Chemical Components in the PDB

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TI5 : Summary

Code

TI5

One-letter code

X

Molecule name

5-methylpyrimidin-4-amine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 5-methylpyrimidin-4-amine

Formula

C5 H7 N3

Formal charge

0

Molecular weight

109.129 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1cncnc1N
SMILES OpenEye OEToolkits 2.0.7 Cc1cncnc1N
Canonical SMILES CACTVS 3.385 Cc1cncnc1N
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1cncnc1N

IUPAC InChI

InChI=1S/C5H7N3/c1-4-2-7-3-8-5(4)6/h2-3H,1H3,(H2,6,7,8)

IUPAC InChI key

XSCYITPLDKUZJB-UHFFFAOYSA-N
TI5

wwPDB Information

Atom count

15 (8 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-01-05

Last modified at

2023-06-02

Status

Released

Obsoleted

Not Assigned



TI5 : Atoms of Molecule

Total Number of Atoms: 15
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C04 C C1 N Y N 0 0.532 -0.687 -0.002
2 C05 C C2 N Y N 0 0.483 0.709 -0.001
3 C06 C C3 N N N 0 1.852 -1.414 0.002
4 C07 C C4 N Y N 0 -0.66 -1.384 -0.002
5 C08 C C5 N Y N 0 -1.815 0.606 0.001
6 N01 N N1 N Y N 0 -0.702 1.311 0.001
7 N02 N N2 N N N 0 1.651 1.454 -0.001
8 N03 N N3 N Y N 0 -1.803 -0.712 0.0
9 H1 H H1 N N N 0 2.172 -1.592 -1.024
10 H2 H H2 N N N 0 2.599 -0.808 0.515
11 H3 H H3 N N N 0 1.74 -2.367 0.519
12 H4 H H4 N N N 0 -0.662 -2.464 -0.003
13 H5 H H5 N N N 0 -2.764 1.122 0.003
14 H6 H H6 N N N 0 2.512 1.006 -0.002
15 H7 H H7 N N N 0 1.609 2.423 0.0



TI5 : Chemical Bonds

Total Number of Bonds: 15
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N02 C05 N C sing 1.39 N N
2 C06 C04 C C sing 1.51 N N
3 C05 C04 C C doub 1.4 N Y
4 C05 N01 C N sing 1.33 N Y
5 C04 C07 C C sing 1.38 N Y
6 N01 C08 N C doub 1.32 N Y
7 C07 N03 C N doub 1.33 N Y
8 C08 N03 C N sing 1.32 N Y
9 C06 H1 C H sing 1.09 N N
10 C06 H2 C H sing 1.09 N N
11 C06 H3 C H sing 1.09 N N
12 C07 H4 C H sing 1.08 N N
13 C08 H5 C H sing 1.08 N N
14 N02 H6 N H sing 0.97 N N
15 N02 H7 N H sing 0.97 N N



TI5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TI5 8c4j Open in New Window Bound ligand 2 1