Chemical Components in the PDB

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OLN : Summary

Code

OLN

One-letter code

X

Molecule name

(S)-2-ACETAMIDO-5-UREIDOPENTANOIC ACID

Synonyms

N-ACETYL-L-CITRULLINE

Systematic names

ProgramVersionName
ACDLabs 10.04 N~2~-acetyl-N~5~-carbamoyl-L-ornithine
OpenEye OEToolkits 1.5.0 (2S)-2-acetamido-5-(aminocarbonylamino)pentanoic acid

Formula

C8 H15 N3 O4

Formal charge

0

Molecular weight

217.222 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(NC(=O)C)CCCNC(=O)N
SMILES CACTVS 3.341 CC(=O)N[CH](CCCNC(N)=O)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 CC(=O)NC(CCCNC(=O)N)C(=O)O
Canonical SMILES CACTVS 3.341 CC(=O)N[C@@H](CCCNC(N)=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(=O)N[C@@H](CCCNC(=O)N)C(=O)O

IUPAC InChI

InChI=1S/C8H15N3O4/c1-5(12)11-6(7(13)14)3-2-4-10-8(9)15/h6H,2-4H2,1H3,(H,11,12)(H,13,14)(H3,9,10,15)/t6-/m0/s1

IUPAC InChI key

WMQMIOYQXNRROC-LURJTMIESA-N
OLN

wwPDB Information

Atom count

30 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-01-10

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



OLN : 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 CA C CA S N N 0 -0.48 -0.333 -1.61
2 C C C N N N 0 -1.501 -0.034 -2.678
3 O O O N N N 0 -2.291 -0.885 -3.013
4 OXT O OXT N N N 0 -1.532 1.175 -3.257
5 CB C CB N N N 0 -1.057 0.024 -0.239
6 CG C CG N N N 0 -0.02 -0.278 0.844
7 CD C CD N N N 0 -0.597 0.079 2.215
8 NE N NE N N N 0 0.395 -0.21 3.253
9 CZ C CZ N N N 0 0.105 0.027 4.548
10 O2 O O2 N N N 0 -0.979 0.483 4.854
11 NH2 N NH2 N N N 0 1.018 -0.239 5.503
12 N1 N N1 N N N 0 0.727 0.458 -1.854
13 C1 C C1 N N N 0 1.716 -0.039 -2.622
14 O1 O O1 N N N 0 1.606 -1.143 -3.111
15 C2 C C2 N N N 0 2.958 0.775 -2.873
16 HA H HA N N N 0 -0.23 -1.394 -1.633
17 HO H HO N N N 0 -2.187 1.367 -3.942
18 HB1 H 1HB N N N 0 -1.307 1.085 -0.216
19 HB2 H 2HB N N N 0 -1.955 -0.564 -0.057
20 HG1 H 1HG N N N 0 0.229 -1.339 0.821
21 HG2 H 2HG N N N 0 0.877 0.311 0.663
22 HD1 H 1HD N N N 0 -0.847 1.14 2.238
23 HD2 H 2HD N N N 0 -1.496 -0.509 2.397
24 HNE H HNE N N N 0 1.26 -0.573 3.009
25 HH21 H 1HH2 N N N 0 0.81 -0.067 6.434
26 HH22 H 2HH2 N N N 0 1.883 -0.602 5.258
27 HN1 H HN1 N N N 0 0.815 1.342 -1.463
28 H21 H 1H2 N N N 0 3.64 0.212 -3.511
29 H22 H 2H2 N N N 0 2.687 1.709 -3.366
30 H23 H 3H2 N N N 0 3.447 0.994 -1.924



OLN : 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 CA C C C sing 1.51 N N
2 CA CB C C sing 1.53 N N
3 CA N1 C N sing 1.46 N N
4 CA HA C H sing 1.09 N N
5 C O C O doub 1.21 N N
6 C OXT C O sing 1.34 N N
7 OXT HO O H sing 0.97 N N
8 CB CG C C sing 1.53 N N
9 CB HB1 C H sing 1.09 N N
10 CB HB2 C H sing 1.09 N N
11 CG CD C C sing 1.53 N N
12 CG HG1 C H sing 1.09 N N
13 CG HG2 C H sing 1.09 N N
14 CD NE C N sing 1.46 N N
15 CD HD1 C H sing 1.09 N N
16 CD HD2 C H sing 1.09 N N
17 NE CZ N C sing 1.35 N N
18 NE HNE N H sing 0.97 N N
19 CZ O2 C O doub 1.22 N N
20 CZ NH2 C N sing 1.35 N N
21 NH2 HH21 N H sing 0.97 N N
22 NH2 HH22 N H sing 0.97 N N
23 N1 C1 N C sing 1.35 N N
24 N1 HN1 N H sing 0.97 N N
25 C1 O1 C O doub 1.21 N N
26 C1 C2 C C sing 1.51 N N
27 C2 H21 C H sing 1.09 N N
28 C2 H22 C H sing 1.09 N N
29 C2 H23 C H sing 1.09 N N



OLN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OLN 3kzk Open in New Window Bound ligand 1 1