Chemical Components in the PDB

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L5J : Summary

Code

L5J

One-letter code

X

Molecule name

(4-{[(1R,2R)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (4-{[(1R,2R)-2-(carboxymethyl)cyclopentyl]methyl}phenyl)acetic acid
OpenEye OEToolkits 2.0.7 2-[4-[[(1~{R},2~{R})-2-(2-hydroxy-2-oxoethyl)cyclopentyl]methyl]phenyl]ethanoic acid

Formula

C16 H20 O4

Formal charge

0

Molecular weight

276.328 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(C(CC(O)=O)CCC1)Cc2ccc(cc2)CC(O)=O
SMILES CACTVS 3.385 OC(=O)C[CH]1CCC[CH]1Cc2ccc(CC(O)=O)cc2
SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1CC2CCCC2CC(=O)O)CC(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)C[C@H]1CCC[C@@H]1Cc2ccc(CC(O)=O)cc2
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C[C@H]2CCC[C@@H]2CC(=O)O)CC(=O)O

IUPAC InChI

InChI=1S/C16H20O4/c17-15(18)9-12-6-4-11(5-7-12)8-13-2-1-3-14(13)10-16(19)20/h4-7,13-14H,1-3,8-10H2,(H,17,18)(H,19,20)/t13-,14-/m1/s1

IUPAC InChI key

QKXFMUHRVZWRPO-ZIAGYGMSSA-N
L5J

wwPDB Information

Atom count

40 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-02-06

Last modified at

2020-02-07

Status

Released

Obsoleted

Not Assigned



L5J : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 R N N 0 -1.482 -0.232 -0.064
2 C13 C C2 N N N 0 -2.291 -2.44 -0.716
3 C11 C C3 R N N 0 -3.011 -0.259 0.108
4 C12 C C4 N N N 0 -1.114 -1.455 -0.93
5 C14 C C5 N N N 0 -3.519 -1.497 -0.659
6 C01 C C6 N Y N 0 2.844 -1.158 0.755
7 C02 C C7 N Y N 0 3.424 0.096 0.814
8 C03 C C8 N Y N 0 2.636 1.211 1.031
9 C04 C C9 N Y N 0 1.27 1.073 1.189
10 C05 C C10 N Y N 0 0.691 -0.181 1.13
11 C06 C C11 N Y N 0 1.478 -1.296 0.913
12 C07 C C12 N N N 0 -0.799 -0.331 1.301
13 C08 C C13 N N N 0 -3.627 1.011 -0.481
14 C09 C C14 N N N 0 -5.107 1.03 -0.197
15 C17 C C15 N N N 0 4.913 0.247 0.643
16 C18 C C16 N N N 0 5.233 0.444 -0.817
17 O15 O O1 N N N 0 -5.616 0.12 0.413
18 O16 O O2 N N N 0 -5.859 2.057 -0.623
19 O19 O O3 N N N 0 6.507 0.602 -1.209
20 O20 O O4 N N N 0 4.343 0.461 -1.633
21 H1 H H1 N N N 0 -1.179 0.686 -0.567
22 H2 H H2 N N N 0 -2.373 -3.132 -1.554
23 H3 H H3 N N N 0 -2.174 -2.983 0.222
24 H4 H H4 N N N 0 -3.266 -0.343 1.164
25 H5 H H5 N N N 0 -1.041 -1.171 -1.98
26 H6 H H6 N N N 0 -0.179 -1.898 -0.587
27 H7 H H7 N N N 0 -3.834 -1.22 -1.665
28 H8 H H8 N N N 0 -4.339 -1.971 -0.119
29 H9 H H9 N N N 0 3.459 -2.029 0.581
30 H10 H H10 N N N 0 3.089 2.191 1.078
31 H11 H H11 N N N 0 0.655 1.945 1.359
32 H12 H H12 N N N 0 1.025 -2.275 0.862
33 H13 H H13 N N N 0 -1.171 0.46 1.952
34 H14 H H14 N N N 0 -1.017 -1.302 1.747
35 H15 H H15 N N N 0 -3.159 1.886 -0.028
36 H16 H H16 N N N 0 -3.463 1.029 -1.558
37 H17 H H17 N N N 0 5.259 1.11 1.211
38 H18 H H18 N N N 0 5.413 -0.651 1.006
39 H19 H H19 N N N 0 -6.803 2.025 -0.417
40 H20 H H20 N N N 0 6.663 0.726 -2.155



L5J : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O20 C18 O C doub 1.21 N N
2 O19 C18 O C sing 1.34 N N
3 C18 C17 C C sing 1.51 N N
4 C17 C02 C C sing 1.51 N N
5 C02 C01 C C doub 1.38 N Y
6 C02 C03 C C sing 1.38 N Y
7 C01 C06 C C sing 1.38 N Y
8 C03 C04 C C doub 1.38 N Y
9 C06 C05 C C doub 1.38 N Y
10 C04 C05 C C sing 1.38 N Y
11 C05 C07 C C sing 1.51 N N
12 O15 C09 O C doub 1.21 N N
13 C07 C10 C C sing 1.53 N N
14 C09 O16 C O sing 1.34 N N
15 C09 C08 C C sing 1.51 N N
16 C12 C10 C C sing 1.54 N N
17 C12 C13 C C sing 1.55 N N
18 C10 C11 C C sing 1.54 N N
19 C11 C08 C C sing 1.53 N N
20 C11 C14 C C sing 1.54 N N
21 C14 C13 C C sing 1.55 N N
22 C10 H1 C H sing 1.09 N N
23 C13 H2 C H sing 1.09 N N
24 C13 H3 C H sing 1.09 N N
25 C11 H4 C H sing 1.09 N N
26 C12 H5 C H sing 1.09 N N
27 C12 H6 C H sing 1.09 N N
28 C14 H7 C H sing 1.09 N N
29 C14 H8 C H sing 1.09 N N
30 C01 H9 C H sing 1.08 N N
31 C03 H10 C H sing 1.08 N N
32 C04 H11 C H sing 1.08 N N
33 C06 H12 C H sing 1.08 N N
34 C07 H13 C H sing 1.09 N N
35 C07 H14 C H sing 1.09 N N
36 C08 H15 C H sing 1.09 N N
37 C08 H16 C H sing 1.09 N N
38 C17 H17 C H sing 1.09 N N
39 C17 H18 C H sing 1.09 N N
40 O16 H19 O H sing 0.97 N N
41 O19 H20 O H sing 0.97 N N



L5J : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
L5J 6nvf Open in New Window Bound ligand 2 1