Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

SJ2 : Summary

Code

SJ2

One-letter code

X

Molecule name

~{N}-[(2~{S})-5-carbamimidamido-1-oxidanyl-pentan-2-yl]-~{N}-methyl-ethanamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{N}-[(2~{S})-5-carbamimidamido-1-oxidanyl-pentan-2-yl]-~{N}-methyl-ethanamide

Formula

C9 H20 N4 O2

Formal charge

0

Molecular weight

216.281 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN([CH](CO)CCCNC(N)=N)C(C)=O
SMILES OpenEye OEToolkits 2.0.7 CC(=O)N(C)C(CCCNC(=N)N)CO
Canonical SMILES CACTVS 3.385 CN([C@H](CO)CCCNC(N)=N)C(C)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 [H]/N=C(/N)\NCCC[C@@H](CO)N(C)C(=O)C

IUPAC InChI

InChI=1S/C9H20N4O2/c1-7(15)13(2)8(6-14)4-3-5-12-9(10)11/h8,14H,3-6H2,1-2H3,(H4,10,11,12)/t8-/m0/s1

IUPAC InChI key

FVJAWAIBRGBBJT-QMMMGPOBSA-N
SJ2

wwPDB Information

Atom count

35 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-11-16

Last modified at

2021-11-26

Status

Released

Obsoleted

Not Assigned



SJ2 : Atoms of Molecule

Total Number of Atoms: 35
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 2.325 -0.037 -1.657
2 C2 C C2 N N N 0 2.424 1.612 0.135
3 C3 C C3 N N N 0 2.84 2.641 -0.885
4 O4 O O1 N N N 0 2.306 1.926 1.3
5 O O O2 N N N 0 2.786 -2.477 -0.488
6 N N N1 N N N 0 2.182 0.343 -0.249
7 CA C C4 S N N 0 1.777 -0.658 0.742
8 C C C5 N N N 0 2.801 -1.794 0.767
9 CB C C6 N N N 0 0.403 -1.218 0.37
10 CG C C7 N N N 0 -0.644 -0.106 0.465
11 CD C C8 N N N 0 -2.018 -0.666 0.093
12 NE N N2 N N N 0 -3.02 0.398 0.185
13 CZ C C9 N N N 0 -4.337 0.13 -0.106
14 NH1 N N3 N N N 0 -5.278 1.129 -0.02
15 NH2 N N4 N N N 0 -4.693 -1.072 -0.464
16 H1 H H1 N N N 0 3.346 -0.368 -1.842
17 H2 H H2 N N N 0 1.633 -0.847 -1.886
18 H3 H H3 N N N 0 2.101 0.822 -2.289
19 H4 H H4 N N N 0 2.062 2.738 -1.642
20 H5 H H5 N N N 0 2.989 3.601 -0.391
21 H6 H H6 N N N 0 3.77 2.327 -1.358
22 H7 H H7 N N N 0 3.412 -3.212 -0.543
23 H8 H H8 N N N 0 1.725 -0.193 1.727
24 H9 H H9 N N N 0 2.549 -2.493 1.565
25 H10 H H10 N N N 0 3.795 -1.383 0.945
26 H11 H H11 N N N 0 0.432 -1.603 -0.65
27 H12 H H12 N N N 0 0.141 -2.024 1.055
28 H13 H H13 N N N 0 -0.673 0.279 1.485
29 H14 H H14 N N N 0 -0.382 0.7 -0.22
30 H15 H H15 N N N 0 -1.989 -1.051 -0.927
31 H16 H H16 N N N 0 -2.28 -1.472 0.778
32 H17 H H17 N N N 0 -2.755 1.293 0.451
33 H18 H H18 N N N 0 -5.012 2.023 0.246
34 H19 H H19 N N N 0 -6.207 0.939 -0.225
35 H20 H H20 N N N 0 -5.622 -1.262 -0.669



SJ2 : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N C N sing 1.47 N N
2 O4 C2 O C doub 1.21 N N
3 C2 N C N sing 1.35 N N
4 C2 C3 C C sing 1.51 N N
5 N CA N C sing 1.47 N N
6 CA C C C sing 1.53 N N
7 CA CB C C sing 1.53 N N
8 C O C O sing 1.43 N N
9 CB CG C C sing 1.53 N N
10 CG CD C C sing 1.53 N N
11 CD NE C N sing 1.46 N N
12 NE CZ N C sing 1.38 N N
13 CZ NH2 C N doub 1.3 N N
14 CZ NH1 C N sing 1.38 N N
15 C1 H1 C H sing 1.09 N N
16 C1 H2 C H sing 1.09 N N
17 C1 H3 C H sing 1.09 N N
18 C3 H4 C H sing 1.09 N N
19 C3 H5 C H sing 1.09 N N
20 C3 H6 C H sing 1.09 N N
21 O H7 O H sing 0.97 N N
22 CA H8 C H sing 1.09 N N
23 C H9 C H sing 1.09 N N
24 C H10 C H sing 1.09 N N
25 CB H11 C H sing 1.09 N N
26 CB H12 C H sing 1.09 N N
27 CG H13 C H sing 1.09 N N
28 CG H14 C H sing 1.09 N N
29 CD H15 C H sing 1.09 N N
30 CD H16 C H sing 1.09 N N
31 NE H17 N H sing 0.97 N N
32 NH1 H18 N H sing 0.97 N N
33 NH1 H19 N H sing 0.97 N N
34 NH2 H20 N H sing 0.97 N N



SJ2 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SJ2 7az7 Open in New Window Polymer component 1 1