Chemical Components in the PDB

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EU0 : Summary

Code

EU0

One-letter code

V

Molecule name

1-[(2~{S})-3-methyl-1-oxidanylidene-butan-2-yl]guanidine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [azanyl-[[(2~{S})-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]amino]methylidene]azanium

Formula

C6 H14 N3 O2

Formal charge

1

Molecular weight

160.194 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(C)[CH](NC(N)=[NH2+])C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC(C)C(C(=O)O)NC(=[NH2+])N
Canonical SMILES CACTVS 3.385 CC(C)[C@H](NC(N)=[NH2+])C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)[C@@H](C(=O)O)NC(=[NH2+])N

IUPAC InChI

InChI=1S/C6H13N3O2/c1-3(2)4(5(10)11)9-6(7)8/h3-4H,1-2H3,(H,10,11)(H4,7,8,9)/p+1/t4-/m0/s1

IUPAC InChI key

KRDSZDZVHLBUMZ-BYPYZUCNSA-O
EU0

wwPDB Information

Atom count

25 (11 without Hydrogen)

Polymer type

Amino Acid

Type description

L-peptide linking

Type code

ATOMP

Is modified

Yes

Standard parent

VAL

Defined at

2022-01-13

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



EU0 : Atoms of Molecule

Total Number of Atoms: 25
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 NT1 N N N N N 1 -2.189 0.596 -1.023
2 CT C CT N N N 0 -2.05 -0.384 -0.131
3 NT2 N NT2 N N N 0 -3.126 -1.011 0.342
4 N N NE N N N 0 -0.803 -0.746 0.299
5 CA C CA S N N 0 0.38 -0.056 -0.221
6 CB C CB N N N 0 0.628 1.215 0.593
7 CG1 C CG1 N N N 0 1.864 1.936 0.05
8 CG2 C CG2 N N N 0 -0.588 2.136 0.484
9 C C C N N N 0 1.579 -0.964 -0.114
10 O O O N N N 0 1.457 -2.073 0.35
11 HT12 H H2 N N N 0 -1.405 1.052 -1.367
12 HT22 H HT22 N N N 0 -4.01 -0.755 0.037
13 HT21 H HT21 N N N 0 -3.025 -1.725 0.991
14 H H HE N N N 0 -0.702 -1.459 0.948
15 HA H HA N N N 0 0.217 0.208 -1.266
16 HB H HB N N N 0 0.792 0.951 1.638
17 HG11 H HG11 N N N 0 1.701 2.2 -0.995
18 HG13 H HG13 N N N 0 2.041 2.841 0.63
19 HG12 H HG12 N N N 0 2.731 1.279 0.128
20 HG23 H HG23 N N N 0 -1.468 1.623 0.871
21 HG22 H HG22 N N N 0 -0.411 3.042 1.064
22 HG21 H HG21 N N N 0 -0.752 2.4 -0.561
23 OXT O OXT N N Y 0 2.781 -0.54 -0.533
24 HXT H H1 N N Y 0 3.52 -1.157 -0.444
25 HT11 H H3 N N N 0 -3.073 0.85 -1.331



EU0 : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NT1 CT N C doub 1.33 N N
2 NT2 CT N C sing 1.33 N N
3 CT N C N sing 1.37 N N
4 N CA N C sing 1.46 N N
5 CA C C C sing 1.51 N N
6 CA CB C C sing 1.53 N N
7 C O C O doub 1.21 N N
8 CG2 CB C C sing 1.53 N N
9 CB CG1 C C sing 1.53 N N
10 NT1 HT12 N H sing 0.97 N N
11 NT2 HT22 N H sing 0.97 N N
12 NT2 HT21 N H sing 0.97 N N
13 N H N H sing 0.97 N N
14 CA HA C H sing 1.09 N N
15 CB HB C H sing 1.09 N N
16 CG1 HG11 C H sing 1.09 N N
17 CG1 HG13 C H sing 1.09 N N
18 CG1 HG12 C H sing 1.09 N N
19 CG2 HG23 C H sing 1.09 N N
20 CG2 HG22 C H sing 1.09 N N
21 CG2 HG21 C H sing 1.09 N N
22 C OXT C O sing 1.34 N N
23 OXT HXT O H sing 0.97 N N
24 HT11 NT1 H N sing 0.97 N N



EU0 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
EU0 7qs6 Open in New Window Polymer component 1 1
EU0 7zax Open in New Window Polymer component 1 1
EU0 7zed Open in New Window Polymer component 1 1
EU0 8onu Open in New Window Polymer component 1 1