Chemical Components in the PDB

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OBF : Summary

Code

OBF

One-letter code

X

Molecule name

(2S)-2-amino-4,4-difluorobutanoic acid

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S)-2-amino-4,4-difluorobutanoic acid
OpenEye OEToolkits 1.5.0 (2S)-2-amino-4,4-difluoro-butanoic acid

Formula

C4 H7 F2 N O2

Formal charge

0

Molecular weight

139.101 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 FC(F)CC(N)C(=O)O
SMILES CACTVS 3.341 N[CH](CC(F)F)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 C(C(C(=O)O)N)C(F)F
Canonical SMILES CACTVS 3.341 N[C@@H](CC(F)F)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C([C@@H](C(=O)O)N)C(F)F

IUPAC InChI

InChI=1S/C4H7F2NO2/c5-3(6)1-2(7)4(8)9/h2-3H,1,7H2,(H,8,9)/t2-/m0/s1

IUPAC InChI key

VIUCNIMDPZQXAD-REOHCLBHSA-N
OBF

wwPDB Information

Atom count

16 (9 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

Yes

Standard parent

UNK

Defined at

2008-03-14

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



OBF : 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 N N N N N N 0 -0.388 -1.651 0.241
2 CA C CA S N N 0 -0.604 -0.218 0.478
3 CB C CB N N N 0 0.449 0.59 -0.283
4 CG C CG N N N 0 1.835 0.289 0.292
5 FG1 F FG1 N N N 0 2.156 -1.052 0.058
6 FG2 F FG2 N N N 0 2.784 1.111 -0.326
7 C C C N N N 0 -1.979 0.169 -0.005
8 O O O N N N 0 -2.559 -0.53 -0.801
9 H H HN N N N 0 -1.031 -2.208 0.783
10 HA H HA N N N 0 -0.522 -0.009 1.544
11 H1B H H1B N N N 0 0.426 0.315 -1.338
12 H2B H H2B N N N 0 0.236 1.654 -0.18
13 HXT H HXT N N Y 0 -3.44 1.498 0.112
14 HG H HG N N N 0 1.832 0.48 1.365
15 H2 H HNA N N Y 0 -0.459 -1.87 -0.742
16 OXT O OXT N N Y 0 -2.558 1.291 0.45



OBF : Chemical Bonds

Total Number of Bonds: 15
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N H2 N H sing 1.01 N N
2 CA N C N sing 1.47 N N
3 CA C C C sing 1.51 N N
4 CA HA C H sing 1.09 N N
5 CB CA C C sing 1.53 N N
6 CG CB C C sing 1.53 N N
7 CG HG C H sing 1.09 N N
8 FG1 CG F C sing 1.4 N N
9 FG2 CG F C sing 1.4 N N
10 C OXT C O sing 1.34 N N
11 O C O C doub 1.21 N N
12 H N H N sing 1.01 N N
13 H1B CB H C sing 1.09 N N
14 H2B CB H C sing 1.09 N N
15 OXT HXT O H sing 0.97 N N



OBF : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
OBF 2k1q Open in New Window Polymer component 1 1
OBF 4y10 Open in New Window Polymer component 1 1
OBF 6tvu Open in New Window Polymer component 1 1
OBF 7qis Open in New Window Polymer component 2 1