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DNK_DROME_1_233

Deoxynucleoside kinase [DCK/DGK family]

Composition of the binding site

Protein chains monomer
A1 (DNK_DROME):29:34, 52, 54, 57, 66, 69, 70, 80, 81, 84, 88, 104:106, 109, 110, 114, 118, 167, 169, 171:17329:34, 52, 54, 57, 66, 69, 70, 80, 81, 84, 88, 104:106, 109, 110, 114, 118, 167, 169, 171:173

Full PDB list

1j90, 1oe0, 1ot3, 1zm7, 1zmx, 2jcs, 2jj8, 2vp0, 2vp2, 2vp4, 2vp5, 2vp6, 2vp9, 2vpp, 2vqs (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
I
2
9
G
3
0
S
3
1
G
3
2
K
3
3
T
3
4
E
5
2
V
5
4
W
5
7
L
6
6
M
6
9
Y
7
0
F
8
0
Q
8
1
V
8
4
M
8
8
E
1
0
4
R
1
0
5
S
1
0
6
S
1
0
9
A
1
1
0
F
1
1
4
M
1
1
8
R
1
6
7
R
1
6
9
E
1
7
2
[1]1ot3.a thm17 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zm7.a ttp29 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1zm7.d mg,ttp30 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2jcs.a mg,ttp30 . . . . . . D . . . . . . . . . . . . . . . . . . .
[1]2jj8.d azz19 . . . . . . . . . . . . . . . . . . . . . . . . - -
[1]2vp2.a dgt31 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vp4.a dcp28 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vp5.b dcz16 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vp6.b 5fu17 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vp9.d doc15 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2vpp.b geo18 . . . . . . . . . . . . . . . . . . . . . . . . - .
[1]2vqs.b bvd19 . . . . . . . . . . . . . . . . . . . . . . . . - -

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

[download in TSV format]
   
PDB.ch
A1
I
2
9
G
3
0
S
3
1
G
3
2
K
3
3
T
3
4
E
5
2
V
5
4
W
5
7
L
6
6
M
6
9
Y
7
0
F
8
0
Q
8
1
V
8
4
M
8
8
E
1
0
4
R
1
0
5
S
1
0
6
S
1
0
9
A
1
1
0
F
1
1
4
M
1
1
8
R
1
6
7
R
1
6
9
E
1
7
1
E
1
7
2
S
1
7
3
[1]1ot3.a . . . . . . . . . . . . . . . . . * . . . . . . . . * .
[1]1zm7.a . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]1zm7.d . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]2jcs.a . . . . . . D . . . . . . . . . . . . . . . . . . . * .
[1]2jj8.d . . . . . . . . . . . . . . . . . * . . . . . . - - - -
[1]2vp2.a . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]2vp4.a . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[1]2vp5.b . . . . . . . . . . . . . . . . . * . . . . . . . . * .
[1]2vp6.b . . . . . . . . . . . . . . . . . * . . . . . . . . * .
[1]2vp9.d . . . . . . . . . . . . . . . . . * . . . . . . . . * .
[1]2vpp.b . . . . . . . . . . . . . . . . . * . . . . . . - . * .
[1]2vqs.b . . . . . . * . . . . . . . . . . * . . . . . . - - - -

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
1ot3.a:thm
1zm7.a:ttp
1zm7.d:mg,ttp
2jcs.a:mg,ttp
2jj8.d:azz
2vp2.a:dgt
2vp4.a:dcp
2vp5.b:dcz
2vp6.b:5fu
2vp9.d:doc
2vpp.b:geo
2vqs.b:bvd
[1] 1ot3.a
0
2.1 2.4 2.3 2.1 2.5 2.1 0.1 0.1 0 0.1 0.2
[1] 1zm7.a 0.3
0
0.3 0.4 1.9 0.5 0.2 0.3 0.2 0.3 0.4 0.6
[1] 1zm7.d 0.3 0
0.3
0.4 1.9 0.5 0.2 0.3 0.2 0.3 0.4 0.6
[1] 2jcs.a 0.5 0 0.2
0.3
2.0 0.5 0.2 0.3 0.2 0.2 0.4 0.2
[1] 2jj8.d 0.1 2.2 2.2 2.3
0
2.2 2.0 0.2 0.3 0 0.1 0.3
[1] 2vp2.a 0.4 0.1 0.2 0.2 1.5
0
0.1 0.2 0.3 0.2 0.3 0.3
[1] 2vp4.a 0.3 0.3 0.4 0.5 1.9 0.8
0.1
0.3 0.1 0.1 0.3 0.4
[1] 2vp5.b 0 2.2 2.0 2.3 1.9 2.1 2.0
0.1
0.1 0 0.1 0.6
[1] 2vp6.b 0.1 2.2 2.3 2.3 1.9 2.6 1.7 0.1
0.2
0 0.1 0.4
[1] 2vp9.d 0.2 1.8 2.0 1.9 1.4 1.8 1.6 0.1 0.1
0
0.2 0.2
[1] 2vpp.b 0.2 2.0 2.3 2.4 1.8 2.3 2.0 0.1 0.2 0
0.1
0.7
[1] 2vqs.b 0.1 2.1 2.3 2.2 0 1.9 1.8 0.2 0.3 0 0.2
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
1ot3.a
1zm7.a
1zm7.d
2jcs.a
2jj8.d
2vp2.a
2vp4.a
2vp5.b
2vp6.b
2vp9.d
2vpp.b
2vqs.b
[1] 1ot3.a
0
.13 .13 .12 .13 .14 .13 .05 .04 .06 .05 .11
[1] 1zm7.a .13
0
0 .01 .19 .04 .04 .10 .14 .13 .13 .18
[1] 1zm7.d .13 0
0
.01 .19 .04 .04 .10 .14 .13 .13 .18
[1] 2jcs.a .12 .01 .01
0
.19 .04 .05 .10 .13 .12 .13 .18
[1] 2jj8.d .13 .19 .19 .19
0
.18 .17 .14 .12 .10 .13 .03
[1] 2vp2.a .14 .04 .04 .04 .18
0
.04 .13 .15 .10 .14 .16
[1] 2vp4.a .13 .04 .04 .05 .17 .04
0
.10 .14 .10 .12 .16
[1] 2vp5.b .05 .10 .10 .10 .14 .13 .10
0
.03 .05 .03 .12
[1] 2vp6.b .04 .14 .14 .13 .12 .15 .14 .03
0
.05 .02 .11
[1] 2vp9.d .06 .13 .13 .12 .10 .10 .10 .05 .05
0
.04 .08
[1] 2vpp.b .05 .13 .13 .13 .13 .14 .12 .03 .02 .04
0
.11
[1] 2vqs.b .11 .18 .18 .18 .03 .16 .16 .12 .11 .08 .11
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1ot3.a
1zm7.a
1zm7.d
2jcs.a
2jj8.d
2vp2.a
2vp4.a
2vp5.b
2vp6.b
2vp9.d
2vpp.b
2vqs.b
[1] 1ot3.a
0
1.3 1.3 1.3 0.6 1.3 1.4 0.9 0.3 0.8 0.3 0.5
[1] 1zm7.a 1.3
0
0 0.2 1.1 0.4 0.4 0.8 1.3 1.3 1.1 1.0
[1] 1zm7.d 1.3 0
0
0.2 1.1 0.4 0.4 0.8 1.3 1.3 1.1 1.0
[1] 2jcs.a 1.3 0.2 0.2
0
1.0 0.4 0.4 0.8 1.2 1.3 1.1 1.0
[1] 2jj8.d 0.6 1.1 1.1 1.0
0
1.0 1.1 0.7 0.6 0.5 0.6 0.4
[1] 2vp2.a 1.3 0.4 0.4 0.4 1.0
0
0.3 0.9 1.3 1.4 1.1 0.9
[1] 2vp4.a 1.4 0.4 0.4 0.4 1.1 0.3
0
0.9 1.4 1.5 1.2 1.0
[1] 2vp5.b 0.9 0.8 0.8 0.8 0.7 0.9 0.9
0
0.8 0.9 0.6 0.6
[1] 2vp6.b 0.3 1.3 1.3 1.2 0.6 1.3 1.4 0.8
0
0.6 0.3 0.5
[1] 2vp9.d 0.8 1.3 1.3 1.3 0.5 1.4 1.5 0.9 0.6
0
0.4 0.4
[1] 2vpp.b 0.3 1.1 1.1 1.1 0.6 1.1 1.2 0.6 0.3 0.4
0
0.5
[1] 2vqs.b 0.5 1.0 1.0 1.0 0.4 0.9 1.0 0.6 0.5 0.4 0.5
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.8 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
1ot3.a
1zm7.a
1zm7.d
2jcs.a
2jj8.d
2vp2.a
2vp4.a
2vp5.b
2vp6.b
2vp9.d
2vpp.b
2vqs.b
[1] 1ot3.a
0
2.6 2.6 2.5 0.6 2.7 2.6 2.2 0.4 2.1 0.5 0.6
[1] 1zm7.a 2.6
0
0.1 0.2 1.6 0.6 0.5 1.4 1.6 1.8 1.6 1.5
[1] 1zm7.d 2.6 0.1
0
0.2 1.6 0.6 0.5 1.4 1.6 1.8 1.5 1.5
[1] 2jcs.a 2.5 0.2 0.2
0
1.3 0.5 0.5 1.1 1.4 1.6 1.3 1.3
[1] 2jj8.d 0.6 1.6 1.6 1.3
0
1.7 1.7 0.9 0.6 0.5 0.7 0.5
[1] 2vp2.a 2.7 0.6 0.6 0.5 1.7
0
0.5 1.6 1.8 2.0 1.7 1.7
[1] 2vp4.a 2.6 0.5 0.5 0.5 1.7 0.5
0
1.5 1.7 2.0 1.7 1.6
[1] 2vp5.b 2.2 1.4 1.4 1.1 0.9 1.6 1.5
0
0.9 1.1 0.6 0.9
[1] 2vp6.b 0.4 1.6 1.6 1.4 0.6 1.8 1.7 0.9
0
0.7 0.6 0.6
[1] 2vp9.d 2.1 1.8 1.8 1.6 0.5 2.0 2.0 1.1 0.7
0
0.6 0.5
[1] 2vpp.b 0.5 1.6 1.5 1.3 0.7 1.7 1.7 0.6 0.6 0.6
0
0.7
[1] 2vqs.b 0.6 1.5 1.5 1.3 0.5 1.7 1.6 0.9 0.6 0.5 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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