Chemical Components in the PDB

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04V : Summary

Code

04V

One-letter code

P

Molecule name

(2S)-pyrrolidine-2-carboximidic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-pyrrolidine-2-carboximidic acid
OpenEye OEToolkits 1.9.2 (2S)-pyrrolidine-2-carboximidic acid

Formula

C5 H10 N2 O

Formal charge

0

Molecular weight

114.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 [N@H]=C(O)C1NCCC1
SMILES CACTVS 3.385 OC(=N)[CH]1CCCN1
SMILES OpenEye OEToolkits 1.9.2 C1CC(NC1)C(=N)O
Canonical SMILES CACTVS 3.385 OC(=N)[C@@H]1CCCN1
Canonical SMILES OpenEye OEToolkits 1.9.2 [H]/N=C(/[C@@H]1CCCN1)\O

IUPAC InChI

InChI=1S/C5H10N2O/c6-5(8)4-2-1-3-7-4/h4,7H,1-3H2,(H2,6,8)/t4-/m0/s1

IUPAC InChI key

VLJNHYLEOZPXFW-BYPYZUCNSA-N

Is part of

4I4
04V

wwPDB Information

Atom count

18 (8 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

PRO

Defined at

2012-10-02

Last modified at

2019-04-14

Status

Released

Obsoleted

Not Assigned



04V : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N7 N N N N N 0 -0.795 -1.137 -0.167
2 C6 C CD N N N 0 -2.208 -0.702 -0.109
3 C5 C CG N N N 0 -2.205 0.802 0.221
4 C4 C CB N N N 0 -0.712 1.192 0.315
5 C3 C CA S N N 0 -0.011 0.079 -0.505
6 C1 C C N N N 0 1.424 -0.076 -0.072
7 N2 N N2 N N N 0 1.839 -1.207 0.391
8 OXT O OXT N N Y 0 2.274 0.966 -0.169
9 H61C H HD2 N N N 0 -2.687 -0.869 -1.074
10 H62C H HD3 N N N 0 -2.734 -1.253 0.67
11 H3 H HA N N N 0 -0.072 0.291 -1.572
12 H51C H HG2 N N N 0 -2.694 1.365 -0.574
13 H52C H HG3 N N N 0 -2.703 0.98 1.174
14 H41C H HB2 N N N 0 -0.54 2.169 -0.136
15 H42C H HB3 N N N 0 -0.374 1.179 1.351
16 H21N H HN2 N N N 0 2.763 -1.307 0.67
17 HXT H HXT N N Y 0 3.172 0.771 0.132
18 H2 H H N N Y 0 -0.5 -1.523 0.717



04V : Chemical Bonds

Total Number of Bonds: 18
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N7 C6 N C sing 1.48 N N
2 N7 C3 N C sing 1.49 N N
3 C6 C5 C C sing 1.54 N N
4 C5 C4 C C sing 1.55 N N
5 C4 C3 C C sing 1.55 N N
6 C3 C1 C C sing 1.51 N N
7 C1 N2 C N doub 1.29 N N
8 C1 OXT C O sing 1.35 N N
9 C6 H61C C H sing 1.09 N N
10 C6 H62C C H sing 1.09 N N
11 C3 H3 C H sing 1.09 N N
12 C5 H51C C H sing 1.09 N N
13 C5 H52C C H sing 1.09 N N
14 C4 H41C C H sing 1.09 N N
15 C4 H42C C H sing 1.09 N N
16 N2 H21N N H sing 0.97 N N
17 OXT HXT O H sing 0.97 N N
18 N7 H2 N H sing 1.01 N N



04V : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct
04V 4bcb Open in New Window Sub-component 1 1