Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PRI : Summary

Code

PRI

One-letter code

X

Molecule name

PYRROLIDINE-2-CARBALDEHYDE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-pyrrolidine-2-carbaldehyde
OpenEye OEToolkits 1.5.0 (2S)-pyrrolidine-2-carbaldehyde

Formula

C5 H9 N O

Formal charge

0

Molecular weight

99.131 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=CC1NCCC1
SMILES CACTVS 3.341 O=C[CH]1CCCN1
SMILES OpenEye OEToolkits 1.5.0 C1CC(NC1)C=O
Canonical SMILES CACTVS 3.341 O=C[C@@H]1CCCN1
Canonical SMILES OpenEye OEToolkits 1.5.0 C1C[C@H](NC1)C=O

IUPAC InChI

InChI=1S/C5H9NO/c7-4-5-2-1-3-6-5/h4-6H,1-3H2/t5-/m0/s1

IUPAC InChI key

JIDDDPVQQUHACU-YFKPBYRVSA-N

Is part of

ZPR
PRI

wwPDB Information

Atom count

16 (7 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-05-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



PRI : Atoms of Molecule

Total Number of Atoms: 16
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CB C CB N N N 0 1.279 -0.027 0.642
2 CG C CG N N N 0 0.513 -0.388 1.931
3 C C C N N N 0 0.47 0.182 -1.719
4 OT1 O OT1 N N N 0 -0.361 -0.455 -2.318
5 N N N N N N 0 -1.074 0.047 0.186
6 CD C CD N N N 0 -0.944 0.046 1.667
7 HCG1 H 1HCG N N N 0 0.561 -1.462 2.111
8 CA C CA S N N 0 0.22 0.595 -0.292
9 HCB1 H 1HCB N N N 0 1.703 -0.924 0.189
10 HCB2 H 2HCB N N N 0 2.065 0.695 0.858
11 HCG2 H 2HCG N N N 0 0.923 0.157 2.781
12 HO'T H THO' N N N 0 1.396 0.452 -2.206
13 HN H HN N N N 0 -1.783 0.727 -0.042
14 HCD1 H 1HCD N N N 0 -1.639 -0.665 2.11
15 HCD2 H 2HCD N N N 0 -1.119 1.047 2.062
16 HCA H AHC N N N 0 0.228 1.682 -0.205



PRI : Chemical Bonds

Total Number of Bonds: 16
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CB CG C C sing 1.54 N N
2 CB CA C C sing 1.54 N N
3 CB HCB1 C H sing 1.09 N N
4 CB HCB2 C H sing 1.09 N N
5 CG CD C C sing 1.54 N N
6 CG HCG1 C H sing 1.09 N N
7 CG HCG2 C H sing 1.09 N N
8 C OT1 C O doub 1.21 N N
9 C CA C C sing 1.51 N N
10 C HO'T C H sing 1.08 N N
11 N CD N C sing 1.49 N N
12 N CA N C sing 1.48 N N
13 N HN N H sing 1.01 N N
14 CD HCD1 C H sing 1.09 N N
15 CD HCD2 C H sing 1.09 N N
16 CA HCA C H sing 1.09 N N



PRI : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
PRI 1h4q Open in New Window Bound ligand 2 1
PRI 2j3m Open in New Window Bound ligand 2 1
PRI 1h2y Open in New Window Sub-component 1 1
PRI 1qfs Open in New Window Sub-component 1 1
PRI 3iuq Open in New Window Sub-component 1 1
PRI 3ivm Open in New Window Sub-component 2 1
PRI 3muo Open in New Window Sub-component 2 1
PRI 5uw6 Open in New Window Sub-component 4 1
PRI 5uzw Open in New Window Sub-component 4 1
PRI 7vgc Open in New Window Sub-component 1 1
PRI 7zaz Open in New Window Sub-component 4 1