Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

0D3 : Summary

Code

0D3

One-letter code

X

Molecule name

N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide
OpenEye OEToolkits 1.6.1 (2S)-N-[(2S)-1-[(2-amino-2-oxo-ethyl)amino]-1-oxo-propan-2-yl]-2-(phenylmethyl)-3-sulfanyl-propanamide

Formula

C15 H21 N3 O3 S

Formal charge

0

Molecular weight

323.411 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N)CNC(=O)C(NC(=O)C(CS)Cc1ccccc1)C
SMILES CACTVS 3.352 C[CH](NC(=O)[CH](CS)Cc1ccccc1)C(=O)NCC(N)=O
Canonical SMILES CACTVS 3.352 C[C@@H](NC(=O)[C@@H](CS)Cc1ccccc1)C(=O)NCC(N)=O

IUPAC InChI

InChI=1S/C15H21N3O3S/c1-10(14(20)17-8-13(16)19)18-15(21)12(9-22)7-11-5-3-2-4-6-11/h2-6,10,12,22H,7-9H2,1H3,(H2,16,19)(H,17,20)(H,18,21)/t10-,12+/m0/s1

IUPAC InChI key

AUJQAKJLNYFOHT-CMPLNLGQSA-N
0D3

wwPDB Information

Atom count

43 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-12-17

Last modified at

2011-07-13

Status

Released

Obsoleted

Not Assigned



0D3 : 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 C1 C C1 N N N 0 0.977 0.44 0.55
2 O1 O O1 N N N 0 1.072 -0.438 1.382
3 C2 C C2 S N N 0 2.219 1.056 -0.04
4 C3 C C3 N N N 0 3.456 0.4 0.576
5 C1' C C4 N Y N 0 3.531 -1.04 0.14
6 C2' C C5 N Y N 0 4.075 -1.363 -1.09
7 C3' C C6 N Y N 0 4.144 -2.684 -1.49
8 C4' C C7 N Y N 0 3.669 -3.683 -0.661
9 C5' C C8 N Y N 0 3.126 -3.361 0.568
10 C6' C C9 N Y N 0 3.061 -2.04 0.971
11 C' C C10 N N N 0 2.235 2.556 0.258
12 S' S S1 N N N 0 3.639 3.327 -0.593
13 N N N1 N N N 0 -0.24 0.859 0.15
14 CA C C11 R N N 0 -1.447 0.256 0.72
15 C C C12 N N N 0 -2.59 0.406 -0.251
16 O O O3 N N N 0 -2.413 0.961 -1.315
17 CB C C13 N N N 0 -1.798 0.96 2.033
18 N1 N N2 N N N 0 -3.808 -0.078 0.062
19 CA1 C C14 N N N 0 -4.919 0.067 -0.882
20 C4 C C15 N N N 0 -6.161 -0.554 -0.296
21 O2 O O5 N N N 0 -6.122 -1.067 0.802
22 N2 N N3 N N N 0 -7.314 -0.539 -0.992
23 H2 H H2 N N N 0 2.224 0.9 -1.119
24 H31 H H3 N N N 0 4.35 0.928 0.244
25 H32 H H4 N N N 0 3.389 0.447 1.663
26 H2' H H5 N N N 0 4.446 -0.582 -1.737
27 H3' H H6 N N N 0 4.569 -2.936 -2.451
28 H4' H H7 N N N 0 3.722 -4.715 -0.974
29 H5' H H8 N N N 0 2.754 -4.141 1.216
30 H6' H H9 N N N 0 2.64 -1.788 1.933
31 H'1 H H10 N N N 0 1.306 3.007 -0.092
32 H'2 H H11 N N N 0 2.331 2.712 1.333
33 HS' H H12 N N N 0 3.529 4.622 -0.247
34 H H H13 N N N 0 -0.316 1.561 -0.515
35 HA H H15 N N N 0 -1.269 -0.802 0.911
36 HB1 H H16 N N N 0 -2.696 0.511 2.457
37 HB2 H H17 N N N 0 -0.972 0.851 2.735
38 HB3 H H18 N N N 0 -1.976 2.018 1.841
39 H1 H H20 N N N 0 -3.949 -0.523 0.912
40 HA2 H H22 N N N 0 -5.097 1.125 -1.073
41 HA3 H H23 N N N 0 -4.669 -0.434 -1.817
42 HN1 H H25 N N N 0 -7.346 -0.128 -1.871
43 HN2 H H26 N N N 0 -8.114 -0.938 -0.615



0D3 : 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 C1 O1 C O doub 1.21 N N
2 C1 C2 C C sing 1.51 N N
3 C2 C3 C C sing 1.53 N N
4 C2 C' C C sing 1.53 N N
5 C2 H2 C H sing 1.09 N N
6 C3 C1' C C sing 1.51 N N
7 C3 H31 C H sing 1.09 N N
8 C3 H32 C H sing 1.09 N N
9 C1' C2' C C doub 1.38 N Y
10 C1' C6' C C sing 1.38 N Y
11 C2' C3' C C sing 1.38 N Y
12 C2' H2' C H sing 1.08 N N
13 C3' C4' C C doub 1.38 N Y
14 C3' H3' C H sing 1.08 N N
15 C4' C5' C C sing 1.38 N Y
16 C4' H4' C H sing 1.08 N N
17 C5' C6' C C doub 1.38 N Y
18 C5' H5' C H sing 1.08 N N
19 C6' H6' C H sing 1.08 N N
20 C' S' C S sing 1.81 N N
21 C' H'1 C H sing 1.09 N N
22 C' H'2 C H sing 1.09 N N
23 S' HS' S H sing 1.34 N N
24 N CA N C sing 1.46 N N
25 N H N H sing 0.97 N N
26 CA C C C sing 1.51 N N
27 CA CB C C sing 1.53 N N
28 CA HA C H sing 1.09 N N
29 C O C O doub 1.21 N N
30 CB HB1 C H sing 1.09 N N
31 CB HB2 C H sing 1.09 N N
32 CB HB3 C H sing 1.09 N N
33 N1 CA1 N C sing 1.47 N N
34 N1 H1 N H sing 0.97 N N
35 CA1 C4 C C sing 1.51 N N
36 CA1 HA2 C H sing 1.09 N N
37 CA1 HA3 C H sing 1.09 N N
38 C4 O2 C O doub 1.21 N N
39 N2 HN1 N H sing 0.97 N N
40 N2 HN2 N H sing 0.97 N N
41 C1 N C N sing 1.35 N N
42 C N1 C N sing 1.35 N N
43 C4 N2 C N sing 1.35 N N



0D3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0D3 1jao Open in New Window Bound ligand 1 1