
V
8
A
9
L
2
2
E
3
0
Y
3
1
F
3
4
T
5
6
V
1
1
5
[1]1dr2.a . . . . . . . . . tap Ca
[1]1dr6.a . . . . . . . . . nap Ca

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
1dr2.a is apo
1dr6.a:hbi
[1] 1dr2.a
-
0.1
[1] 1dr6.a -
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
1dr2.a
1dr6.a
[1] 1dr2.a
0
.01
[1] 1dr6.a .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
1dr2.a
1dr6.a
[1] 1dr2.a
0
0.2
[1] 1dr6.a 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
1dr2.a
1dr6.a
[1] 1dr2.a
0
0.9
[1] 1dr6.a 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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