Chemical Components in the PDB

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W5D : Summary

Code

W5D

One-letter code

X

Molecule name

4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine

Systematic names

ProgramVersionName
ACDLabs 12.01 4-(1,4-oxazonan-4-yl)-7H-pyrrolo[2,3-d]pyrimidine
OpenEye OEToolkits 2.0.7 4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)-1,4-oxazonane

Formula

C13 H18 N4 O

Formal charge

0

Molecular weight

246.308 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c2(c1ccnc1ncn2)N3CCOCCCCC3
SMILES CACTVS 3.385 C1CCOCCN(CC1)c2ncnc3[nH]ccc23
SMILES OpenEye OEToolkits 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCCCOCC3
Canonical SMILES CACTVS 3.385 C1CCOCCN(CC1)c2ncnc3[nH]ccc23
Canonical SMILES OpenEye OEToolkits 2.0.7 c1c[nH]c2c1c(ncn2)N3CCCCCOCC3

IUPAC InChI

InChI=1S/C13H18N4O/c1-2-6-17(7-9-18-8-3-1)13-11-4-5-14-12(11)15-10-16-13/h4-5,10H,1-3,6-9H2,(H,14,15,16)

IUPAC InChI key

UZDOXWRWKJXTPZ-UHFFFAOYSA-N
W5D

wwPDB Information

Atom count

36 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-29

Last modified at

2020-12-11

Status

Released

Obsoleted

Not Assigned



W5D : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 -0.853 0.586 0.138
2 C17 C C2 N Y N 0 -1.791 -1.832 -0.399
3 C01 C C3 N N N 0 3.934 -1.125 -0.311
4 C03 C C4 N N N 0 2.222 -1.263 1.315
5 C04 C C5 N N N 0 0.762 -0.814 1.144
6 C05 C C6 N N N 0 3.99 0.415 -0.302
7 C06 C C7 N N N 0 2.941 0.884 -1.365
8 C12 C C10 N Y N 0 -2.546 2.143 0.318
9 C07 C C8 N N N 0 2.057 1.932 -0.657
10 C08 C C9 N N N 0 1.321 1.45 0.611
11 C14 C C11 N Y N 0 -3.177 -0.022 -0.137
12 C16 C C12 N Y N 0 -3.066 -2.223 -0.561
13 C18 C C13 N Y N 0 -1.821 -0.398 -0.12
14 N09 N N1 N N N 0 0.492 0.266 0.165
15 N11 N N2 N Y N 0 -1.262 1.833 0.349
16 N13 N N3 N Y N 0 -3.487 1.255 0.082
17 N15 N N4 N Y N 0 -3.904 -1.149 -0.407
18 O02 O O1 N N N 0 2.662 -1.735 -0.004
19 H171 H H1 N N N 0 -0.913 -2.458 -0.462
20 H011 H H2 N N N 0 4.24 -1.466 -1.3
21 H012 H H3 N N N 0 4.666 -1.492 0.408
22 H031 H H4 N N N 0 2.837 -0.423 1.637
23 H032 H H5 N N N 0 2.282 -2.073 2.042
24 H041 H H6 N N N 0 0.177 -1.686 0.851
25 H1 H H7 N N N 0 0.398 -0.483 2.116
26 H2 H H8 N N N 0 3.722 0.796 0.683
27 H051 H H9 N N N 0 4.987 0.757 -0.581
28 H061 H H10 N N N 0 3.448 1.336 -2.218
29 H062 H H11 N N N 0 2.334 0.04 -1.691
30 H071 H H12 N N N 0 2.687 2.779 -0.383
31 H072 H H13 N N N 0 1.312 2.285 -1.369
32 H081 H H14 N N N 0 2.04 1.143 1.371
33 H082 H H15 N N N 0 0.676 2.24 0.996
34 H121 H H16 N N N 0 -2.835 3.169 0.495
35 H161 H H17 N N N 0 -3.383 -3.231 -0.78
36 H151 H H18 N N N 0 -4.871 -1.183 -0.479



W5D : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C18 C C doub 1.4 N Y
2 C10 N09 C N sing 1.38 N N
3 C10 N11 C N sing 1.33 N Y
4 C17 C16 C C doub 1.34 N Y
5 C17 C18 C C sing 1.46 N Y
6 C01 C05 C C sing 1.54 N N
7 C01 O02 C O sing 1.44 N N
8 C03 C04 C C sing 1.54 N N
9 C03 O02 C O sing 1.47 N N
10 C04 N09 C N sing 1.48 N N
11 C05 C06 C C sing 1.57 N N
12 C06 C07 C C sing 1.54 N N
13 C07 C08 C C sing 1.54 N N
14 C08 N09 C N sing 1.51 N N
15 C12 N11 C N doub 1.32 N Y
16 C12 N13 C N sing 1.32 N Y
17 C14 C18 C C sing 1.41 N Y
18 C14 N13 C N doub 1.33 N Y
19 C14 N15 C N sing 1.37 N Y
20 C16 N15 C N sing 1.37 N Y
21 C17 H171 C H sing 1.08 N N
22 C01 H011 C H sing 1.09 N N
23 C01 H012 C H sing 1.09 N N
24 C03 H031 C H sing 1.09 N N
25 C03 H032 C H sing 1.09 N N
26 C04 H041 C H sing 1.09 N N
27 C04 H1 C H sing 1.09 N N
28 C05 H2 C H sing 1.09 N N
29 C05 H051 C H sing 1.09 N N
30 C06 H061 C H sing 1.09 N N
31 C06 H062 C H sing 1.09 N N
32 C07 H071 C H sing 1.09 N N
33 C07 H072 C H sing 1.09 N N
34 C08 H081 C H sing 1.09 N N
35 C08 H082 C H sing 1.09 N N
36 C12 H121 C H sing 1.08 N N
37 C16 H161 C H sing 1.08 N N
38 N15 H151 N H sing 0.97 N N



W5D : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
W5D 5rsi Open in New Window Bound ligand 1 1