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5NTD_HUMAN_24_549

5'-nucleotidase [5'-nucleotidase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (5NTD_HUMAN):R: Substrate binding (500, 506)
36, 38, 47, 52, 85, 116:118, 121, 184:186, 220, 243, 245, 282, 354, 390, 392, 393, 395, 417, 446, 447
36, 38, 47, 52, 85, 116:118, 121, 184:186, 220, 243, 245, 282, 354, 390, 392, 393, 395, 417, 446, 447, 500, 506

Full PDB list

4h1s, 4h1y, 4h2b, 4h2f, 4h2g, 4h2i (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
D
3
6
H
3
8
D
4
7
D
8
5
N
1
1
7
H
1
1
8
H
2
2
0
H
2
4
3
N
2
4
5
R
3
5
4
N
3
9
0
G
3
9
2
G
3
9
3
R
3
9
5
F
4
1
7
G
4
4
7
F
5
0
0
D
5
0
6
[1]4h1y.p 0yq33 . . . . . . . . . . . . . . . . . .
[1]4h2b.a 0xe32 . . . . . . . . . . . . . . . . . .
[1]4h2f.a adn19 . . . . . . . . . . . . . . . . . .
[1]4h2i.a a12,zn,zn29 . . . . . . . . . . . . . . . . . .
[2]4h1s.a zn,zn2 . . . . . . . . . . . . . . . . . .

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
D
3
6
H
3
8
D
4
7
V
5
2
D
8
5
G
1
1
6
N
1
1
7
H
1
1
8
D
1
2
1
L
1
8
4
S
1
8
5
N
1
8
6
H
2
2
0
H
2
4
3
N
2
4
5
A
2
8
2
R
3
5
4
N
3
9
0
G
3
9
2
G
3
9
3
R
3
9
5
F
4
1
7
T
4
4
6
G
4
4
7
F
5
0
0
D
5
0
6
[1]4h1y.p . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4h2b.a . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]4h2f.a . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4h2i.a . . . . * . . * . . . . . . . . . . . . . . . . . .
[2]4h1s.a . * . . * . . * . . . . . . . . . . . . . . . . . .

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
4h1y.p:0yq
4h2b.a:0xe
4h2f.a:adn
4h2i.a:a12,zn
4h1s.a:zn
[1] 4h1y.p
0.1
0.1 0.2 0.5 0
[1] 4h2b.a 0.5
0.1
0.8 1.1 0
[1] 4h2f.a 0.1 0.1
0.1
0.2 0
[1] 4h2i.a 3.1 0.5 0.1
1.1
0.6
[2] 4h1s.a 6.8 1.4 0.3 4.2
0.6
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
4h1y.p
4h2b.a
4h2f.a
4h2i.a
4h1s.a
[1] 4h1y.p
0
.02 .03 .20 .30
[1] 4h2b.a .02
0
.05 .22 .32
[1] 4h2f.a .03 .05
0
.17 .31
[1] 4h2i.a .20 .22 .17
0
.24
[2] 4h1s.a .30 .32 .31 .24
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 6.2 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
4h1y.p
4h2b.a
4h2f.a
4h2i.a
4h1s.a
[1] 4h1y.p
0
0.3 6.1 25 25
[1] 4h2b.a 0.3
0
6.2 25 25
[1] 4h2f.a 6.1 6.2
0
29 30
[1] 4h2i.a 25 25 29
0
2.0
[2] 4h1s.a 25 25 30 2.0
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 6.2 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
4h1y.p
4h2b.a
4h2f.a
4h2i.a
4h1s.a
[1] 4h1y.p
0
0.4 6.1 24 25
[1] 4h2b.a 0.4
0
6.2 24 24
[1] 4h2f.a 6.1 6.2
0
29 29
[1] 4h2i.a 24 24 29
0
2.1
[2] 4h1s.a 25 24 29 2.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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