Chemical Components in the PDB

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04X : Summary

Code

04X

One-letter code

X

Molecule name

(2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid
OpenEye OEToolkits 1.9.2 (2S)-5-(morpholin-4-ylmethyl)-1,2,3,6-tetrahydropyridine-2-carboxylic acid

Formula

C11 H18 N2 O3

Formal charge

0

Molecular weight

226.272 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C1NCC(=CC1)CN2CCOCC2
SMILES CACTVS 3.385 OC(=O)[CH]1CC=C(CN1)CN2CCOCC2
SMILES OpenEye OEToolkits 1.9.2 C1COCCN1CC2=CCC(NC2)C(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)[C@@H]1CC=C(CN1)CN2CCOCC2
Canonical SMILES OpenEye OEToolkits 1.9.2 C1COCCN1CC2=CC[C@H](NC2)C(=O)O

IUPAC InChI

InChI=1S/C11H18N2O3/c14-11(15)10-2-1-9(7-12-10)8-13-3-5-16-6-4-13/h1,10,12H,2-8H2,(H,14,15)/t10-/m0/s1

IUPAC InChI key

IIQVKGCHPWVHMA-JTQLQIEISA-N
04X

wwPDB Information

Atom count

34 (16 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2014-06-19

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



04X : Atoms of Molecule

Total Number of Atoms: 34
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N N N 0 4.558 -0.132 0.823
2 C C C N N N 0 -3.994 0.466 0.29
3 N1 N N1 N N N 0 2.274 -0.49 0.019
4 C1 C C1 N N N 0 3.636 -1.044 0.009
5 O1 O O1 N N N 0 4.508 1.192 0.283
6 CA C CA S N N 0 -2.51 0.21 0.224
7 N N N N N N 0 -2.229 -1.178 0.627
8 O O O N N N 0 -4.768 -0.461 0.278
9 C4 C C4 N N N 0 2.261 0.869 -0.541
10 CB C CB N N N 0 -2.018 0.408 -1.212
11 CG C CG N N N 0 -0.612 -0.109 -1.341
12 CD C CD N N N 0 -0.07 -0.903 -0.469
13 CE C CE N N N 0 -0.781 -1.383 0.763
14 C0 C C0 N N N 0 1.344 -1.367 -0.705
15 C3 C C3 N N N 0 3.197 1.762 0.278
16 H4 H H4 N N N 0 4.228 -0.114 1.862
17 H5 H H5 N N N 0 5.58 -0.508 0.771
18 H15 H H15 N N N 0 3.997 -1.104 -1.018
19 H16 H H16 N N N 0 3.627 -2.04 0.451
20 HA H H18 N N N 0 -1.99 0.898 0.891
21 H32 H H32 N N N 0 2.6 0.839 -1.577
22 H33 H H33 N N N 0 1.248 1.269 -0.501
23 H39 H H39 N N N 0 -2.669 -0.136 -1.896
24 H40 H H40 N N N 0 -2.038 1.469 -1.459
25 H41 H H41 N N N 0 -0.028 0.192 -2.198
26 H44 H H44 N N N 0 -0.418 -0.828 1.629
27 H45 H H45 N N N 0 -0.579 -2.444 0.907
28 H55 H H55 N N N 0 1.566 -1.33 -1.772
29 H56 H H56 N N N 0 1.456 -2.39 -0.346
30 H63 H H63 N N N 0 2.827 1.835 1.301
31 H64 H H64 N N N 0 3.234 2.756 -0.168
32 OXT O OXT N N Y 0 -4.456 1.724 0.363
33 HXT H HXT N N Y 0 -5.415 1.839 0.404
34 H H H2 N N Y 0 -2.709 -1.41 1.484



04X : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 C1 C C sing 1.53 N N
2 C2 O1 C O sing 1.43 N N
3 C CA C C sing 1.51 N N
4 C O C O doub 1.21 N N
5 N1 C1 N C sing 1.47 N N
6 N1 C0 N C sing 1.47 N N
7 N1 C4 N C sing 1.47 N N
8 O1 C3 O C sing 1.43 N N
9 CA N C N sing 1.47 N N
10 CA CB C C sing 1.53 N N
11 N CE N C sing 1.47 N N
12 C4 C3 C C sing 1.53 N N
13 CB CG C C sing 1.5 N N
14 CG CD C C doub 1.3 N N
15 CD CE C C sing 1.5 N N
16 CD C0 C C sing 1.51 N N
17 C2 H4 C H sing 1.09 N N
18 C2 H5 C H sing 1.09 N N
19 C1 H15 C H sing 1.09 N N
20 C1 H16 C H sing 1.09 N N
21 CA HA C H sing 1.09 N N
22 C4 H32 C H sing 1.09 N N
23 C4 H33 C H sing 1.09 N N
24 CB H39 C H sing 1.09 N N
25 CB H40 C H sing 1.09 N N
26 CG H41 C H sing 1.08 N N
27 CE H44 C H sing 1.09 N N
28 CE H45 C H sing 1.09 N N
29 C0 H55 C H sing 1.09 N N
30 C0 H56 C H sing 1.09 N N
31 C3 H63 C H sing 1.09 N N
32 C3 H64 C H sing 1.09 N N
33 C OXT C O sing 1.34 N N
34 OXT HXT O H sing 0.97 N N
35 N H N H sing 1.01 N N



04X : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
04X 4u1v Open in New Window Polymer component 2 1
04X 4u27 Open in New Window Polymer component 2 1