Chemical Components in the PDB

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PAF : Summary

Code

PAF

One-letter code

X

Molecule name

PANTOATE

Synonyms

2,4-DIHYDROXY-3,3-DIMETHYL-BUTYRATE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R)-2,4-dihydroxy-3,3-dimethylbutanoate
OpenEye OEToolkits 1.5.0 (2R)-2,4-dihydroxy-3,3-dimethyl-butanoate

Formula

C6 H11 O4

Formal charge

-1

Molecular weight

147.149 Da

SMILES

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

IUPAC InChI

InChI=1S/C6H12O4/c1-6(2,3-7)4(8)5(9)10/h4,7-8H,3H2,1-2H3,(H,9,10)/p-1/t4-/m0/s1

IUPAC InChI key

OTOIIPJYVQJATP-BYPYZUCNSA-M

Is part of

0JR
PAF

wwPDB Information

Atom count

21 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2002-11-05

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



PAF : 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 C1 C C1 N N N 0 1.772 0.196 0.118
2 C2 C C2 R N N 0 0.52 -0.442 0.662
3 C3 C C3 N N N 0 -0.704 0.167 -0.025
4 C4 C C4 N N N 0 -0.618 -0.081 -1.533
5 C5 C C5 N N N 0 -0.741 1.673 0.242
6 C6 C C6 N N N 0 -1.975 -0.481 0.527
7 H21 H 1H2 N N N 0 0.459 -0.265 1.736
8 H41 H 1H4 N N N 0 0.288 0.38 -1.926
9 H42 H 2H4 N N N 0 -0.591 -1.154 -1.723
10 H43 H 3H4 N N N 0 -1.49 0.353 -2.023
11 H51 H 1H5 N N N 0 -1.613 2.108 -0.248
12 H52 H 2H5 N N N 0 -0.802 1.85 1.316
13 H53 H 3H5 N N N 0 0.165 2.135 -0.152
14 H61 H 1H6 N N N 0 -1.948 -1.553 0.337
15 H62 H 2H6 N N N 0 -2.036 -0.303 1.601
16 HO31 H 1HO3 N N N 0 0.608 -1.962 -0.546
17 HO41 H 1HO4 N N N 0 -3.895 -0.346 0.261
18 O1 O O1 N N N -1 2.573 -0.474 -0.512
19 O2 O O2 N N N 0 1.984 1.382 0.308
20 O3 O O3 N N N 0 0.555 -1.849 0.413
21 O4 O O4 N N N 0 -3.117 0.089 -0.115



PAF : 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 O1 C1 O C sing 1.22 N N
2 C1 O2 C O doub 1.22 N N
3 C1 C2 C C sing 1.51 N N
4 C2 O3 C O sing 1.43 N N
5 C2 C3 C C sing 1.53 N N
6 C2 H21 C H sing 1.09 N N
7 O3 HO31 O H sing 0.97 N N
8 C3 C4 C C sing 1.53 N N
9 C3 C5 C C sing 1.53 N N
10 C3 C6 C C sing 1.53 N N
11 C4 H41 C H sing 1.09 N N
12 C4 H42 C H sing 1.09 N N
13 C4 H43 C H sing 1.09 N N
14 C5 H51 C H sing 1.09 N N
15 C5 H52 C H sing 1.09 N N
16 C5 H53 C H sing 1.09 N N
17 C6 O4 C O sing 1.43 N N
18 C6 H61 C H sing 1.09 N N
19 C6 H62 C H sing 1.09 N N
20 O4 HO41 O H sing 0.97 N N



PAF : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
PAF 1n2b Open in New Window Bound ligand 1 1
PAF 1n2e Open in New Window Bound ligand 1 1
PAF 1n2j Open in New Window Bound ligand 2 1
PAF 2ofp Open in New Window Bound ligand 2 1
PAF 3guz Open in New Window Bound ligand 3 1
PAF 3q12 Open in New Window Bound ligand 4 1
PAF 4nq8 Open in New Window Bound ligand 2 1
PAF 4pak Open in New Window Bound ligand 1 1
PAF 4xeq Open in New Window Bound ligand 4 1
PAF 4gi7 Open in New Window Sub-component 5 1