Chemical Components in the PDB

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2KY : Summary

Code

2KY

One-letter code

X

Molecule name

(2S)-amino(cyclopentyl)ethanoic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-amino(cyclopentyl)ethanoic acid
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-2-cyclopentyl-ethanoic acid

Formula

C7 H13 N O2

Formal charge

0

Molecular weight

143.184 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)C1CCCC1
SMILES CACTVS 3.385 N[CH](C1CCCC1)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 C1CCC(C1)C(C(=O)O)N
Canonical SMILES CACTVS 3.385 N[C@@H](C1CCCC1)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1CCC(C1)[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C7H13NO2/c8-6(7(9)10)5-3-1-2-4-5/h5-6H,1-4,8H2,(H,9,10)/t6-/m0/s1

IUPAC InChI key

XBPKRVHTESHFAA-LURJTMIESA-N

Is part of

4P2
2KY

wwPDB Information

Atom count

23 (10 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2013-11-22

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



2KY : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C5 N N N 0 1.842 -0.313 0.032
2 CA C C6 S N N 0 0.711 0.587 0.459
3 N N N7 N N N 0 1.073 1.986 0.196
4 O O O32 N N N 0 2.672 0.089 -0.748
5 C33 C C33 N N N 0 -0.551 0.229 -0.329
6 C34 C C34 N N N 0 -1.725 1.138 0.09
7 C35 C C35 N N N 0 -2.986 0.256 0.089
8 C36 C C36 N N N 0 -2.534 -1.158 -0.331
9 C37 C C37 N N N 0 -1.028 -1.199 0.032
10 HA H H6 N N N 0 0.524 0.454 1.525
11 H H H7 N N N 0 1.251 2.135 -0.786
12 H33 H H33 N N N 0 -0.367 0.313 -1.4
13 H341 H H341 N N N 0 -1.55 1.537 1.089
14 H342 H H342 N N N 0 -1.839 1.954 -0.623
15 H352 H H352 N N N 0 -3.422 0.227 1.088
16 H351 H H351 N N N 0 -3.712 0.643 -0.625
17 H361 H H361 N N N 0 -3.082 -1.916 0.229
18 H362 H H362 N N N 0 -2.674 -1.301 -1.403
19 H371 H H371 N N N 0 -0.507 -1.944 -0.569
20 H372 H H372 N N N 0 -0.892 -1.395 1.095
21 H2 H H2 N N Y 0 0.358 2.614 0.532
22 OXT O OXT N N Y 0 1.929 -1.559 0.522
23 HXT H HXT N N Y 0 2.672 -2.099 0.219



2KY : Chemical Bonds

Total Number of Bonds: 23
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C O C doub 1.21 N N
2 C CA C C sing 1.51 N N
3 N CA N C sing 1.47 N N
4 CA C33 C C sing 1.53 N N
5 C33 C34 C C sing 1.54 N N
6 C33 C37 C C sing 1.55 N N
7 C34 C35 C C sing 1.54 N N
8 C37 C36 C C sing 1.55 N N
9 C35 C36 C C sing 1.54 N N
10 CA HA C H sing 1.09 N N
11 N H N H sing 1.01 N N
12 C33 H33 C H sing 1.09 N N
13 C34 H341 C H sing 1.09 N N
14 C34 H342 C H sing 1.09 N N
15 C35 H352 C H sing 1.09 N N
16 C35 H351 C H sing 1.09 N N
17 C36 H361 C H sing 1.09 N N
18 C36 H362 C H sing 1.09 N N
19 C37 H371 C H sing 1.09 N N
20 C37 H372 C H sing 1.09 N N
21 N H2 N H sing 1.01 N N
22 C OXT C O sing 1.34 N N
23 OXT HXT O H sing 0.97 N N



2KY : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
2KY 6b5q Open in New Window Polymer component 2 1
2KY 8qke Open in New Window Polymer component 2 1
2KY 6fe6 Open in New Window Sub-component 1 1