Chemical Components in the PDB

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DC0 : Summary

Code

DC0

One-letter code

X

Molecule name

N-[(2S)-2-amino-4-methylpentyl]-L-phenylalanine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(2S)-2-amino-4-methylpentyl]-L-phenylalanine
OpenEye OEToolkits 1.7.0 (2S)-2-[[(2S)-2-azanyl-4-methyl-pentyl]amino]-3-phenyl-propanoic acid

Formula

C15 H24 N2 O2

Formal charge

0

Molecular weight

264.363 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(NCC(N)CC(C)C)Cc1ccccc1
SMILES CACTVS 3.370 CC(C)C[CH](N)CN[CH](Cc1ccccc1)C(O)=O
SMILES OpenEye OEToolkits 1.7.0 CC(C)CC(CNC(Cc1ccccc1)C(=O)O)N
Canonical SMILES CACTVS 3.370 CC(C)C[C@H](N)CN[C@@H](Cc1ccccc1)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CC(C)C[C@@H](CN[C@@H](Cc1ccccc1)C(=O)O)N

IUPAC InChI

InChI=1S/C15H24N2O2/c1-11(2)8-13(16)10-17-14(15(18)19)9-12-6-4-3-5-7-12/h3-7,11,13-14,17H,8-10,16H2,1-2H3,(H,18,19)/t13-,14-/m0/s1

IUPAC InChI key

ZTDJCNPVROYUSY-KBPBESRZSA-N
DC0

wwPDB Information

Atom count

43 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-10-09

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



DC0 : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 -1.707 1.403 0.713
2 CA C C1 S N N 0 -2.17 0.105 0.205
3 C2 C C2 N N N 0 -1.011 -0.613 -0.49
4 C3 C C3 N N N 0 -3.307 0.324 -0.794
5 C4 C C4 N N N 0 -4.512 0.928 -0.071
6 C5 C C5 N N N 0 -5.604 1.262 -1.09
7 C6 C C6 N N N 0 -5.055 -0.08 0.945
8 N2 N N2 N N N 0 0.126 -0.716 0.434
9 C7 C C7 S N N 0 1.26 -1.401 -0.201
10 C C C N N N 0 1.091 -2.892 -0.057
11 O O O N N N 0 0.125 -3.338 0.515
12 C9 C C9 N N N 0 2.562 -0.968 0.477
13 C10 C C10 N Y N 0 2.793 0.5 0.229
14 C11 C C11 N Y N 0 2.292 1.438 1.112
15 C12 C C12 N Y N 0 3.511 0.909 -0.88
16 C13 C C13 N Y N 0 2.504 2.784 0.884
17 C14 C C14 N Y N 0 3.724 2.256 -1.107
18 C15 C C15 N Y N 0 3.218 3.194 -0.227
19 OXT O OXT N N Y 0 2.013 -3.724 -0.565
20 H H H N N N 0 -1.37 1.986 -0.038
21 HA H H1 N N N 0 -2.528 -0.504 1.036
22 H3 H H3 N N N 0 -1.329 -1.612 -0.789
23 H4 H H4 N N N 0 -0.711 -0.048 -1.373
24 H5 H H5 N N N 0 -2.976 1.004 -1.579
25 H6 H H6 N N N 0 -3.59 -0.631 -1.238
26 H7 H H7 N N N 0 -4.207 1.837 0.446
27 H8 H H8 N N N 0 -5.909 0.352 -1.607
28 H9 H H9 N N N 0 -6.462 1.692 -0.575
29 H10 H H10 N N N 0 -5.217 1.979 -1.814
30 H11 H H11 N N N 0 -4.277 -0.318 1.671
31 H12 H H12 N N N 0 -5.913 0.35 1.46
32 H13 H H13 N N N 0 -5.36 -0.989 0.428
33 H14 H H14 N N N 0 0.398 0.193 0.776
34 H15 H H15 N N N 0 1.297 -1.14 -1.258
35 H16 H H16 N N N 0 2.49 -1.149 1.55
36 H17 H H17 N N N 0 3.393 -1.542 0.067
37 H18 H H18 N N N 0 1.735 1.118 1.98
38 H19 H H19 N N N 0 3.907 0.176 -1.567
39 H20 H H20 N N N 0 2.112 3.517 1.574
40 H21 H H21 N N N 0 4.285 2.575 -1.973
41 H22 H H22 N N N 0 3.384 4.246 -0.405
42 H2 H H2 N N Y 0 -2.437 1.869 1.232
43 HXT H HXT N N Y 0 1.861 -4.672 -0.449



DC0 : Chemical Bonds

Total Number of Bonds: 43
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 CA C2 C C sing 1.53 N N
4 CA C3 C C sing 1.53 N N
5 CA HA C H sing 1.09 N N
6 C2 H3 C H sing 1.09 N N
7 C2 H4 C H sing 1.09 N N
8 C2 N2 C N sing 1.47 N N
9 C3 C4 C C sing 1.53 N N
10 C3 H5 C H sing 1.09 N N
11 C3 H6 C H sing 1.09 N N
12 C4 C5 C C sing 1.53 N N
13 C4 C6 C C sing 1.53 N N
14 C4 H7 C H sing 1.09 N N
15 C5 H8 C H sing 1.09 N N
16 C5 H9 C H sing 1.09 N N
17 C5 H10 C H sing 1.09 N N
18 C6 H11 C H sing 1.09 N N
19 C6 H12 C H sing 1.09 N N
20 C6 H13 C H sing 1.09 N N
21 N2 C7 N C sing 1.47 N N
22 N2 H14 N H sing 1.01 N N
23 C7 C C C sing 1.51 N N
24 C7 C9 C C sing 1.53 N N
25 C7 H15 C H sing 1.09 N N
26 C O C O doub 1.21 N N
27 C OXT C O sing 1.34 N N
28 C9 C10 C C sing 1.51 N N
29 C9 H16 C H sing 1.09 N N
30 C9 H17 C H sing 1.09 N N
31 C10 C11 C C doub 1.38 N Y
32 C10 C12 C C sing 1.38 N Y
33 C11 C13 C C sing 1.38 N Y
34 C11 H18 C H sing 1.08 N N
35 C12 C14 C C doub 1.38 N Y
36 C12 H19 C H sing 1.08 N N
37 C13 C15 C C doub 1.38 N Y
38 C13 H20 C H sing 1.08 N N
39 C14 C15 C C sing 1.38 N Y
40 C14 H21 C H sing 1.08 N N
41 C15 H22 C H sing 1.08 N N
42 OXT HXT O H sing 0.97 N N
43 N H2 N H sing 1.01 N N



DC0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DC0 4gzf Open in New Window Polymer component 1 1