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DNPH1_RAT_9_152

2'-deoxynucleoside 5'-phosphate N-hydrolase 1 [2'-deoxynucleoside 5'-phosphate N- hydrolase 1 family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (DNPH1_RAT):R: Substrate binding (15:19)
20, 44:46, 51:58, 60, 64, 65, 68, 69, 87, 89, 90, 93
15:20, 44:46, 51:58, 60, 64, 65, 68, 69, 87, 89, 90, 93
A2 (DNPH1_RAT):R: Substrate binding
shared with homodimeric partner (117:119)
117:119

Full PDB list

4fyh, 4fyi, 4fyk, 4kxl, 4kxm, 4kxn, 4p5d (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2
C
1
5
G
1
6
S
1
7
I
1
8
R
1
9
G
2
0
E
4
4
H
4
5
V
4
6
L
5
1
E
5
2
E
5
7
A
5
8
F
6
4
I
6
5
Q
6
8
D
6
9
S
8
7
G
8
9
V
9
0
E
9
3
S
1
1
7
A
1
1
8
M
1
1
9
[1]4fyh.d tr527 . . . . . . . . . - - - - . . . N . . . . . . .
[1]4fyk.a sra23 . . . . . . . . - - - - - . . . N . . . . . . .
[1]4kxl.a 6c628 . . . . . . . . . - - . . . . . N . . . . . . .
[1]4kxm.c 6ia28 . . . . . . . . . - - - - . . . N . . . . . . .
[1]4kxn.a 6k629 . . . . . . . . . - - - - . . . N . . . . . . .
[1]4p5d.a n6p32 . . . . . . . . . . . . . . . . N . . . . . . .

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 A2
C
1
5
G
1
6
S
1
7
I
1
8
R
1
9
G
2
0
E
4
4
H
4
5
V
4
6
L
5
1
E
5
2
P
5
3
L
5
4
G
5
5
E
5
6
E
5
7
A
5
8
G
6
0
F
6
4
I
6
5
Q
6
8
D
6
9
S
8
7
G
8
9
V
9
0
E
9
3
S
1
1
7
A
1
1
8
M
1
1
9
[1]4fyh.d . . . . . . . . . - - - - - - - - . . . . N . . . . . . .
[1]4fyk.a . . . . . . . . - - - - - - - - - . . . . N . . . . . . .
[1]4kxl.a . . . . . . . . . - - - - - - . . . . . . N . . . . . . .
[1]4kxm.c . . . . . . . * . - - - - - - - - . . . . N . . . . . . .
[1]4kxn.a . . . . . . . . . - - - - - - - - . . . . N . . . . . . .
[1]4p5d.a . . . . . . . . . . . . . . . . . . . . . N . . . . . . .

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
4fyh.d:tr5
4fyk.a:sra
4kxl.a:6c6
4kxm.c:6ia
4kxn.a:6k6
4p5d.a:n6p
[1] 4fyh.d
0.1
0.8 0.2 0.2 1.7 0.3
[1] 4fyk.a 0.3
0.1
0.2 0.1 0.1 0.2
[1] 4kxl.a 0.1 0.6
0
0.5 1.8 0.6
[1] 4kxm.c 0.1 1.1 0.3
0
1.2 0.3
[1] 4kxn.a 0.1 0.1 0.1 0
0.1
0.1
[1] 4p5d.a 0.1 0.6 0.1 0.2 0.9
0.2
[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
4fyh.d
4fyk.a
4kxl.a
4kxm.c
4kxn.a
4p5d.a
[1] 4fyh.d
0
.07 .03 .02 .06 .04
[1] 4fyk.a .07
0
.08 .06 .01 .03
[1] 4kxl.a .03 .08
0
.04 .08 .04
[1] 4kxm.c .02 .06 .04
0
.05 .03
[1] 4kxn.a .06 .01 .08 .05
0
.04
[1] 4p5d.a .04 .03 .04 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
4fyh.d
4fyk.a
4kxl.a
4kxm.c
4kxn.a
4p5d.a
[1] 4fyh.d
0
1.1 1.2 0.8 1.2 0.5
[1] 4fyk.a 1.1
0
1.6 1.1 1.6 1.1
[1] 4kxl.a 1.2 1.6
0
1.6 0.3 1.7
[1] 4kxm.c 0.8 1.1 1.6
0
1.5 0.6
[1] 4kxn.a 1.2 1.6 0.3 1.5
0
1.3
[1] 4p5d.a 0.5 1.1 1.7 0.6 1.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
4fyh.d
4fyk.a
4kxl.a
4kxm.c
4kxn.a
4p5d.a
[1] 4fyh.d
0
1.9 1.2 1.1 1.5 0.9
[1] 4fyk.a 1.9
0
2.1 1.9 2.3 1.8
[1] 4kxl.a 1.2 2.1
0
1.3 0.9 1.6
[1] 4kxm.c 1.1 1.9 1.3
0
1.4 0.7
[1] 4kxn.a 1.5 2.3 0.9 1.4
0
1.3
[1] 4p5d.a 0.9 1.8 1.6 0.7 1.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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