Chemical Components in the PDB

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1HD : Summary

Code

1HD

One-letter code

X

Molecule name

N-[(2S)-2-amino-3-hydroxypropyl]acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(2S)-2-amino-3-hydroxypropyl]acetamide
OpenEye OEToolkits 1.7.6 N-[(2S)-2-azanyl-3-oxidanyl-propyl]ethanamide

Formula

C5 H12 N2 O2

Formal charge

0

Molecular weight

132.161 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCC(N)CO)C
SMILES CACTVS 3.370 CC(=O)NC[CH](N)CO
SMILES OpenEye OEToolkits 1.7.6 CC(=O)NCC(CO)N
Canonical SMILES CACTVS 3.370 CC(=O)NC[C@H](N)CO
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(=O)NC[C@@H](CO)N

IUPAC InChI

InChI=1S/C5H12N2O2/c1-4(9)7-2-5(6)3-8/h5,8H,2-3,6H2,1H3,(H,7,9)/t5-/m0/s1

IUPAC InChI key

FGWRNRQRNIHEGV-YFKPBYRVSA-N
1HD

wwPDB Information

Atom count

21 (9 without Hydrogen)

Polymer type

Amino Acid

Type description

peptide-like

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2013-02-05

Last modified at

2013-02-15

Status

Released

Obsoleted

Not Assigned



1HD : Atoms of Molecule

Total Number of Atoms: 21
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 2.527 -0.729 -0.085
2 CD C CD N N N 0 -2.358 -0.114 0.029
3 N N N N N N 0 1.393 1.39 -0.555
4 OE1 O OE1 N N N 0 -2.554 -1.259 -0.319
5 CA C CA S N N 0 1.342 0.172 0.266
6 CB C CB N N N 0 0.035 -0.573 -0.0090
7 C1 C C1 N N N 0 -3.523 0.814 0.257
8 N1 N N1 N N N 0 -1.098 0.329 0.212
9 O1 O O1 N N Y 0 3.746 -0.079 0.281
10 H1 H H1 N N N 0 1.35 1.165 -1.538
11 H2 H H2 N N N 0 0.658 2.031 -0.297
12 H4 H H4 N N N 0 1.391 0.443 1.321
13 H5 H H5 N N N 0 0.025 -0.921 -1.042
14 H6 H H6 N N N 0 -0.045 -1.428 0.663
15 H7 H H7 N N N 0 -3.845 0.746 1.296
16 H8 H H8 N N N 0 -3.221 1.838 0.037
17 H9 H H9 N N N 0 -4.347 0.531 -0.398
18 H10 H H10 N N N 0 -0.941 1.245 0.491
19 H11 H H11 N N N 0 4.54 -0.594 0.087
20 H12 H H12 N N N 0 2.441 -1.671 0.459
21 H13 H H13 N N N 0 2.528 -0.928 -1.156



1HD : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C CA C C sing 1.53 N N
2 CA CB C C sing 1.53 N N
3 CA N C N sing 1.47 N N
4 CB N1 C N sing 1.46 N N
5 OE1 CD O C doub 1.21 N N
6 N1 CD N C sing 1.35 N N
7 CD C1 C C sing 1.51 N N
8 C O1 C O sing 1.43 N N
9 N H1 N H sing 1.01 N N
10 N H2 N H sing 1.01 N N
11 CA H4 C H sing 1.09 N N
12 CB H5 C H sing 1.09 N N
13 CB H6 C H sing 1.09 N N
14 C1 H7 C H sing 1.09 N N
15 C1 H8 C H sing 1.09 N N
16 C1 H9 C H sing 1.09 N N
17 N1 H10 N H sing 0.97 N N
18 O1 H11 O H sing 0.97 N N
19 C H12 C H sing 1.09 N N
20 C H13 C H sing 1.09 N N



1HD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1HD 4imq Open in New Window Polymer component 1 1