Chemical Components in the PDB

pdbe.org/chem
spacer

V8W : Summary

Code

V8W

One-letter code

X

Molecule name

(R)-azanyl-[(2S)-pyrrolidin-2-yl]methanol

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 (R)-azanyl-[(2S)-pyrrolidin-2-yl]methanol

Formula

C5 H12 N2 O

Formal charge

0

Molecular weight

116.162 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 N[CH](O)[CH]1CCCN1
SMILES OpenEye OEToolkits 1.7.6 C1CC(NC1)C(N)O
Canonical SMILES CACTVS 3.370 N[C@H](O)[C@@H]1CCCN1
Canonical SMILES OpenEye OEToolkits 1.7.6 C1C[C@H](NC1)[C@H](N)O

Is part of

JKT
V8W

wwPDB Information

Atom count

20 (8 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-23

Last modified at

2013-04-26

Status

Released

Obsoleted

Not Assigned



V8W : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N7 N N7 N N N 0 0.506 -1.007 -0.447
2 C3 C C3 S N N 0 -0.0010 -0.109 0.623
3 C1 C C1 R N N 0 -1.43 0.34 0.31
4 N2 N N2 N N N 0 -2.332 -0.818 0.373
5 C4 C C4 N N N 0 0.96 1.099 0.604
6 C5 C C5 N N N 0 2.265 0.564 -0.019
7 C6 C C6 N N N 0 1.984 -0.923 -0.324
8 OXT O OXT N N Y 0 -1.474 0.909 -1.0
9 H3 H H3 N N N 0 0.036 -0.611 1.59
10 H61C H H61C N N N 0 2.333 -1.552 0.495
11 H62C H H62C N N N 0 2.46 -1.217 -1.259
12 H41C H H41C N N N 0 0.548 1.9 -0.01
13 H42C H H42C N N N 0 1.142 1.454 1.618
14 H21N H H21N N N N 0 -2.061 -1.523 -0.296
15 H22N H H22N N N N 0 -2.367 -1.199 1.306
16 H51C H H51C N N N 0 2.495 1.102 -0.939
17 H52C H H52C N N N 0 3.089 0.656 0.69
18 HOXT H HOXT N N N 0 -2.352 1.217 -1.265
19 H1C H H1C N N N 0 -1.744 1.086 1.041
20 H2 H H2 N N Y 0 0.184 -1.953 -0.307



V8W : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N7 C3 N C sing 1.49 N N
2 N7 C6 N C sing 1.49 N N
3 C3 C1 C C sing 1.53 N N
4 C3 C4 C C sing 1.54 N N
5 C1 N2 C N sing 1.47 N N
6 C1 OXT C O sing 1.43 N N
7 C4 C5 C C sing 1.54 N N
8 C5 C6 C C sing 1.54 N N
9 C3 H3 C H sing 1.09 N N
10 C6 H61C C H sing 1.09 N N
11 C6 H62C C H sing 1.09 N N
12 C4 H41C C H sing 1.09 N N
13 C4 H42C C H sing 1.09 N N
14 N2 H21N N H sing 1.01 N N
15 N2 H22N N H sing 1.01 N N
16 C5 H51C C H sing 1.09 N N
17 C5 H52C C H sing 1.09 N N
18 OXT HOXT O H sing 0.97 N N
19 C1 H1C C H sing 1.09 N N
20 N7 H2 N H sing 1.01 N N



V8W : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct
V8W 4bcc Open in New Window Sub-component 1 1