Chemical Components in the PDB

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L1Y : Summary

Code

L1Y

One-letter code

X

Molecule name

4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 4-[(1S,2R)-2-(carboxymethyl)cyclopentane-1-carbonyl]benzoic acid
OpenEye OEToolkits 2.0.7 4-[(1~{S},2~{R})-2-(2-hydroxy-2-oxoethyl)cyclopentyl]carbonylbenzoic acid

Formula

C15 H16 O5

Formal charge

0

Molecular weight

276.285 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(C(CCC1)CC(=O)O)C(c2ccc(cc2)C(O)=O)=O
SMILES CACTVS 3.385 OC(=O)C[CH]1CCC[CH]1C(=O)c2ccc(cc2)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C(=O)C2CCCC2CC(=O)O)C(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)C[C@H]1CCC[C@@H]1C(=O)c2ccc(cc2)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(ccc1C(=O)[C@H]2CCC[C@@H]2CC(=O)O)C(=O)O

IUPAC InChI

InChI=1S/C15H16O5/c16-13(17)8-11-2-1-3-12(11)14(18)9-4-6-10(7-5-9)15(19)20/h4-7,11-12H,1-3,8H2,(H,16,17)(H,19,20)/t11-,12+/m1/s1

IUPAC InChI key

AIBKYDBZFDNIIN-NEPJUHHUSA-N
L1Y

wwPDB Information

Atom count

36 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-01-31

Last modified at

2020-01-31

Status

Released

Obsoleted

Not Assigned



L1Y : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 S N N 0 -1.304 0.523 0.563
2 C12 C C2 N N N 0 -1.443 1.809 1.402
3 C14 C C3 N N N 0 -3.633 1.343 0.484
4 O17 O O1 N N N 0 -4.983 -0.695 -0.995
5 C01 C C4 N Y N 0 2.857 -0.47 1.051
6 C02 C C5 N Y N 0 3.776 -0.271 0.019
7 C03 C C6 N Y N 0 3.352 0.26 -1.201
8 C04 C C7 N Y N 0 2.026 0.587 -1.387
9 C05 C C8 N Y N 0 1.106 0.388 -0.354
10 C06 C C9 N Y N 0 1.531 -0.149 0.865
11 C07 C C10 N N N 0 -0.312 0.738 -0.552
12 C08 C C11 N N N 0 -3.192 -1.135 0.471
13 C09 C C12 N N N 0 -4.498 -1.468 -0.203
14 C11 C C13 R N N 0 -2.696 0.226 -0.021
15 C13 C C14 N N N 0 -2.68 2.522 0.803
16 C18 C C15 N N N 0 5.199 -0.621 0.218
17 O15 O O2 N N N 0 -5.123 -2.622 0.077
18 O16 O O3 N N N 0 -0.681 1.198 -1.61
19 O19 O O4 N N N 0 6.086 -0.429 -0.778
20 O20 O O5 N N N 0 5.569 -1.082 1.279
21 H1 H H1 N N N 0 -0.981 -0.303 1.196
22 H2 H H2 N N N 0 -1.614 1.565 2.45
23 H3 H H3 N N N 0 -0.555 2.432 1.295
24 H4 H H4 N N N 0 -4.343 1.626 -0.293
25 H5 H H5 N N N 0 -4.16 1.022 1.383
26 H6 H H6 N N N 0 3.186 -0.88 1.995
27 H7 H H7 N N N 0 4.063 0.414 -1.999
28 H8 H H8 N N N 0 1.699 0.998 -2.33
29 H9 H H9 N N N 0 0.82 -0.303 1.664
30 H10 H H10 N N N 0 -3.338 -1.1 1.55
31 H11 H H11 N N N 0 -2.453 -1.9 0.229
32 H12 H H12 N N N 0 -2.655 0.237 -1.11
33 H13 H H13 N N N 0 -3.13 3.195 1.533
34 H14 H H14 N N N 0 -2.414 3.06 -0.107
35 H15 H H15 N N N 0 -5.958 -2.792 -0.38
36 H16 H H16 N N N 0 7.004 -0.673 -0.601



L1Y : Chemical Bonds

Total Number of Bonds: 37
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O17 C09 O C doub 1.21 N N
2 O16 C07 O C doub 1.21 N N
3 C08 C09 C C sing 1.51 N N
4 C08 C11 C C sing 1.53 N N
5 C09 O15 C O sing 1.34 N N
6 C07 C10 C C sing 1.51 N N
7 C07 C05 C C sing 1.47 N N
8 C10 C11 C C sing 1.54 N N
9 C10 C12 C C sing 1.54 N N
10 C06 C05 C C doub 1.4 N Y
11 C06 C01 C C sing 1.38 N Y
12 C11 C14 C C sing 1.54 N N
13 C12 C13 C C sing 1.55 N N
14 C05 C04 C C sing 1.4 N Y
15 C13 C14 C C sing 1.55 N N
16 C01 C02 C C doub 1.4 N Y
17 C04 C03 C C doub 1.38 N Y
18 C02 C03 C C sing 1.4 N Y
19 C02 C18 C C sing 1.48 N N
20 O20 C18 O C doub 1.21 N N
21 C18 O19 C O sing 1.35 N N
22 C10 H1 C H sing 1.09 N N
23 C12 H2 C H sing 1.09 N N
24 C12 H3 C H sing 1.09 N N
25 C14 H4 C H sing 1.09 N N
26 C14 H5 C H sing 1.09 N N
27 C01 H6 C H sing 1.08 N N
28 C03 H7 C H sing 1.08 N N
29 C04 H8 C H sing 1.08 N N
30 C06 H9 C H sing 1.08 N N
31 C08 H10 C H sing 1.09 N N
32 C08 H11 C H sing 1.09 N N
33 C11 H12 C H sing 1.09 N N
34 C13 H13 C H sing 1.09 N N
35 C13 H14 C H sing 1.09 N N
36 O15 H15 O H sing 0.97 N N
37 O19 H16 O H sing 0.97 N N



L1Y : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
L1Y 6nu6 Open in New Window Bound ligand 4 1