Chemical Components in the PDB

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2YC : Summary

Code

2YC

One-letter code

X

Molecule name

N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine

Systematic names

ProgramVersionName
ACDLabs 12.01 N~6~-{[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
OpenEye OEToolkits 1.7.6 (2S)-2-azanyl-6-[[(2S,3S)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonylamino]hexanoic acid

Formula

C12 H21 N3 O3

Formal charge

0

Molecular weight

255.313 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NCCCCC(C(=O)O)N)C1N=CCC1C
SMILES CACTVS 3.385 C[CH]1CC=N[CH]1C(=O)NCCCC[CH](N)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC1CC=NC1C(=O)NCCCCC(C(=O)O)N
Canonical SMILES CACTVS 3.385 C[C@H]1CC=N[C@@H]1C(=O)NCCCC[C@H](N)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H]1CC=N[C@@H]1C(=O)NCCCC[C@@H](C(=O)O)N

IUPAC InChI

InChI=1S/C12H21N3O3/c1-8-5-7-14-10(8)11(16)15-6-3-2-4-9(13)12(17)18/h7-10H,2-6,13H2,1H3,(H,15,16)(H,17,18)/t8-,9-,10-/m0/s1

IUPAC InChI key

ZFOMKMMPBOQKMC-GUBZILKMSA-N
2YC

wwPDB Information

Atom count

39 (18 without Hydrogen)

Polymer type

Amino Acid

Type description

L-PEPTIDE LINKING

Type code

ATOMP

Is modified

No

Standard parent

Not Assigned

Defined at

2014-04-14

Last modified at

2014-04-22

Status

Released

Obsoleted

Not Assigned



2YC : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N Y 0 -6.295 -0.263 -1.525
2 C6 C C6 N N N 0 -5.879 -0.322 -0.25
3 O1 O O1 N N N 0 -6.462 -1.022 0.544
4 C5 C C5 S N N 0 -4.685 0.485 0.191
5 N1 N N1 N N N 0 -4.712 0.64 1.651
6 C4 C C4 N N N 0 -3.401 -0.238 -0.221
7 C3 C C3 N N N 0 -2.193 0.638 0.114
8 C2 C C2 N N N 0 -0.909 -0.085 -0.298
9 C1 C C1 N N N 0 0.3 0.791 0.038
10 N N N N N N 0 1.53 0.1 -0.357
11 C C C N N N 0 2.727 0.685 -0.156
12 O O O N N N 0 2.786 1.785 0.352
13 C7 C C7 S N N 0 3.991 -0.027 -0.562
14 C10 C C10 S N N 0 4.423 -1.025 0.537
15 C11 C C11 N N N 0 3.993 -2.451 0.188
16 C9 C C9 N N N 0 5.963 -0.876 0.478
17 C8 C C8 N N N 0 6.168 0.498 -0.122
18 N2 N N2 N N N 0 5.101 0.927 -0.668
19 H1 H H1 N N N 0 -7.066 -0.798 -1.761
20 H2 H H2 N N Y 0 -4.716 1.467 -0.28
21 H3 H H3 N N N 0 -5.518 1.171 1.944
22 H4 H H4 N N N 0 -4.684 -0.257 2.111
23 H6 H H6 N N N 0 -3.326 -1.182 0.318
24 H7 H H7 N N N 0 -3.422 -0.433 -1.294
25 H8 H H8 N N N 0 -2.267 1.582 -0.425
26 H9 H H9 N N N 0 -2.172 0.833 1.186
27 H10 H H10 N N N 0 -0.834 -1.029 0.241
28 H11 H H11 N N N 0 -0.929 -0.279 -1.37
29 H12 H H12 N N N 0 0.225 1.736 -0.502
30 H13 H H13 N N N 0 0.321 0.986 1.11
31 H14 H H14 N N N 0 1.482 -0.78 -0.764
32 H15 H H15 N N N 0 3.846 -0.545 -1.51
33 H16 H H16 N N N 0 4.036 -0.728 1.512
34 H17 H H17 N N N 0 4.417 -3.147 0.912
35 H18 H H18 N N N 0 2.905 -2.52 0.213
36 H19 H H19 N N N 0 4.35 -2.704 -0.811
37 H20 H H20 N N N 0 6.391 -0.925 1.479
38 H21 H H21 N N N 0 6.397 -1.642 -0.164
39 H22 H H22 N N N 0 7.099 1.044 -0.089



2YC : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 C10 C C sing 1.53 N N
2 C10 C9 C C sing 1.55 N N
3 C10 C7 C C sing 1.55 N N
4 C9 C8 C C sing 1.51 N N
5 O C O C doub 1.21 N N
6 C7 C C C sing 1.51 N N
7 C7 N2 C N sing 1.47 N N
8 O1 C6 O C doub 1.21 N N
9 C N C N sing 1.35 N N
10 C8 N2 C N doub 1.27 N N
11 C6 O2 C O sing 1.34 N N
12 C6 C5 C C sing 1.51 N N
13 N C1 N C sing 1.47 N N
14 C2 C1 C C sing 1.53 N N
15 C2 C3 C C sing 1.53 N N
16 C4 C5 C C sing 1.53 N N
17 C4 C3 C C sing 1.53 N N
18 C5 N1 C N sing 1.47 N N
19 O2 H1 O H sing 0.97 N N
20 C5 H2 C H sing 1.09 N N
21 N1 H3 N H sing 1.01 N N
22 N1 H4 N H sing 1.01 N N
23 C4 H6 C H sing 1.09 N N
24 C4 H7 C H sing 1.09 N N
25 C3 H8 C H sing 1.09 N N
26 C3 H9 C H sing 1.09 N N
27 C2 H10 C H sing 1.09 N N
28 C2 H11 C H sing 1.09 N N
29 C1 H12 C H sing 1.09 N N
30 C1 H13 C H sing 1.09 N N
31 N H14 N H sing 0.97 N N
32 C7 H15 C H sing 1.09 N N
33 C10 H16 C H sing 1.09 N N
34 C11 H17 C H sing 1.09 N N
35 C11 H18 C H sing 1.09 N N
36 C11 H19 C H sing 1.09 N N
37 C9 H20 C H sing 1.09 N N
38 C9 H21 C H sing 1.09 N N
39 C8 H22 C H sing 1.08 N N



2YC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
2YC 4q3a Open in New Window Bound ligand 4 1