Chemical Components in the PDB

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XDT : Summary

Code

XDT

One-letter code

T

Molecule name

O-methyl-D-allothreonine

Systematic names

ProgramVersionName
ACDLabs 12.01 O-methyl-D-allothreonine
OpenEye OEToolkits 2.0.6 (2~{R})-2-azanyl-3-methoxy-butanoic acid

Formula

C5 H11 N O3

Formal charge

0

Molecular weight

133.146 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 NC(C(=O)O)C(OC)C
SMILES CACTVS 3.385 CO[CH](C)[CH](N)C(O)=O
SMILES OpenEye OEToolkits 2.0.6 CC(C(C(=O)O)N)OC
Canonical SMILES CACTVS 3.385 CO[C@H](C)[C@@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.6 CC([C@H](C(=O)O)N)OC

IUPAC InChI

InChI=1S/C5H11NO3/c1-3(9-2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t3-,4-/m1/s1

IUPAC InChI key

FYCWLJLGIAUCCL-QWWZWVQMSA-N
XDT

wwPDB Information

Atom count

20 (9 without Hydrogen)

Polymer type

Amino Acid

Type description

D-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

DTH

Defined at

2013-06-06

Last modified at

2018-01-16

Status

Released

Obsoleted

Not Assigned



XDT : 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 N N N N N N 0 -1.024 1.967 -0.067
2 CA C CA R N N 0 -0.478 0.7 0.438
3 C C C N N N 0 -1.395 -0.432 0.054
4 O O O N N N 0 -2.181 -0.291 -0.854
5 CB C CB R N N 0 0.907 0.464 -0.169
6 OG1 O OG1 N N N 0 1.438 -0.768 0.323
7 CG2 C CG2 N N N 0 1.838 1.613 0.222
8 CD1 C CD1 N N N 0 2.317 -1.428 -0.59
9 OXT O OXT N N Y 0 -1.339 -1.596 0.719
10 H H H N N N 0 -1.11 1.948 -1.072
11 H2 H H2 N N Y 0 -1.91 2.178 0.368
12 HCA H HCA N N N 0 -0.395 0.748 1.524
13 HB H HB N N N 0 0.824 0.416 -1.254
14 HG21 H HG21 N N N 0 1.433 2.553 -0.153
15 HG22 H HG22 N N N 0 1.921 1.661 1.308
16 HG23 H HG23 N N N 0 2.824 1.445 -0.21
17 HD11 H HD11 N N N 0 1.781 -1.654 -1.512
18 HD12 H HD12 N N N 0 3.164 -0.778 -0.813
19 HD13 H HD13 N N N 0 2.678 -2.354 -0.143
20 HXT H HXT N N Y 0 -1.947 -2.293 0.436



XDT : Chemical Bonds

Total Number of Bonds: 19
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 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 CA C C C sing 1.51 N N
5 CA CB C C sing 1.53 N N
6 CA HCA C H sing 1.09 N N
7 C O C O doub 1.21 N N
8 C OXT C O sing 1.34 N N
9 CB OG1 C O sing 1.43 N N
10 CB CG2 C C sing 1.53 N N
11 CB HB C H sing 1.09 N N
12 OG1 CD1 O C sing 1.43 N N
13 CG2 HG21 C H sing 1.09 N N
14 CG2 HG22 C H sing 1.09 N N
15 CG2 HG23 C H sing 1.09 N N
16 CD1 HD11 C H sing 1.09 N N
17 CD1 HD12 C H sing 1.09 N N
18 CD1 HD13 C H sing 1.09 N N
19 OXT HXT O H sing 0.97 N N



XDT : Used in PDB Entries

Total Number of PDB Entries: 0
Ligand Code PDB Entry ID Type Total Distinct