Chemical Components in the PDB

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QXV : Summary

Code

QXV

One-letter code

X

Molecule name

D-methioninamide

Systematic names

ProgramVersionName
ACDLabs 12.01 D-methioninamide
OpenEye OEToolkits 2.0.7 (2~{R})-2-azanyl-4-methylsulfanyl-butanamide

Formula

C5 H12 N2 O S

Formal charge

0

Molecular weight

148.227 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(C(N)=O)CCSC
SMILES CACTVS 3.385 CSCC[CH](N)C(N)=O
SMILES OpenEye OEToolkits 2.0.7 CSCCC(C(=O)N)N
Canonical SMILES CACTVS 3.385 CSCC[C@@H](N)C(N)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CSCC[C@H](C(=O)N)N

IUPAC InChI

InChI=1S/C5H12N2OS/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H2,7,8)/t4-/m1/s1

IUPAC InChI key

GSYTVXOARWSQSV-SCSAIBSYSA-N
QXV

wwPDB Information

Atom count

21 (9 without Hydrogen)

Polymer type

Amino Acid

Type description

D-peptide linking

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2020-01-13

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



QXV : Atoms of Molecule

Total Number of Atoms: 21
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N N N 0 -1.256 1.812 0.15
2 CA C C1 R N N 0 -1.238 0.383 0.489
3 C C C2 N N N 0 -2.515 -0.262 0.016
4 O O O1 N N N 0 -3.183 0.275 -0.842
5 CB C C3 N N N 0 -0.044 -0.288 -0.193
6 CG C C4 N N N 0 1.256 0.281 0.379
7 SD S S1 N N N 0 2.672 -0.515 -0.431
8 CE C C5 N N N 0 4.096 0.277 0.367
9 NXT N N2 N N N 0 -2.914 -1.435 0.546
10 H1 H H1 N N N 0 -1.336 1.946 -0.847
11 H2 H H2 N N Y 0 -1.997 2.291 0.64
12 H4 H H4 N N N 0 -1.151 0.268 1.57
13 H5 H H5 N N N 0 -0.08 -1.362 -0.015
14 H6 H H6 N N N 0 -0.084 -0.096 -1.266
15 H7 H H7 N N N 0 1.293 1.356 0.2
16 H8 H H8 N N N 0 1.296 0.089 1.451
17 H9 H H9 N N N 0 4.061 1.352 0.188
18 H10 H H10 N N N 0 4.064 0.086 1.439
19 H11 H H11 N N N 0 5.017 -0.13 -0.048
20 H12 H H12 N N N 0 -2.379 -1.864 1.233
21 H13 H H13 N N N 0 -3.736 -1.85 0.242



QXV : 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 N CA N C sing 1.47 N N
2 CA C C C sing 1.51 N N
3 CA CB C C sing 1.53 N N
4 O C O C doub 1.21 N N
5 C NXT C N sing 1.35 N N
6 CG CB C C sing 1.53 N N
7 CG SD C S sing 1.82 N N
8 CE SD C S sing 1.81 N N
9 N H1 N H sing 1.01 N N
10 N H2 N H sing 1.01 N N
11 CA H4 C H sing 1.09 N N
12 CB H5 C H sing 1.09 N N
13 CB H6 C H sing 1.09 N N
14 CG H7 C H sing 1.09 N N
15 CG H8 C H sing 1.09 N N
16 CE H9 C H sing 1.09 N N
17 CE H10 C H sing 1.09 N N
18 CE H11 C H sing 1.09 N N
19 NXT H12 N H sing 0.97 N N
20 NXT H13 N H sing 0.97 N N



QXV : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
QXV 6lw5 Open in New Window Polymer component 1 1
QXV 6omm Open in New Window Polymer component 1 1
QXV 7t6u Open in New Window Polymer component 1 1