Chemical Components in the PDB

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KNA : Summary

Code

KNA

One-letter code

X

Molecule name

nonanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 nonanoic acid
OpenEye OEToolkits 1.7.2 nonanoic acid

Formula

C9 H18 O2

Formal charge

0

Molecular weight

158.238 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CCCCCCCC
SMILES CACTVS 3.370 CCCCCCCCC(O)=O
SMILES OpenEye OEToolkits 1.7.2 CCCCCCCCC(=O)O
Canonical SMILES CACTVS 3.370 CCCCCCCCC(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.2 CCCCCCCCC(=O)O

IUPAC InChI

InChI=1S/C9H18O2/c1-2-3-4-5-6-7-8-9(10)11/h2-8H2,1H3,(H,10,11)

IUPAC InChI key

FBUKVWPVBMHYJY-UHFFFAOYSA-N
KNA

wwPDB Information

Atom count

29 (11 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-09-30

Last modified at

2012-03-16

Status

Released

Obsoleted

Not Assigned



KNA : Atoms of Molecule

Total Number of Atoms: 29
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 3.924 -0.101 0.0010
2 C2 C C2 N N N 0 2.663 0.724 0.0
3 C3 C C3 N N N 0 1.446 -0.204 0.0010
4 C4 C C4 N N N 0 0.166 0.634 -0.0010
5 C5 C C5 N N N 0 -1.051 -0.294 0.0010
6 C6 C C6 N N N 0 -2.331 0.544 -0.0010
7 C7 C C7 N N N 0 -3.547 -0.384 0.0010
8 C8 C C8 N N N 0 -4.828 0.453 -0.0010
9 C9 C C9 N N N 0 -6.044 -0.475 0.0010
10 H2 H H2 N N N 0 2.64 1.355 0.888
11 H2A H H2A N N N 0 2.64 1.352 -0.891
12 H3 H H3 N N N 0 1.469 -0.834 -0.888
13 H3A H H3A N N N 0 1.469 -0.831 0.892
14 H4 H H4 N N N 0 0.143 1.264 0.888
15 H4A H H4A N N N 0 0.143 1.261 -0.892
16 H5 H H5 N N N 0 -1.028 -0.924 -0.888
17 H5A H H5A N N N 0 -1.028 -0.921 0.892
18 H6 H H6 N N N 0 -2.354 1.174 0.888
19 H6A H H6A N N N 0 -2.353 1.171 -0.892
20 H7 H H7 N N N 0 -3.525 -1.015 -0.888
21 H7A H H7A N N N 0 -3.525 -1.012 0.892
22 H8 H H8 N N N 0 -4.851 1.084 0.888
23 H8A H H8A N N N 0 -4.85 1.081 -0.892
24 H9 H H9 N N N 0 -6.021 -1.105 -0.888
25 H9A H H9A N N N 0 -6.022 -1.102 0.891
26 H9B H H9B N N N 0 -6.956 0.122 -0.0010
27 HO1 H HO1 N N N 0 5.902 -0.067 0.0020
28 O1 O O1 N N N 0 5.122 0.504 0.0
29 O2 O O2 N N N 0 3.856 -1.307 -0.0020



KNA : Chemical Bonds

Total Number of Bonds: 28
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C1 O C doub 1.21 N N
2 C1 C2 C C sing 1.51 N N
3 C1 O1 C O sing 1.34 N N
4 O1 HO1 O H sing 0.97 N N
5 C3 C2 C C sing 1.53 N N
6 C2 H2 C H sing 1.09 N N
7 C2 H2A C H sing 1.09 N N
8 C3 C4 C C sing 1.53 N N
9 C3 H3 C H sing 1.09 N N
10 C3 H3A C H sing 1.09 N N
11 C5 C4 C C sing 1.53 N N
12 C4 H4 C H sing 1.09 N N
13 C4 H4A C H sing 1.09 N N
14 C5 C6 C C sing 1.53 N N
15 C5 H5 C H sing 1.09 N N
16 C5 H5A C H sing 1.09 N N
17 C6 C7 C C sing 1.53 N N
18 C6 H6 C H sing 1.09 N N
19 C6 H6A C H sing 1.09 N N
20 C7 C8 C C sing 1.53 N N
21 C7 H7 C H sing 1.09 N N
22 C7 H7A C H sing 1.09 N N
23 C8 C9 C C sing 1.53 N N
24 C8 H8 C H sing 1.09 N N
25 C8 H8A C H sing 1.09 N N
26 C9 H9 C H sing 1.09 N N
27 C9 H9A C H sing 1.09 N N
28 C9 H9B C H sing 1.09 N N



KNA : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
KNA 3sz1 Open in New Window Bound ligand 2 1
KNA 4em9 Open in New Window Bound ligand 4 1
KNA 5ugm Open in New Window Bound ligand 2 1
KNA 6aug Open in New Window Bound ligand 1 1
KNA 6avi Open in New Window Bound ligand 3 1
KNA 6c1i Open in New Window Bound ligand 2 1
KNA 6ci6 Open in New Window Bound ligand 1 1
KNA 6dh9 Open in New Window Bound ligand 1 1
KNA 6dha Open in New Window Bound ligand 2 1
KNA 6o67 Open in New Window Bound ligand 1 1
KNA 6u4r Open in New Window Bound ligand 1 1