Chemical Components in the PDB

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M3Z : Summary

Code

M3Z

One-letter code

X

Molecule name

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

Systematic names

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

Formula

C13 H15 N3 O2

Formal charge

0

Molecular weight

245.277 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(CC1=NC(=O)NC(=O)C1)Cc2ccccc2
SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccccc1)CC2=NC(=O)NC(=O)C2
Canonical SMILES CACTVS 3.385 CN(CC1=NC(=O)NC(=O)C1)Cc2ccccc2
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(Cc1ccccc1)CC2=NC(=O)NC(=O)C2

IUPAC InChI

InChI=1S/C13H15N3O2/c1-16(8-10-5-3-2-4-6-10)9-11-7-12(17)15-13(18)14-11/h2-6H,7-9H2,1H3,(H,15,17,18)

IUPAC InChI key

RNBXCVLIBKJIGQ-UHFFFAOYSA-N
M3Z

wwPDB Information

Atom count

33 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-10-03

Last modified at

2020-02-28

Status

Released

Obsoleted

Not Assigned



M3Z : 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 CAC C C1 N N N 0 0.675 -0.09 1.46
2 CAF C C2 N Y N 0 4.852 0.554 0.945
3 CAG C C3 N Y N 0 3.759 -0.29 1.018
4 CAH C C4 N Y N 0 5.255 1.058 -0.277
5 CAI C C5 N Y N 0 3.473 -0.124 -1.354
6 CAJ C C6 N N N 0 -3.151 -1.296 -0.186
7 CAK C C7 N N N 0 1.879 -1.549 -0.052
8 CAL C C8 N N N 0 -0.542 -1.586 -0.004
9 CAQ C C9 N Y N 0 3.07 -0.629 -0.131
10 CAR C C10 N N N 0 -1.763 -0.704 -0.035
11 CAS C C11 N Y N 0 4.566 0.719 -1.426
12 CAT C C12 N N N 0 -4.303 -0.307 -0.204
13 CAU C C13 N N N 0 -2.716 1.402 0.043
14 NAO N N1 N N N 0 -1.659 0.584 0.067
15 NAP N N2 N N N 0 -3.988 1.002 -0.085
16 NAX N N3 N N N 0 0.659 -0.755 0.15
17 OAD O O1 N N N 0 -5.452 -0.675 -0.321
18 OAE O O2 N N N 0 -2.508 2.595 0.146
19 H1 H H1 N N N 0 0.667 -0.842 2.249
20 H2 H H2 N N N 0 1.575 0.519 1.548
21 H3 H H3 N N N 0 -0.205 0.546 1.555
22 H4 H H4 N N N 0 5.387 0.822 1.844
23 H5 H H5 N N N 0 3.444 -0.684 1.973
24 H6 H H6 N N N 0 6.109 1.718 -0.333
25 H7 H H7 N N N 0 2.935 -0.39 -2.252
26 H8 H H8 N N N 0 -3.178 -1.865 -1.115
27 H9 H H9 N N N 0 -3.316 -1.989 0.639
28 H10 H H10 N N N 0 1.794 -2.114 -0.98
29 H11 H H11 N N N 0 2.006 -2.237 0.783
30 H12 H H12 N N N 0 -0.615 -2.278 0.835
31 H13 H H13 N N N 0 -0.477 -2.149 -0.935
32 H14 H H14 N N N 0 4.881 1.114 -2.381
33 H15 H H15 N N N 0 -4.696 1.665 -0.092



M3Z : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAD CAT O C doub 1.21 N N
2 CAT NAP C N sing 1.35 N N
3 CAT CAJ C C sing 1.52 N N
4 NAP CAU N C sing 1.34 N N
5 CAJ CAR C C sing 1.52 N N
6 CAU OAE C O doub 1.22 N N
7 CAU NAO C N sing 1.34 N N
8 CAR NAO C N doub 1.3 N N
9 CAR CAL C C sing 1.51 N N
10 CAF CAG C C doub 1.38 N Y
11 CAF CAH C C sing 1.38 N Y
12 CAG CAQ C C sing 1.38 N Y
13 CAL NAX C N sing 1.47 N N
14 NAX CAC N C sing 1.47 N N
15 NAX CAK N C sing 1.47 N N
16 CAH CAS C C doub 1.38 N Y
17 CAQ CAK C C sing 1.51 N N
18 CAQ CAI C C doub 1.38 N Y
19 CAS CAI C C sing 1.38 N Y
20 CAC H1 C H sing 1.09 N N
21 CAC H2 C H sing 1.09 N N
22 CAC H3 C H sing 1.09 N N
23 CAF H4 C H sing 1.08 N N
24 CAG H5 C H sing 1.08 N N
25 CAH H6 C H sing 1.08 N N
26 CAI H7 C H sing 1.08 N N
27 CAJ H8 C H sing 1.09 N N
28 CAJ H9 C H sing 1.09 N N
29 CAK H10 C H sing 1.09 N N
30 CAK H11 C H sing 1.09 N N
31 CAL H12 C H sing 1.09 N N
32 CAL H13 C H sing 1.09 N N
33 CAS H14 C H sing 1.08 N N
34 NAP H15 N H sing 0.97 N N



M3Z : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
M3Z 6szr Open in New Window Bound ligand 1 1