Chemical Components in the PDB

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XDV : Summary

Code

XDV

One-letter code

X

Molecule name

2-[2-(2-aminoethoxy)ethoxy]acetamide

Systematic names

ProgramVersionName
ACDLabs 12.01 2-[2-(2-aminoethoxy)ethoxy]acetamide
OpenEye OEToolkits 2.0.7 2-[2-(2-azanylethoxy)ethoxy]ethanamide

Formula

C6 H14 N2 O3

Formal charge

0

Molecular weight

162.187 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(COCCOCCN)=O
SMILES CACTVS 3.385 NCCOCCOCC(N)=O
SMILES OpenEye OEToolkits 2.0.7 C(COCCOCC(=O)N)N
Canonical SMILES CACTVS 3.385 NCCOCCOCC(N)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C(COCCOCC(=O)N)N

IUPAC InChI

InChI=1S/C6H14N2O3/c7-1-2-10-3-4-11-5-6(8)9/h1-5,7H2,(H2,8,9)

IUPAC InChI key

CDFONQZJZPNQML-UHFFFAOYSA-N
XDV

wwPDB Information

Atom count

25 (11 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-12-11

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



XDV : 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 N10 N N1 N N N 0 4.411 0.743 -0.434
2 C02 C C1 N N N 0 -3.678 1.169 0.322
3 C03 C C2 N N N 0 -3.064 -0.17 0.733
4 C05 C C3 N N N 0 -1.145 -1.566 0.392
5 C06 C C4 N N N 0 0.183 -1.64 -0.364
6 C08 C C5 N N N 0 2.33 -0.589 -0.541
7 C09 C C6 N N N 0 3.162 0.531 0.026
8 N01 N N2 N N N 0 -3.99 1.145 -1.114
9 O04 O O1 N N N 0 -1.807 -0.34 0.075
10 O07 O O2 N N N 0 1.055 -0.609 0.104
11 O11 O O3 N N N 0 2.709 1.243 0.897
12 H101 H H1 N N N 0 4.774 0.174 -1.131
13 H102 H H2 N N N 0 4.946 1.467 -0.071
14 H021 H H3 N N N 0 -4.593 1.339 0.89
15 H022 H H4 N N N 0 -2.969 1.972 0.526
16 H032 H H5 N N N 0 -2.914 -0.186 1.812
17 H031 H H6 N N N 0 -3.735 -0.98 0.447
18 H052 H H7 N N N 0 -1.777 -2.405 0.1
19 H051 H H8 N N N 0 -0.956 -1.61 1.464
20 H062 H H9 N N N 0 0.645 -2.612 -0.193
21 H061 H H10 N N N 0 0.002 -1.507 -1.431
22 H082 H H11 N N N 0 2.193 -0.434 -1.612
23 H081 H H12 N N N 0 2.836 -1.539 -0.374
24 H1 H H13 N N N 0 -4.595 0.37 -1.339
25 H2 H H14 N N Y 0 -4.397 2.02 -1.41



XDV : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N01 C02 N C sing 1.47 N N
2 C02 C03 C C sing 1.53 N N
3 O04 C03 O C sing 1.43 N N
4 O04 C05 O C sing 1.43 N N
5 C05 C06 C C sing 1.53 N N
6 C06 O07 C O sing 1.43 N N
7 O07 C08 O C sing 1.43 N N
8 C08 C09 C C sing 1.51 N N
9 O11 C09 O C doub 1.21 N N
10 C09 N10 C N sing 1.35 N N
11 N10 H101 N H sing 0.97 N N
12 N10 H102 N H sing 0.97 N N
13 C02 H021 C H sing 1.09 N N
14 C02 H022 C H sing 1.09 N N
15 C03 H032 C H sing 1.09 N N
16 C03 H031 C H sing 1.09 N N
17 C05 H052 C H sing 1.09 N N
18 C05 H051 C H sing 1.09 N N
19 C06 H062 C H sing 1.09 N N
20 C06 H061 C H sing 1.09 N N
21 C08 H082 C H sing 1.09 N N
22 C08 H081 C H sing 1.09 N N
23 N01 H1 N H sing 1.01 N N
24 N01 H2 N H sing 1.01 N N



XDV : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
XDV 7kzl Open in New Window Polymer component 1 1
XDV 7uid Open in New Window Polymer component 2 1