Chemical Components in the PDB

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W0C : Summary

Code

W0C

One-letter code

X

Molecule name

N-(pentan-3-yl)-N'-(pyridin-3-yl)urea

Systematic names

ProgramVersionName
ACDLabs 12.01 N-(pentan-3-yl)-N'-(pyridin-3-yl)urea
OpenEye OEToolkits 2.0.7 1-pentan-3-yl-3-pyridin-3-yl-urea

Formula

C11 H17 N3 O

Formal charge

0

Molecular weight

207.272 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(Nc1cccnc1)NC(CC)CC
SMILES CACTVS 3.385 CCC(CC)NC(=O)Nc1cccnc1
SMILES OpenEye OEToolkits 2.0.7 CCC(CC)NC(=O)Nc1cccnc1
Canonical SMILES CACTVS 3.385 CCC(CC)NC(=O)Nc1cccnc1
Canonical SMILES OpenEye OEToolkits 2.0.7 CCC(CC)NC(=O)Nc1cccnc1

IUPAC InChI

InChI=1S/C11H17N3O/c1-3-9(4-2)13-11(15)14-10-6-5-7-12-8-10/h5-9H,3-4H2,1-2H3,(H2,13,14,15)

IUPAC InChI key

AVWZCVALHDIHNF-UHFFFAOYSA-N
W0C

wwPDB Information

Atom count

32 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-02

Last modified at

2022-10-28

Status

Released

Obsoleted

Not Assigned



W0C : Atoms of Molecule

Total Number of Atoms: 32
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 -0.603 0.788 0.685
2 C7 C C1 N Y N 0 -2.197 0.15 -1.027
3 C8 C C2 N Y N 0 -3.501 -0.176 -1.357
4 N2 N N2 N Y N 0 -4.16 0.109 0.881
5 C9 C C3 N Y N 0 -4.466 -0.187 -0.367
6 C1 C C4 N N N 0 4.095 0.668 0.066
7 C5 C C5 N N N 0 0.449 0.199 0.083
8 C6 C C6 N Y N 0 -1.906 0.452 0.302
9 C4 C C7 N N N 0 1.871 -2.471 0.157
10 C3 C C8 N N N 0 3.071 -1.575 0.47
11 C2 C C9 N N N 0 2.845 -0.19 -0.139
12 O O O1 N N N 0 0.27 -0.56 -0.85
13 N N N3 N N N 0 1.701 0.451 0.515
14 C C C10 N N N 0 3.918 2.008 -0.65
15 C10 C C11 N Y N 0 -2.929 0.415 1.24
16 H1 H H1 N N N 0 -0.457 1.442 1.387
17 H2 H H2 N N N 0 -1.423 0.166 -1.78
18 H3 H H3 N N N 0 -3.762 -0.42 -2.376
19 H4 H H4 N N N 0 -5.485 -0.441 -0.619
20 H5 H H5 N N N 0 4.246 0.842 1.131
21 H6 H H6 N N N 0 4.962 0.149 -0.343
22 H7 H H7 N N N 0 2.032 -3.458 0.591
23 H8 H H8 N N N 0 0.968 -2.031 0.581
24 H9 H H9 N N N 0 1.758 -2.564 -0.923
25 H10 H H10 N N N 0 3.183 -1.483 1.551
26 H11 H H11 N N N 0 3.974 -2.015 0.047
27 H12 H H12 N N N 0 2.644 -0.29 -1.206
28 H13 H H13 N N N 0 1.844 1.056 1.259
29 H14 H H14 N N N 0 3.767 1.834 -1.716
30 H15 H H15 N N N 0 3.05 2.527 -0.241
31 H16 H H16 N N N 0 4.808 2.619 -0.504
32 H17 H H17 N N N 0 -2.716 0.647 2.273



W0C : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C3 C C sing 1.53 N N
2 C3 C2 C C sing 1.53 N N
3 C2 C1 C C sing 1.53 N N
4 C2 N C N sing 1.47 N N
5 C1 C C C sing 1.53 N N
6 N C5 N C sing 1.35 N N
7 C5 N1 C N sing 1.35 N N
8 C5 O C O doub 1.22 N N
9 N1 C6 N C sing 1.4 N N
10 C10 C6 C C doub 1.39 N Y
11 C10 N2 C N sing 1.32 N Y
12 C6 C7 C C sing 1.39 N Y
13 N2 C9 N C doub 1.32 N Y
14 C7 C8 C C doub 1.38 N Y
15 C9 C8 C C sing 1.38 N Y
16 N1 H1 N H sing 0.97 N N
17 C7 H2 C H sing 1.08 N N
18 C8 H3 C H sing 1.08 N N
19 C9 H4 C H sing 1.08 N N
20 C1 H5 C H sing 1.09 N N
21 C1 H6 C H sing 1.09 N N
22 C4 H7 C H sing 1.09 N N
23 C4 H8 C H sing 1.09 N N
24 C4 H9 C H sing 1.09 N N
25 C3 H10 C H sing 1.09 N N
26 C3 H11 C H sing 1.09 N N
27 C2 H12 C H sing 1.09 N N
28 N H13 N H sing 0.97 N N
29 C H14 C H sing 1.09 N N
30 C H15 C H sing 1.09 N N
31 C H16 C H sing 1.09 N N
32 C10 H17 C H sing 1.08 N N



W0C : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W0C 7fne Open in New Window Bound ligand 1 1