Chemical Components in the PDB

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LN5 : Summary

Code

LN5

One-letter code

X

Molecule name

N5-(1-iminopropyl)-L-ornithine

Synonyms

(2S)-2-azanyl-5-(propanimidoylamino)pentanoic acid

Systematic names

ProgramVersionName
ACDLabs 10.04 N~5~-[(1Z)-propanimidoyl]-L-ornithine
OpenEye OEToolkits 1.5.0 (2S)-2-amino-5-(propanimidoylamino)pentanoic acid

Formula

C8 H17 N3 O2

Formal charge

0

Molecular weight

187.239 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)C(N)CCCNC(=[N@H])CC
SMILES CACTVS 3.341 CCC(=N)NCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 [H]N=C(CC)NCCCC(C(=O)O)N
Canonical SMILES CACTVS 3.341 CCC(=N)NCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C(/CC)\NCCC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C8H17N3O2/c1-2-7(10)11-5-3-4-6(9)8(12)13/h6H,2-5,9H2,1H3,(H2,10,11)(H,12,13)/t6-/m0/s1

IUPAC InChI key

ZYIBCZWVLDODOL-LURJTMIESA-N
LN5

wwPDB Information

Atom count

30 (13 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-07-07

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



LN5 : 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 CT1 C CT1 N N N 0 -5.944 0.134 0.064
2 CH1 C CH1 N N N 0 -4.708 -0.623 -0.427
3 CZ C CZ N N N 0 -3.465 0.099 0.025
4 NH2 N NH2 N N N 0 -3.564 1.185 0.719
5 NE N NE N N N 0 -2.229 -0.396 -0.3
6 CD C CD N N N 0 -1.02 0.305 0.14
7 CG C CG N N N 0 0.215 -0.451 -0.352
8 CB C CB N N N 0 1.478 0.281 0.107
9 CA C CA S N N 0 2.714 -0.476 -0.385
10 C C C N N N 0 3.953 0.309 -0.039
11 OA2 O OA2 N N N 0 4.612 0.003 0.927
12 OA1 O OA1 N N N 0 4.326 1.347 -0.805
13 N N N N N N 0 2.771 -1.793 0.263
14 H1H2 H H1H2 N N N 0 -2.763 1.65 1.01
15 H1T1 H H1T1 N N N 0 -6.843 -0.388 -0.263
16 H2T1 H H2T1 N N N 0 -5.929 0.185 1.153
17 H3T1 H H3T1 N N N 0 -5.939 1.143 -0.347
18 H1H1 H H1H1 N N N 0 -4.713 -1.632 -0.016
19 H2H1 H H2H1 N N N 0 -4.723 -0.674 -1.516
20 HNE H HNE N N N 0 -2.155 -1.211 -0.821
21 H1D H H1D N N N 0 -1.016 1.314 -0.272
22 H2D H H2D N N N 0 -1.006 0.356 1.228
23 H1G H H1G N N N 0 0.211 -1.461 0.059
24 H2G H H2G N N N 0 0.201 -0.503 -1.441
25 H1B H H1B N N N 0 1.482 1.29 -0.305
26 H2B H H2B N N N 0 1.492 0.332 1.196
27 HA H HA N N N 0 2.654 -0.605 -1.465
28 H15 H H15 N N N 0 5.128 1.819 -0.543
29 H1N H H1N N N N 0 2.826 -1.7 1.266
30 H2N H H2N N N N 0 1.982 -2.362 -0.004



LN5 : 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 CH1 CT1 C C sing 1.53 N N
2 CZ CH1 C C sing 1.51 N N
3 CZ NH2 C N doub 1.29 N N
4 NH2 H1H2 N H sing 0.97 N N
5 NE CZ N C sing 1.37 N N
6 CD NE C N sing 1.47 N N
7 CG CD C C sing 1.53 N N
8 CB CG C C sing 1.53 N N
9 CA C C C sing 1.51 N N
10 CA CB C C sing 1.53 N N
11 C OA1 C O sing 1.34 N N
12 OA2 C O C doub 1.21 N N
13 N CA N C sing 1.47 N N
14 CT1 H1T1 C H sing 1.09 N N
15 CT1 H2T1 C H sing 1.09 N N
16 CT1 H3T1 C H sing 1.09 N N
17 CH1 H1H1 C H sing 1.09 N N
18 CH1 H2H1 C H sing 1.09 N N
19 NE HNE N H sing 0.97 N N
20 CD H1D C H sing 1.09 N N
21 CD H2D C H sing 1.09 N N
22 CG H1G C H sing 1.09 N N
23 CG H2G C H sing 1.09 N N
24 CB H1B C H sing 1.09 N N
25 CB H2B C H sing 1.09 N N
26 CA HA C H sing 1.09 N N
27 OA1 H15 O H sing 0.97 N N
28 N H1N N H sing 1.01 N N
29 N H2N N H sing 1.01 N N



LN5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LN5 3i4a Open in New Window Bound ligand 2 1