Chemical Components in the PDB

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VZP : Summary

Code

VZP

One-letter code

X

Molecule name

N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea

Systematic names

ProgramVersionName
ACDLabs 12.01 N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N-methyl-N'-propan-2-ylurea
OpenEye OEToolkits 2.0.7 1-[(3~{R})-1,1-bis(oxidanylidene)thiolan-3-yl]-1-methyl-3-propan-2-yl-urea

Formula

C9 H18 N2 O3 S

Formal charge

0

Molecular weight

234.316 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N(C1CCS(C1)(=O)=O)(C(=O)NC(C)C)C
SMILES CACTVS 3.385 CC(C)NC(=O)N(C)[CH]1CC[S](=O)(=O)C1
SMILES OpenEye OEToolkits 2.0.7 CC(C)NC(=O)N(C)C1CCS(=O)(=O)C1
Canonical SMILES CACTVS 3.385 CC(C)NC(=O)N(C)[C@@H]1CC[S](=O)(=O)C1
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)NC(=O)N(C)[C@@H]1CCS(=O)(=O)C1

IUPAC InChI

InChI=1S/C9H18N2O3S/c1-7(2)10-9(12)11(3)8-4-5-15(13,14)6-8/h7-8H,4-6H2,1-3H3,(H,10,12)/t8-/m1/s1

IUPAC InChI key

RMWFRPZNASSVCZ-MRVPVSSYSA-N
VZP

wwPDB Information

Atom count

33 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-24

Last modified at

2021-01-08

Status

Released

Obsoleted

Not Assigned



VZP : Atoms of Molecule

Total Number of Atoms: 33
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 0.619 -0.362 0.221
2 C4 C C1 N N N 0 0.612 -1.71 0.794
3 C5 C C2 R N N 0 -0.64 0.37 0.055
4 C6 C C3 N N N 0 -1.319 0.548 1.424
5 C7 C C4 N N N 0 -2.77 1.018 1.142
6 C8 C C5 N N N 0 -1.585 -0.428 -0.865
7 O2 O O1 N N N 0 -3.953 0.733 -1.229
8 S S S1 N N N 0 -3.27 -0.051 -0.261
9 O1 O O2 N N N 0 -3.869 -1.237 0.242
10 C3 C C6 N N N 0 1.783 0.208 -0.147
11 O O O3 N N N 0 1.788 1.33 -0.618
12 N N N2 N N N 0 2.941 -0.464 0.005
13 C1 C C7 N N N 0 4.206 0.156 -0.396
14 C2 C C8 N N N 0 4.732 1.027 0.747
15 C C C9 N N N 0 5.229 -0.936 -0.717
16 H1 H H1 N N N 0 0.503 -2.444 -0.005
17 H2 H H2 N N N 0 1.55 -1.885 1.322
18 H3 H H3 N N N 0 -0.22 -1.805 1.491
19 H4 H H4 N N N 0 -0.441 1.347 -0.385
20 H5 H H5 N N N 0 -1.332 -0.401 1.961
21 H6 H H6 N N N 0 -0.789 1.3 2.009
22 H7 H H7 N N N 0 -3.408 0.844 2.008
23 H8 H H8 N N N 0 -2.786 2.07 0.856
24 H9 H H9 N N N 0 -1.472 -0.101 -1.899
25 H10 H H10 N N N 0 -1.382 -1.496 -0.783
26 H11 H H11 N N N 0 2.936 -1.358 0.381
27 H12 H H12 N N N 0 4.044 0.773 -1.279
28 H13 H H13 N N N 0 4.893 0.41 1.63
29 H14 H H14 N N N 0 5.673 1.488 0.448
30 H15 H H15 N N N 0 4.003 1.805 0.975
31 H16 H H16 N N N 0 4.855 -1.557 -1.531
32 H17 H H17 N N N 0 6.171 -0.475 -1.015
33 H18 H H18 N N N 0 5.391 -1.553 0.167



VZP : Chemical Bonds

Total Number of Bonds: 33
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 S O S doub 1.42 N N
2 C4 N1 C N sing 1.46 N N
3 S O2 S O doub 1.42 N N
4 S C7 S C sing 1.83 N N
5 S C8 S C sing 1.83 N N
6 C7 C6 C C sing 1.55 N N
7 C8 C5 C C sing 1.54 N N
8 N1 C5 N C sing 1.47 N N
9 N1 C3 N C sing 1.35 N N
10 C5 C6 C C sing 1.54 N N
11 N C3 N C sing 1.35 N N
12 N C1 N C sing 1.46 N N
13 C3 O C O doub 1.22 N N
14 C C1 C C sing 1.53 N N
15 C2 C1 C C sing 1.53 N N
16 C4 H1 C H sing 1.09 N N
17 C4 H2 C H sing 1.09 N N
18 C4 H3 C H sing 1.09 N N
19 C5 H4 C H sing 1.09 N N
20 C6 H5 C H sing 1.09 N N
21 C6 H6 C H sing 1.09 N N
22 C7 H7 C H sing 1.09 N N
23 C7 H8 C H sing 1.09 N N
24 C8 H9 C H sing 1.09 N N
25 C8 H10 C H sing 1.09 N N
26 N H11 N H sing 0.97 N N
27 C1 H12 C H sing 1.09 N N
28 C2 H13 C H sing 1.09 N N
29 C2 H14 C H sing 1.09 N N
30 C2 H15 C H sing 1.09 N N
31 C H16 C H sing 1.09 N N
32 C H17 C H sing 1.09 N N
33 C H18 C H sing 1.09 N N



VZP : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
VZP 5s2k Open in New Window Bound ligand 1 1
VZP 5sbt Open in New Window Bound ligand 1 1