Chemical Components in the PDB

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GN1 : Summary

Code

GN1

One-letter code

X

Molecule name

2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

Synonyms

2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE
N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE
N-acetyl-1-O-phosphono-alpha-D-glucosamine
2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose
2-acetamido-2-deoxy-1-O-phosphono-D-glucose
2-acetamido-2-deoxy-1-O-phosphono-glucose

Systematic names

ProgramVersionName
ACDLabs 10.04 2-(acetylamino)-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
OpenEye OEToolkits 1.5.0 [(2R,3R,4R,5S,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl] dihydrogen phosphate

Formula

C8 H16 N O9 P

Formal charge

0

Molecular weight

301.188 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)O
SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)O

IUPAC InChI

InChI=1S/C8H16NO9P/c1-3(11)9-5-7(13)6(12)4(2-10)17-8(5)18-19(14,15)16/h4-8,10,12-13H,2H2,1H3,(H,9,11)(H2,14,15,16)/t4-,5-,6-,7-,8-/m1/s1

IUPAC InChI key

FZLJPEPAYPUMMR-FMDGEEDCSA-N
GN1

wwPDB Information

Atom count

35 (19 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

Yes

Standard parent

NDG

Defined at

2007-01-25

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GN1 : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1' R N N 0 2.368 0.767 1.447
2 OP1 O OP1 N N N 0 2.826 3.482 2.563
3 P P P N N N 0 1.602 2.599 3.143
4 OP2 O OP2 N N N 0 2.311 1.67 4.261
5 OP3 O OP3 N N N 0 0.419 3.383 3.629
6 C2 C C2' R N N 0 2.137 0.436 -0.031
7 C3 C C3' R N N 0 0.949 -0.515 -0.197
8 C4 C C4' S N N 0 1.107 -1.734 0.716
9 C5 C C5' R N N 0 1.425 -1.314 2.156
10 C6 C C6' N N N 0 1.759 -2.511 3.042
11 C8 C C8' N N N 0 2.6 3.542 -2.151
12 O1 O O1' N N N 0 1.289 1.548 1.958
13 O3 O O3' N N N 0 0.906 -0.961 -1.554
14 O4 O O4' N N N 0 -0.109 -2.477 0.674
15 O5 O O5' N N N 0 2.557 -0.438 2.193
16 N2 N N2' N N N 0 1.961 1.638 -0.813
17 C7 C C7' N N N 0 3.014 2.331 -1.384
18 O6 O O6' N N N 0 2.05 -2.04 4.344
19 O7 O O7' N N N 0 4.201 2.037 -1.311
20 H1 H H1' N N N 0 3.277 1.368 1.559
21 HOP1 H HOP1 N N N 0 3.154 4.242 3.09
22 HOP2 H HOP2 N N N 0 2.522 2.058 5.137
23 H2 H H2' N N N 0 3.032 -0.052 -0.435
24 H3 H H3' N N N 0 -0.0030 -0.0050 -0.0030
25 H4 H H4' N N N 0 1.9 -2.383 0.324
26 H5 H H5' N N N 0 0.56 -0.813 2.608
27 H61 H H6'1 N N N 0 2.628 -3.035 2.645
28 H62 H H6'2 N N N 0 0.907 -3.19 3.085
29 H81 H H8'1 N N N 0 3.057 4.465 -1.758
30 H82 H H8'2 N N N 0 2.905 3.494 -3.209
31 H83 H H8'3 N N N 0 1.517 3.741 -2.17
32 HO3 H HO3' N N Y 0 1.705 -1.49 -1.693
33 HO4 H HO4' N N Y 0 -0.383 -2.504 -0.255
34 HN2 H HN2' N N N 0 1.019 1.992 -0.952
35 HO6 H HO6' N N Y 0 2.976 -2.268 4.531



GN1 : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O sing 1.43 N N
2 C1 O5 C O sing 1.43 N N
3 C1 C2 C C sing 1.53 N N
4 C1 H1 C H sing 1.1 N N
5 OP1 P O P sing 1.62 N N
6 OP1 HOP1 O H sing 0.98 N N
7 P OP3 P O doub 1.5 N N
8 P OP2 P O sing 1.62 N N
9 P O1 P O sing 1.61 N N
10 OP2 HOP2 O H sing 0.98 N N
11 C2 C3 C C sing 1.53 N N
12 C2 N2 C N sing 1.44 N N
13 C2 H2 C H sing 1.1 N N
14 C3 C4 C C sing 1.53 N N
15 C3 O3 C O sing 1.43 N N
16 C3 H3 C H sing 1.1 N N
17 C4 C5 C C sing 1.53 N N
18 C4 O4 C O sing 1.43 N N
19 C4 H4 C H sing 1.1 N N
20 C5 C6 C C sing 1.53 N N
21 C5 O5 C O sing 1.43 N N
22 C5 H5 C H sing 1.1 N N
23 C6 O6 C O sing 1.41 N N
24 C6 H61 C H sing 1.09 N N
25 C6 H62 C H sing 1.09 N N
26 C8 C7 C C sing 1.49 N N
27 C8 H81 C H sing 1.1 N N
28 C8 H82 C H sing 1.1 N N
29 C8 H83 C H sing 1.1 N N
30 O3 HO3 O H sing 0.97 N N
31 O4 HO4 O H sing 0.97 N N
32 N2 C7 N C sing 1.38 N N
33 N2 HN2 N H sing 1.02 N N
34 C7 O7 C O doub 1.23 N N
35 O6 HO6 O H sing 0.97 N N



GN1 : Used in PDB Entries

Total Number of PDB Entries: 14
Ligand Code PDB Entry ID Type Total Distinct
GN1 2oi7 Open in New Window Bound ligand 2 1
GN1 2qkx Open in New Window Bound ligand 1 1
GN1 2yqh Open in New Window Bound ligand 2 1
GN1 4g3s Open in New Window Bound ligand 1 1
GN1 4hcq Open in New Window Bound ligand 2 1
GN1 4k6r Open in New Window Bound ligand 2 1
GN1 4oco Open in New Window Bound ligand 1 1
GN1 4ocp Open in New Window Bound ligand 1 1
GN1 4rgg Open in New Window Bound ligand 2 1
GN1 5dq9 Open in New Window s 3 1
GN1 5dqd Open in New Window s 1 1
GN1 6dfe Open in New Window s 2 1
GN1 6ryn Open in New Window Bound ligand 1 1
GN1 6tn3 Open in New Window Bound ligand 1 1