Chemical Components in the PDB

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LHC : Summary

Code

LHC

One-letter code

X

Molecule name

(2S)-2-amino-4-(4-amino-2-oxopyrimidin-1(2H)-yl)butanoic acid

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2-amino-4-(4-amino-2-oxopyrimidin-1(2H)-yl)butanoic acid
OpenEye OEToolkits 1.5.0 (2S)-2-amino-4-(4-amino-2-oxo-pyrimidin-1-yl)butanoic acid

Formula

C8 H12 N4 O3

Formal charge

0

Molecular weight

212.206 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(C=CN1CCC(C(=O)O)N)N
SMILES CACTVS 3.341 N[CH](CCN1C=CC(=NC1=O)N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)N=C1N)CCC(C(=O)O)N
Canonical SMILES CACTVS 3.341 N[C@@H](CCN1C=CC(=NC1=O)N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)N=C1N)CC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C8H12N4O3/c9-5(7(13)14)1-3-12-4-2-6(10)11-8(12)15/h2,4-5H,1,3,9H2,(H,13,14)(H2,10,11,15)/t5-/m0/s1

IUPAC InChI key

FKWFMIJKLRYFAG-YFKPBYRVSA-N
LHC

wwPDB Information

Atom count

27 (15 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

UNK

Defined at

2008-02-12

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



LHC : Atoms of Molecule

Total Number of Atoms: 27
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 -2.961 -1.497 0.993
2 CA C CA S N N 0 -2.675 -0.128 0.545
3 CB C CB N N N 0 -1.261 -0.065 -0.035
4 CG C CG N N N 0 -0.243 -0.35 1.072
5 N1 N N1 N N N 0 1.112 -0.29 0.517
6 C6 C C6 N N N 0 1.685 -1.415 0.005
7 C5 C C5 N N N 0 2.937 -1.347 -0.506
8 C4 C C4 N N N 0 3.613 -0.109 -0.493
9 N4 N N4 N N N 0 4.886 -0.012 -1.006
10 N3 N N3 N N N 0 3.015 0.96 0.016
11 C2 C C2 N N N 0 1.781 0.878 0.51
12 O2 O O2 N N N 0 1.25 1.876 0.967
13 C C C N N N 0 -3.67 0.272 -0.514
14 O O O N N N 0 -4.283 -0.576 -1.118
15 OXT O OXT N N Y 0 -3.875 1.571 -0.786
16 H H HN N N N 0 -2.896 -2.149 0.225
17 HA H HA N N N 0 -2.751 0.554 1.392
18 HB H HB N N N 0 -1.158 -0.81 -0.823
19 HBA H HBA N N N 0 -1.081 0.928 -0.447
20 HG H HG N N N 0 -0.346 0.396 1.86
21 HGA H HGA N N N 0 -0.423 -1.342 1.484
22 H6 H H6 N N N 0 1.146 -2.351 0.007
23 H5 H H5 N N N 0 3.411 -2.226 -0.916
24 HN4 H HN4 N N N 0 5.321 -0.795 -1.377
25 HN4A H HN4A N N N 0 5.349 0.841 -0.996
26 H2 H HNA N N Y 0 -2.348 -1.766 1.748
27 HXT H HXT N N Y 0 -4.523 1.778 -1.473



LHC : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N H N H sing 1.01 N N
2 N CA N C sing 1.47 N N
3 N H2 N H sing 1.01 N N
4 C CA C C sing 1.51 N N
5 CA HA C H sing 1.09 N N
6 CA CB C C sing 1.53 N N
7 HBA CB H C sing 1.09 N N
8 CB HB C H sing 1.09 N N
9 CB CG C C sing 1.53 N N
10 HG CG H C sing 1.09 N N
11 CG HGA C H sing 1.09 N N
12 CG N1 C N sing 1.47 N N
13 N1 C2 N C sing 1.35 N N
14 N1 C6 N C sing 1.36 N N
15 H6 C6 H C sing 1.08 N N
16 C6 C5 C C doub 1.35 N N
17 C5 C4 C C sing 1.41 N N
18 C5 H5 C H sing 1.08 N N
19 N3 C4 N C doub 1.33 N N
20 C4 N4 C N sing 1.38 N N
21 N4 HN4 N H sing 0.97 N N
22 N4 HN4A N H sing 0.97 N N
23 C2 N3 C N sing 1.33 N N
24 O2 C2 O C doub 1.22 N N
25 O C O C doub 1.21 N N
26 C OXT C O sing 1.34 N N
27 OXT HXT O H sing 0.97 N N



LHC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LHC 3c1p Open in New Window Polymer component 8 2