Chemical Components in the PDB

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PA1 : Summary

Code

PA1

One-letter code

X

Molecule name

2-amino-2-deoxy-alpha-D-glucopyranose

Systematic names

ProgramVersionName
ACDLabs 10.04 2-amino-2-deoxy-alpha-D-glucopyranose
OpenEye OEToolkits 1.5.0 (2S,3R,4R,5S,6R)-3-amino-6-(hydroxymethyl)oxane-2,4,5-triol

Formula

C6 H13 N O5

Formal charge

0

Molecular weight

179.171 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC1C(O)C(OC(O)C1N)CO
SMILES CACTVS 3.341 N[CH]1[CH](O)O[CH](CO)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C(C1C(C(C(C(O1)O)N)O)O)O
Canonical SMILES CACTVS 3.341 N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)N)O)O)O

IUPAC InChI

InChI=1S/C6H13NO5/c7-3-5(10)4(9)2(1-8)12-6(3)11/h2-6,8-11H,1,7H2/t2-,3-,4-,5-,6+/m1/s1

IUPAC InChI key

MSWZFWKMSRAUBD-UKFBFLRUSA-N
PA1

wwPDB Information

Atom count

25 (12 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide, alpha linking

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2021-08-24

Status

Released

Obsoleted

Not Assigned



PA1 : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 S N N 0 1.564 0.223 0.505
2 O1 O O1 N N Y 0 1.77 -1.188 0.422
3 C2 C C2 R N N 0 0.529 0.524 1.591
4 N2 N N2 N N N 0 1.026 0.047 2.889
5 C3 C C3 R N N 0 -0.78 -0.193 1.249
6 O3 O O3 N N N 0 -1.802 0.195 2.169
7 C4 C C4 S N N 0 -1.194 0.194 -0.174
8 O4 O O4 N N N 0 -2.33 -0.576 -0.571
9 C5 C C5 R N N 0 -0.029 -0.081 -1.127
10 O5 O O5 N N N 0 1.098 0.707 -0.753
11 C6 C C6 N N N 0 -0.447 0.274 -2.556
12 O6 O O6 N N N 0 0.636 0.011 -3.449
13 H1 H H1 N N N 0 2.505 0.713 0.755
14 HO1 H HO1 N N Y 0 2.427 -1.334 -0.271
15 H2 H H2 N N N 0 0.354 1.599 1.64
16 HN21 H HN21 N N N 0 1.886 0.543 3.07
17 HN22 H HN22 N N Y 0 0.363 0.355 3.584
18 H3 H H3 N N N 0 -0.629 -1.271 1.304
19 HO3 H HO3 N N Y 0 -1.501 -0.067 3.049
20 H4 H H4 N N N 0 -1.446 1.255 -0.203
21 HO4 H HO4 N N Y 0 -2.552 -0.304 -1.472
22 H5 H H5 N N N 0 0.235 -1.137 -1.08
23 H61 H H61 N N N 0 -1.309 -0.327 -2.843
24 H62 H H62 N N N 0 -0.709 1.331 -2.605
25 HO6 H HO6 N N Y 0 0.332 0.248 -4.335



PA1 : Chemical Bonds

Total Number of Bonds: 25
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 C2 C C sing 1.53 N N
3 C1 O5 C O sing 1.43 N N
4 C1 H1 C H sing 1.09 N N
5 O1 HO1 O H sing 0.97 N N
6 C2 N2 C N sing 1.47 N N
7 C2 C3 C C sing 1.53 N N
8 C2 H2 C H sing 1.09 N N
9 N2 HN21 N H sing 1.01 N N
10 N2 HN22 N H sing 1.01 N N
11 C3 O3 C O sing 1.43 N N
12 C3 C4 C C sing 1.53 N N
13 C3 H3 C H sing 1.09 N N
14 O3 HO3 O H sing 0.97 N N
15 C4 O4 C O sing 1.43 N N
16 C4 C5 C C sing 1.53 N N
17 C4 H4 C H sing 1.09 N N
18 O4 HO4 O H sing 0.97 N N
19 C5 O5 C O sing 1.43 N N
20 C5 C6 C C sing 1.53 N N
21 C5 H5 C H sing 1.09 N N
22 C6 O6 C O sing 1.43 N N
23 C6 H61 C H sing 1.09 N N
24 C6 H62 C H sing 1.09 N N
25 O6 HO6 O H sing 0.97 N N



PA1 : Used in PDB Entries

Total Number of PDB Entries: 20
Ligand Code PDB Entry ID Type Total Distinct
PA1 1fi1 Open in New Window s 1 1
PA1 1pbr Open in New Window Bound ligand 1 1
PA1 1qff Open in New Window s 1 1
PA1 1qfg Open in New Window s 1 1
PA1 1qkc Open in New Window s 1 1
PA1 3fxi Open in New Window s 3 3
PA1 3v0w Open in New Window s 1 1
PA1 4cu4 Open in New Window s 1 1
PA1 4y9t Open in New Window Bound ligand 1 1
PA1 5kgp Open in New Window s 2 1
PA1 5tv4 Open in New Window s 2 2
PA1 5w7b Open in New Window s 2 1
PA1 6bpl Open in New Window Bound ligand 1 1
PA1 6bpp Open in New Window s 1 1
PA1 6ry6 Open in New Window Bound ligand 1 1
PA1 7wld Open in New Window Bound ligand 1 1
PA1 8imx Open in New Window Bound ligand 1 1
PA1 8imy Open in New Window Bound ligand 1 1
PA1 8k9r Open in New Window Bound ligand 1 1
PA1 8k9t Open in New Window Bound ligand 1 1