Chemical Components in the PDB

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LLD : Summary

Code

LLD

One-letter code

X

Molecule name

2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate

Formula

C21 H25 N3 O5 S

Formal charge

0

Molecular weight

431.505 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O=C(NCCOC(=O)[CH]1CCCCN1[S](=O)(=O)Cc2ccccc2)c3cccnc3
SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)CS(=O)(=O)N2CCCCC2C(=O)OCCNC(=O)c3cccnc3
Canonical SMILES CACTVS 3.385 O=C(NCCOC(=O)[C@@H]1CCCCN1[S](=O)(=O)Cc2ccccc2)c3cccnc3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(cc1)CS(=O)(=O)N2CCCC[C@H]2C(=O)OCCNC(=O)c3cccnc3

IUPAC InChI

InChI=1S/C21H25N3O5S/c25-20(18-9-6-11-22-15-18)23-12-14-29-21(26)19-10-4-5-13-24(19)30(27,28)16-17-7-2-1-3-8-17/h1-3,6-9,11,15,19H,4-5,10,12-14,16H2,(H,23,25)/t19-/m0/s1

IUPAC InChI key

YBYJEZJXJIOQAP-IBGZPJMESA-N
LLD

wwPDB Information

Atom count

55 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-01

Last modified at

2020-02-07

Status

Released

Obsoleted

Not Assigned



LLD : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N Y N 0 -5.877 0.684 -0.068
2 C17 C C2 N Y N 0 -8.213 0.178 -0.067
3 C20 C C3 N Y N 0 -5.699 -0.342 0.86
4 C24 C C4 N Y N 0 4.475 1.019 0.707
5 C26 C C5 N Y N 0 4.668 3.395 0.932
6 C28 C C6 N Y N 0 6.582 2.091 0.325
7 C04 C C7 N N N 0 2.618 -3.249 -0.947
8 C05 C C8 N N N 0 2.456 -4.149 0.282
9 C06 C C9 N N N 0 0.979 -4.201 0.68
10 C07 C C10 N N N 0 0.498 -2.795 1.044
11 C08 C C11 S N N 0 0.638 -1.879 -0.176
12 C09 C C12 N N N 0 0.296 -0.464 0.213
13 C11 C C13 N N N 0 -1.065 1.491 0.122
14 C12 C C14 N N N 0 -2.342 1.991 -0.556
15 C14 C C15 N N N 0 -4.723 1.474 -0.547
16 C16 C C16 N Y N 0 -7.167 0.95 -0.543
17 C18 C C17 N Y N 0 -7.953 -0.821 0.853
18 C23 C C18 N N N 0 3.64 -0.235 0.767
19 C25 C C19 N Y N 0 3.902 2.245 0.987
20 C27 C C20 N Y N 0 6.007 3.318 0.599
21 C29 C C21 N Y N 0 5.816 0.941 0.38
22 N03 N N1 N N N 0 2.025 -1.936 -0.657
23 N13 N N2 N N N 0 -3.486 1.209 -0.082
24 N19 N N3 N Y N 0 -6.727 -1.049 1.283
25 O01 O O1 N N N 0 1.933 0.441 -1.169
26 O10 O O2 N N N 0 -0.797 0.126 -0.296
27 O21 O O3 N N N 0 -4.889 2.363 -1.359
28 O22 O O4 N N N 0 1.005 0.14 0.983
29 O30 O O5 N N N 0 3.909 -0.906 -1.802
30 S02 S S1 N N N 0 2.905 -0.549 -0.862
31 H1 H H1 N N N 0 -9.222 0.355 -0.411
32 H2 H H2 N N N 0 -4.71 -0.559 1.235
33 H3 H H3 N N N 0 4.219 4.353 1.15
34 H4 H H4 N N N 0 7.629 2.03 0.07
35 H5 H H5 N N N 0 3.677 -3.129 -1.175
36 H6 H H6 N N N 0 2.109 -3.699 -1.8
37 H7 H H7 N N N 0 2.804 -5.155 0.044
38 H8 H H8 N N N 0 3.042 -3.747 1.107
39 H9 H H9 N N N 0 0.391 -4.581 -0.155
40 H10 H H10 N N N 0 0.858 -4.86 1.539
41 H11 H H11 N N N 0 -0.548 -2.836 1.35
42 H12 H H12 N N N 0 1.102 -2.405 1.863
43 H13 H H13 N N N 0 -0.035 -2.216 -0.965
44 H14 H H14 N N N 0 -0.228 2.129 -0.162
45 H15 H H15 N N N 0 -1.193 1.52 1.204
46 H16 H H16 N N N 0 -2.494 3.043 -0.313
47 H17 H H17 N N N 0 -2.247 1.878 -1.636
48 H18 H H18 N N N 0 -7.342 1.737 -1.261
49 H19 H H19 N N N 0 -8.767 -1.425 1.226
50 H20 H H20 N N N 0 4.27 -1.078 1.05
51 H21 H H21 N N N 0 2.848 -0.109 1.505
52 H22 H H22 N N N 0 2.855 2.305 1.247
53 H23 H H23 N N N 0 6.605 4.216 0.557
54 H24 H H24 N N N 0 6.265 -0.018 0.166
55 H25 H H25 N N N 0 -3.353 0.5 0.567



LLD : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O01 S02 O S doub 1.42 N N
2 O30 S02 O S doub 1.42 N N
3 C07 C06 C C sing 1.53 N N
4 C07 C08 C C sing 1.53 N N
5 S02 N03 S N sing 1.66 N N
6 S02 C23 S C sing 1.81 N N
7 C06 C05 C C sing 1.53 N N
8 C05 C04 C C sing 1.53 N N
9 C08 N03 C N sing 1.47 N N
10 C08 C09 C C sing 1.51 N N
11 N03 C04 N C sing 1.47 N N
12 C28 C29 C C doub 1.38 N Y
13 C28 C27 C C sing 1.38 N Y
14 C29 C24 C C sing 1.38 N Y
15 C27 C26 C C doub 1.38 N Y
16 C24 C23 C C sing 1.51 N N
17 C24 C25 C C doub 1.38 N Y
18 C09 O22 C O doub 1.21 N N
19 C09 O10 C O sing 1.34 N N
20 C26 C25 C C sing 1.38 N Y
21 O10 C11 O C sing 1.45 N N
22 C11 C12 C C sing 1.53 N N
23 C20 N19 C N doub 1.32 N Y
24 C20 C15 C C sing 1.39 N Y
25 O21 C14 O C doub 1.22 N N
26 N19 C18 N C sing 1.32 N Y
27 C14 C15 C C sing 1.48 N N
28 C14 N13 C N sing 1.35 N N
29 C12 N13 C N sing 1.46 N N
30 C15 C16 C C doub 1.4 N Y
31 C18 C17 C C doub 1.38 N Y
32 C16 C17 C C sing 1.38 N Y
33 C17 H1 C H sing 1.08 N N
34 C20 H2 C H sing 1.08 N N
35 C26 H3 C H sing 1.08 N N
36 C28 H4 C H sing 1.08 N N
37 C04 H5 C H sing 1.09 N N
38 C04 H6 C H sing 1.09 N N
39 C05 H7 C H sing 1.09 N N
40 C05 H8 C H sing 1.09 N N
41 C06 H9 C H sing 1.09 N N
42 C06 H10 C H sing 1.09 N N
43 C07 H11 C H sing 1.09 N N
44 C07 H12 C H sing 1.09 N N
45 C08 H13 C H sing 1.09 N N
46 C11 H14 C H sing 1.09 N N
47 C11 H15 C H sing 1.09 N N
48 C12 H16 C H sing 1.09 N N
49 C12 H17 C H sing 1.09 N N
50 C16 H18 C H sing 1.08 N N
51 C18 H19 C H sing 1.08 N N
52 C23 H20 C H sing 1.09 N N
53 C23 H21 C H sing 1.09 N N
54 C25 H22 C H sing 1.08 N N
55 C27 H23 C H sing 1.08 N N
56 C29 H24 C H sing 1.08 N N
57 N13 H25 N H sing 0.97 N N



LLD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LLD 6o4a Open in New Window Bound ligand 4 1