Chemical Components in the PDB

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I58 : Summary

Code

I58

One-letter code

K

Molecule name

4R-FLUORO-N6-ETHANIMIDOYL-L-LYSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 (4R)-N~6~-[(1Z)-ethanimidoyl]-4-fluoro-L-lysine
OpenEye OEToolkits 1.5.0 (2S,4R)-2-amino-6-(ethanimidoylamino)-4-fluoro-hexanoic acid

Formula

C8 H16 F N3 O2

Formal charge

0

Molecular weight

205.23 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 FC(CCNC(=[N@H])C)CC(N)C(=O)O
SMILES CACTVS 3.341 CC(=N)NCC[CH](F)C[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.5.0 [H]N=C(C)NCCC(CC(C(=O)O)N)F
Canonical SMILES CACTVS 3.341 CC(=N)NCC[C@@H](F)C[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 [H]/N=C(/C)\NCC[C@H](C[C@@H](C(=O)O)N)F

IUPAC InChI

InChI=1S/C8H16FN3O2/c1-5(10)12-3-2-6(9)4-7(11)8(13)14/h6-7H,2-4,11H2,1H3,(H2,10,12)(H,13,14)/t6-,7+/m1/s1

IUPAC InChI key

LTCJJIZTKXNFGK-RQJHMYQMSA-N
I58

wwPDB Information

Atom count

30 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

Yes

Standard parent

LYS

Defined at

2003-10-28

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



I58 : 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 C C C N N N 0 -4.055 -0.323 0.072
2 CA C CA S N N 0 -2.781 0.474 -0.045
3 CB C CB N N N 0 -1.579 -0.464 0.083
4 CD C CD N N N 0 0.916 -0.585 0.09
5 CE C CE N N N 0 2.204 0.233 -0.031
6 CG C CG R N N 0 -0.29 0.323 -0.16
7 CT C CT N N N 0 5.815 -1.014 0.398
8 CX C CX N N N 0 4.627 -0.12 0.152
9 F F F N N N 0 -0.264 0.779 -1.482
10 H H 1HN N N N 0 -2.762 0.976 1.898
11 H2 H 2HN N N Y 0 -1.825 1.916 0.971
12 HA H HA N N N 0 -2.752 0.972 -1.014
13 HB2 H 1HB N N N 0 -1.662 -1.263 -0.655
14 HB3 H 2HB N N N 0 -1.559 -0.895 1.084
15 HD2 H 1HD N N N 0 0.926 -1.388 -0.647
16 HD3 H 2HD N N N 0 0.849 -1.011 1.091
17 HE2 H 1HE N N N 0 2.194 1.037 0.706
18 HE3 H 2HE N N N 0 2.271 0.66 -1.032
19 HG H HG N N N 0 -0.251 1.174 0.519
20 HNX H HNX N N N 0 5.702 1.498 -0.152
21 HT1 H 1HT N N N 0 6.732 -0.431 0.312
22 HT2 H 2HT N N N 0 5.748 -1.44 1.399
23 HT3 H 3HT N N N 0 5.824 -1.817 -0.339
24 HXT H HXT N N Y 0 -5.336 -1.518 -0.911
25 HZ H 1HZ N N N 0 3.226 -1.576 0.406
26 N N N N N N 0 -2.733 1.48 1.024
27 NX N NX N N N 0 4.804 1.134 -0.112
28 NZ N NZ N N N 0 3.359 -0.635 0.208
29 O O O N N N 0 -4.659 -0.347 1.118
30 OXT O OXT N N Y 0 -4.519 -1.007 -0.986



I58 : 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 N CA N C sing 1.47 N N
2 N H N H sing 1.01 N N
3 N H2 N H sing 1.01 N N
4 C O C O doub 1.21 N N
5 C OXT C O sing 1.34 N N
6 C CA C C sing 1.51 N N
7 OXT HXT O H sing 0.97 N N
8 CA CB C C sing 1.53 N N
9 CA HA C H sing 1.09 N N
10 CB CG C C sing 1.53 N N
11 CB HB2 C H sing 1.09 N N
12 CB HB3 C H sing 1.09 N N
13 CG F C F sing 1.4 N N
14 CG CD C C sing 1.53 N N
15 CG HG C H sing 1.09 N N
16 CD CE C C sing 1.53 N N
17 CD HD2 C H sing 1.09 N N
18 CD HD3 C H sing 1.09 N N
19 CE NZ C N sing 1.46 N N
20 CE HE2 C H sing 1.09 N N
21 CE HE3 C H sing 1.09 N N
22 NZ CX N C sing 1.37 N N
23 NZ HZ N H sing 0.97 N N
24 CX NX C N doub 1.29 N N
25 CX CT C C sing 1.51 N N
26 NX HNX N H sing 0.97 N N
27 CT HT1 C H sing 1.09 N N
28 CT HT2 C H sing 1.09 N N
29 CT HT3 C H sing 1.09 N N



I58 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
I58 1r35 Open in New Window Bound ligand 2 1