Chemical Components in the PDB

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TDA : Summary

Code

TDA

One-letter code

X

Molecule name

N-TRIDECANOIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 tridecanoic acid
OpenEye OEToolkits 1.5.0 tridecanoic acid

Formula

C13 H26 O2

Formal charge

0

Molecular weight

214.344 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)CCCCCCCCCCCC
SMILES CACTVS 3.341 CCCCCCCCCCCCC(O)=O
SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCC(=O)O
Canonical SMILES CACTVS 3.341 CCCCCCCCCCCCC(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCC(=O)O

IUPAC InChI

InChI=1S/C13H26O2/c1-2-3-4-5-6-7-8-9-10-11-12-13(14)15/h2-12H2,1H3,(H,14,15)

IUPAC InChI key

SZHOJFHSIKHZHA-UHFFFAOYSA-N
TDA

wwPDB Information

Atom count

41 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-09-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



TDA : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O21 O O21 N N N 0 0.439 0.0 -7.555
2 O22 O O22 N N N 0 -1.354 0.0 -6.265
3 C21 C C21 N N N 0 -0.149 0.0 -6.349
4 C22 C C22 N N N 0 0.693 0.0 -5.099
5 C23 C C23 N N N 0 -0.218 0.0 -3.87
6 C24 C C24 N N N 0 0.637 0.0 -2.601
7 C25 C C25 N N N 0 -0.274 0.0 -1.372
8 C26 C C26 N N N 0 0.581 0.0 -0.103
9 C27 C C27 N N N 0 -0.33 0.0 1.125
10 C28 C C28 N N N 0 0.525 0.0 2.394
11 C29 C C29 N N N 0 -0.386 0.0 3.623
12 C30 C C30 N N N 0 0.469 0.0 4.892
13 C31 C C31 N N N 0 -0.442 0.0 6.121
14 C32 C C32 N N N 0 0.413 0.0 7.389
15 C33 C C33 N N N 0 -0.498 0.0 8.619
16 H21 H H21 N N N 0 -0.1 0.0 -8.357
17 H222 H 2H22 N N N 0 1.322 0.89 -5.085
18 H221 H 1H22 N N N 0 1.322 -0.89 -5.085
19 H232 H 2H23 N N N 0 -0.847 -0.89 -3.884
20 H231 H 1H23 N N N 0 -0.847 0.89 -3.884
21 H242 H 2H24 N N N 0 1.266 0.89 -2.587
22 H241 H 1H24 N N N 0 1.266 -0.89 -2.587
23 H252 H 2H25 N N N 0 -0.903 -0.89 -1.386
24 H251 H 1H25 N N N 0 -0.903 0.89 -1.386
25 H262 H 2H26 N N N 0 1.21 0.89 -0.089
26 H261 H 1H26 N N N 0 1.21 -0.89 -0.089
27 H272 H 2H27 N N N 0 -0.959 -0.89 1.111
28 H271 H 1H27 N N N 0 -0.959 0.89 1.111
29 H282 H 2H28 N N N 0 1.154 0.89 2.408
30 H281 H 1H28 N N N 0 1.154 -0.89 2.408
31 H292 H 2H29 N N N 0 -1.015 -0.89 3.609
32 H291 H 1H29 N N N 0 -1.015 0.89 3.609
33 H302 H 2H30 N N N 0 1.098 0.89 4.906
34 H301 H 1H30 N N N 0 1.098 -0.89 4.906
35 H312 H 2H31 N N N 0 -1.071 -0.89 6.107
36 H311 H 1H31 N N N 0 -1.071 0.89 6.107
37 H322 H 2H32 N N N 0 1.042 0.89 7.404
38 H321 H 1H32 N N N 0 1.042 -0.89 7.404
39 H333 H 3H33 N N N 0 0.111 0.0 9.522
40 H332 H 2H33 N N N 0 -1.127 0.89 8.604
41 H331 H 1H33 N N N 0 -1.127 -0.89 8.604



TDA : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O21 C21 O C sing 1.34 N N
2 O21 H21 O H sing 0.97 N N
3 O22 C21 O C doub 1.21 N N
4 C21 C22 C C sing 1.51 N N
5 C22 C23 C C sing 1.53 N N
6 C22 H222 C H sing 1.09 N N
7 C22 H221 C H sing 1.09 N N
8 C23 C24 C C sing 1.53 N N
9 C23 H232 C H sing 1.09 N N
10 C23 H231 C H sing 1.09 N N
11 C24 C25 C C sing 1.53 N N
12 C24 H242 C H sing 1.09 N N
13 C24 H241 C H sing 1.09 N N
14 C25 C26 C C sing 1.53 N N
15 C25 H252 C H sing 1.09 N N
16 C25 H251 C H sing 1.09 N N
17 C26 C27 C C sing 1.53 N N
18 C26 H262 C H sing 1.09 N N
19 C26 H261 C H sing 1.09 N N
20 C27 C28 C C sing 1.53 N N
21 C27 H272 C H sing 1.09 N N
22 C27 H271 C H sing 1.09 N N
23 C28 C29 C C sing 1.53 N N
24 C28 H282 C H sing 1.09 N N
25 C28 H281 C H sing 1.09 N N
26 C29 C30 C C sing 1.53 N N
27 C29 H292 C H sing 1.09 N N
28 C29 H291 C H sing 1.09 N N
29 C30 C31 C C sing 1.53 N N
30 C30 H302 C H sing 1.09 N N
31 C30 H301 C H sing 1.09 N N
32 C31 C32 C C sing 1.53 N N
33 C31 H312 C H sing 1.09 N N
34 C31 H311 C H sing 1.09 N N
35 C32 C33 C C sing 1.53 N N
36 C32 H322 C H sing 1.09 N N
37 C32 H321 C H sing 1.09 N N
38 C33 H333 C H sing 1.09 N N
39 C33 H332 C H sing 1.09 N N
40 C33 H331 C H sing 1.09 N N



TDA : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
TDA 1qll Open in New Window Bound ligand 2 1
TDA 1tc8 Open in New Window Bound ligand 1 1
TDA 1tp2 Open in New Window Bound ligand 2 1
TDA 4rw3 Open in New Window Bound ligand 1 1
TDA 4rw5 Open in New Window Bound ligand 1 1
TDA 4xu6 Open in New Window Bound ligand 2 1
TDA 6ghh Open in New Window Bound ligand 1 1
TDA 7a9y Open in New Window Bound ligand 1 1
TDA 7fg1 Open in New Window Bound ligand 1 1