Chemical Components in the PDB

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YV4 : Summary

Code

YV4

One-letter code

X

Molecule name

(3S)-3-aminopyrrolidin-2-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-3-aminopyrrolidin-2-one
OpenEye OEToolkits 2.0.7 (3~{S})-3-azanylpyrrolidin-2-one

Formula

C4 H8 N2 O

Formal charge

0

Molecular weight

100.119 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NCCC1N
SMILES CACTVS 3.385 N[CH]1CCNC1=O
SMILES OpenEye OEToolkits 2.0.7 C1CNC(=O)C1N
Canonical SMILES CACTVS 3.385 N[C@H]1CCNC1=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C1CNC(=O)[C@H]1N

IUPAC InChI

InChI=1S/C4H8N2O/c5-3-1-2-6-4(3)7/h3H,1-2,5H2,(H,6,7)/t3-/m0/s1

IUPAC InChI key

YNDAMDVOGKACTP-VKHMYHEASA-N
YV4

wwPDB Information

Atom count

15 (7 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-04-01

Last modified at

2021-06-18

Status

Released

Obsoleted

Not Assigned



YV4 : Atoms of Molecule

Total Number of Atoms: 15
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N01 N N1 N N N 0 -1.541 1.34 0.251
2 C02 C C1 S N N 0 -0.418 0.706 -0.451
3 C03 C C2 N N N 0 0.926 1.305 0.026
4 C04 C C3 N N N 0 1.847 0.066 0.009
5 N05 N N2 N N N 0 0.955 -1.088 0.175
6 C06 C C4 N N N 0 -0.322 -0.758 -0.082
7 O07 O O1 N N N 0 -1.262 -1.523 -0.025
8 H012 H H1 N N N 0 -2.418 0.913 -0.008
9 H1 H H2 N N N 0 -1.407 1.311 1.251
10 H021 H H4 N N N 0 -0.528 0.821 -1.529
11 H032 H H5 N N N 0 1.282 2.066 -0.669
12 H031 H H6 N N N 0 0.836 1.712 1.033
13 H042 H H7 N N N 0 2.374 0.001 -0.943
14 H041 H H8 N N N 0 2.56 0.115 0.832
15 H051 H H9 N N N 0 1.25 -1.974 0.437



YV4 : Chemical Bonds

Total Number of Bonds: 15
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C02 N01 C N sing 1.47 N N
2 C03 C02 C C sing 1.55 N N
3 C04 C03 C C sing 1.54 N N
4 N05 C04 N C sing 1.47 N N
5 C06 N05 C N sing 1.34 N N
6 O07 C06 O C doub 1.21 N N
7 C02 C06 C C sing 1.51 N N
8 N01 H012 N H sing 1.01 N N
9 N01 H1 N H sing 1.01 N N
10 C02 H021 C H sing 1.09 N N
11 C03 H032 C H sing 1.09 N N
12 C03 H031 C H sing 1.09 N N
13 C04 H042 C H sing 1.09 N N
14 C04 H041 C H sing 1.09 N N
15 N05 H051 N H sing 0.97 N N



YV4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
YV4 5s9k Open in New Window Bound ligand 1 1