Chemical Components in the PDB

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19W : Summary

Code

19W

One-letter code

X

Molecule name

5-(aminooxy)-L-norvaline

Systematic names

ProgramVersionName
ACDLabs 12.01 5-(aminooxy)-L-norvaline
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-5-azanyloxy-pentanoic acid

Formula

C5 H12 N2 O3

Formal charge

0

Molecular weight

148.16 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCCON
SMILES CACTVS 3.385 NOCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 C(CC(C(=O)O)N)CON
Canonical SMILES CACTVS 3.385 NOCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C(C[C@@H](C(=O)O)N)CON

IUPAC InChI

InChI=1S/C5H12N2O3/c6-4(5(8)9)2-1-3-10-7/h4H,1-3,6-7H2,(H,8,9)/t4-/m0/s1

IUPAC InChI key

GFOZTGXHZSBIOB-BYPYZUCNSA-N
19W

wwPDB Information

Atom count

22 (10 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2012-11-12

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



19W : Atoms of Molecule

Total Number of Atoms: 22
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 -1.427 1.794 -0.206
2 CA C CA S N N 0 -1.395 0.352 -0.485
3 C C C N N N 0 -2.66 -0.286 0.029
4 O O O N N N 0 -3.324 0.277 0.867
5 H H H1 N N N 0 -1.498 1.969 0.785
6 CB C CB N N N 0 -0.187 -0.276 0.213
7 CG C CG N N N 0 1.101 0.282 -0.397
8 CD C CD N N N 0 2.309 -0.346 0.301
9 OE O OE N N N 0 3.511 0.175 -0.268
10 NZ N NZ N N N 0 4.734 -0.363 0.33
11 H2 H H2 N N Y 0 -0.619 2.256 -0.598
12 HA H H4 N N N 0 -1.318 0.191 -1.56
13 H6 H H6 N N N 0 -0.218 -0.039 1.276
14 H7 H H7 N N N 0 -0.213 -1.358 0.08
15 H8 H H8 N N N 0 1.132 0.045 -1.46
16 H9 H H9 N N N 0 1.126 1.363 -0.264
17 H10 H H10 N N N 0 2.278 -0.11 1.365
18 H13 H H13 N N N 0 5.554 0.035 -0.104
19 H11 H H11 N N N 0 2.283 -1.428 0.169
20 H12 H H12 N N N 0 4.749 -1.37 0.278
21 HXT H HXT N N Y 0 -3.868 -1.85 -0.085
22 OXT O OXT N N Y 0 -3.05 -1.48 -0.445



19W : Chemical Bonds

Total Number of Bonds: 21
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C O C doub 1.21 N N
2 C CA C C sing 1.51 N N
3 CA N C N sing 1.47 N N
4 CA CB C C sing 1.53 N N
5 CG CB C C sing 1.53 N N
6 CG CD C C sing 1.53 N N
7 CD OE C O sing 1.43 N N
8 OE NZ O N sing 1.46 N N
9 N H N H sing 1.01 N N
10 N H2 N H sing 1.01 N N
11 CA HA C H sing 1.09 N N
12 CB H6 C H sing 1.09 N N
13 CB H7 C H sing 1.09 N N
14 CG H8 C H sing 1.09 N N
15 CG H9 C H sing 1.09 N N
16 CD H10 C H sing 1.09 N N
17 CD H11 C H sing 1.09 N N
18 NZ H12 N H sing 1.01 N N
19 NZ H13 N H sing 1.01 N N
20 C OXT C O sing 1.34 N N
21 OXT HXT O H sing 0.97 N N



19W : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
19W 4hu5 Open in New Window Polymer component 2 1
19W 4hu6 Open in New Window Polymer component 4 1
19W 5khy Open in New Window Polymer component 1 1