Chemical Components in the PDB

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6DN : Summary

Code

6DN

One-letter code

K

Molecule name

(2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 (2~{S})-2-azanyl-6-(2-hydroxy-2-oxoethylamino)hexanoic acid

Formula

C8 H16 N2 O4

Formal charge

0

Molecular weight

204.224 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 N[CH](CCCCNCC(O)=O)C(O)=O
SMILES OpenEye OEToolkits 2.0.5 C(CCNCC(=O)O)CC(C(=O)O)N
Canonical SMILES CACTVS 3.385 N[C@@H](CCCCNCC(O)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.5 C(CCNCC(=O)O)C[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C8H16N2O4/c9-6(8(13)14)3-1-2-4-10-5-7(11)12/h6,10H,1-5,9H2,(H,11,12)(H,13,14)/t6-/m0/s1

IUPAC InChI key

NUXSIDPKKIEIMI-LURJTMIESA-N
6DN

wwPDB Information

Atom count

30 (14 without Hydrogen)

Polymer type

Amino Acid

Type description

NON-POLYMER

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

2016-03-30

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



6DN : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1 O O1 N N N 0
2 O2 O O2 N N N 0
3 CB C C1 N N N 0
4 CA C C2 S N N 0
5 C C C3 N N N 0
6 O O O3 N N N 0
7 N N N1 N N N 0
8 CG C C4 N N N 0
9 CD C C5 N N N 0
10 CE C C6 N N N 0
11 NZ N N2 N N N 0
12 CX1 C C7 N N N 0
13 CX2 C C8 N N N 0
14 OXT O O4 N N Y 0
15 H1 H H1 N N N 0
16 HB2 H H2 N N N 0
17 HB3 H H3 N N N 0
18 HA H H4 N N N 0
19 H H H5 N N N 0
20 H2 H H6 N N Y 0
21 HG2 H H8 N N N 0
22 HG3 H H9 N N N 0
23 HD2 H H10 N N N 0
24 HD3 H H11 N N N 0
25 HE2 H H12 N N N 0
26 HE3 H H13 N N N 0
27 HZ1 H H14 N N N 0
28 H16 H H16 N N N 0
29 H17 H H17 N N N 0
30 HXT H H18 N N Y 0



6DN : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 CX2 O C doub N N
2 NZ CE N C sing N N
3 NZ CX1 N C sing N N
4 CX2 O1 C O sing N N
5 CX2 CX1 C C sing N N
6 CE CD C C sing N N
7 CD CG C C sing N N
8 CG CB C C sing N N
9 CB CA C C sing N N
10 CA C C C sing N N
11 CA N C N sing N N
12 C O C O doub N N
13 C OXT C O sing N N
14 O1 H1 O H sing N N
15 CB HB2 C H sing N N
16 CB HB3 C H sing N N
17 CA HA C H sing N N
18 N H N H sing N N
19 N H2 N H sing N N
20 CG HG2 C H sing N N
21 CG HG3 C H sing N N
22 CD HD2 C H sing N N
23 CD HD3 C H sing N N
24 CE HE2 C H sing N N
25 CE HE3 C H sing N N
26 NZ HZ1 N H sing N N
27 CX1 H16 C H sing N N
28 CX1 H17 C H sing N N
29 OXT HXT O H sing N N



6DN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6DN 5j2s Open in New Window Polymer component 2 1