Chemical Components in the PDB

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P0K : Summary

Code

P0K

One-letter code

X

Molecule name

6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 6-[[furan-2-ylmethyl(methyl)amino]methyl]-5~{H}-pyrimidine-2,4-dione

Formula

C11 H13 N3 O3

Formal charge

0

Molecular weight

235.239 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(CC1=NC(=O)NC(=O)C1)Cc2occc2
SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccco1)CC2=NC(=O)NC(=O)C2
Canonical SMILES CACTVS 3.385 CN(CC1=NC(=O)NC(=O)C1)Cc2occc2
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccco1)CC2=NC(=O)NC(=O)C2

IUPAC InChI

InChI=1S/C11H13N3O3/c1-14(7-9-3-2-4-17-9)6-8-5-10(15)13-11(16)12-8/h2-4H,5-7H2,1H3,(H,13,15,16)

IUPAC InChI key

PWXNLVGSEBBXAV-UHFFFAOYSA-N
P0K

wwPDB Information

Atom count

30 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-04-14

Last modified at

2020-07-10

Status

Released

Obsoleted

Not Assigned



P0K : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 1.508 -0.701 0.019
2 C01 C C2 N N N 0 -0.908 0.024 -1.462
3 C03 C C3 N N N 0 -2.159 -1.431 0.015
4 C04 C C4 N Y N 0 -3.32 -0.477 0.115
5 C05 C C5 N Y N 0 -4.058 -0.024 -0.914
6 C06 C C6 N Y N 0 -5.033 0.843 -0.37
7 C07 C C7 N Y N 0 -4.834 0.867 0.96
8 C09 C C8 N N N 0 0.259 -1.544 -0.034
9 C11 C C9 N N N 0 2.877 -1.341 0.15
10 C12 C C10 N N N 0 4.059 -0.39 0.193
11 C14 C C11 N N N 0 2.526 1.374 -0.003
12 N02 N N1 N N N 0 -0.915 -0.672 -0.168
13 N13 N N2 N N N 0 3.785 0.932 0.111
14 N15 N N3 N N N 0 1.444 0.591 -0.052
15 O08 O O1 N Y N 0 -3.798 0.062 1.249
16 O16 O O2 N N N 0 2.356 2.576 -0.078
17 O17 O O3 N N N 0 5.196 -0.796 0.296
18 H1 H H1 N N N 0 -0.923 -0.708 -2.268
19 H2 H H2 N N N 0 -1.788 0.663 -1.535
20 H3 H H3 N N N 0 -0.008 0.635 -1.541
21 H4 H H4 N N N 0 -2.093 -2.022 0.929
22 H5 H H5 N N N 0 -2.307 -2.096 -0.837
23 H6 H H6 N N N 0 -3.929 -0.273 -1.957
24 H7 H H7 N N N 0 -5.793 1.382 -0.916
25 H8 H H8 N N N 0 -5.411 1.435 1.675
26 H9 H H9 N N N 0 0.312 -2.217 -0.889
27 H10 H H10 N N N 0 0.176 -2.127 0.883
28 H11 H H11 N N N 0 2.887 -1.936 1.063
29 H12 H H12 N N N 0 3.018 -2.015 -0.694
30 H14 H H14 N N N 0 4.514 1.571 0.135



P0K : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O17 C12 O C doub 1.21 N N
2 C12 C11 C C sing 1.52 N N
3 C12 N13 C N sing 1.35 N N
4 C11 C10 C C sing 1.52 N N
5 N13 C14 N C sing 1.34 N N
6 C10 C09 C C sing 1.51 N N
7 C10 N15 C N doub 1.3 N N
8 C14 N15 C N sing 1.34 N N
9 C14 O16 C O doub 1.22 N N
10 C09 N02 C N sing 1.47 N N
11 C01 N02 C N sing 1.47 N N
12 N02 C03 N C sing 1.47 N N
13 O08 C07 O C sing 1.34 N Y
14 O08 C04 O C sing 1.34 N Y
15 C07 C06 C C doub 1.35 N Y
16 C04 C03 C C sing 1.51 N N
17 C04 C05 C C doub 1.34 N Y
18 C06 C05 C C sing 1.41 N Y
19 C01 H1 C H sing 1.09 N N
20 C01 H2 C H sing 1.09 N N
21 C01 H3 C H sing 1.09 N N
22 C03 H4 C H sing 1.09 N N
23 C03 H5 C H sing 1.09 N N
24 C05 H6 C H sing 1.08 N N
25 C06 H7 C H sing 1.08 N N
26 C07 H8 C H sing 1.08 N N
27 C09 H9 C H sing 1.09 N N
28 C09 H10 C H sing 1.09 N N
29 C11 H11 C H sing 1.09 N N
30 C11 H12 C H sing 1.09 N N
31 N13 H14 N H sing 0.97 N N



P0K : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
P0K 6ynk Open in New Window Bound ligand 2 1