Chemical Components in the PDB

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NFM : Summary

Code

NFM

One-letter code

X

Molecule name

N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide

Systematic names

ProgramVersionName
ACDLabs 11.02 N-[(4-amino-2-methylpyrimidin-5-yl)methyl]formamide
OpenEye OEToolkits 1.6.1 N-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]methanamide

Formula

C7 H10 N4 O

Formal charge

0

Molecular weight

166.18 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=CNCc1cnc(nc1N)C
SMILES CACTVS 3.352 Cc1ncc(CNC=O)c(N)n1
SMILES OpenEye OEToolkits 1.7.0 Cc1ncc(c(n1)N)CNC=O
Canonical SMILES CACTVS 3.352 Cc1ncc(CNC=O)c(N)n1
Canonical SMILES OpenEye OEToolkits 1.7.0 Cc1ncc(c(n1)N)CNC=O

IUPAC InChI

InChI=1S/C7H10N4O/c1-5-10-3-6(2-9-4-12)7(8)11-5/h3-4H,2H2,1H3,(H,9,12)(H2,8,10,11)

IUPAC InChI key

PVWNFAGYFUUDRC-UHFFFAOYSA-N
NFM

wwPDB Information

Atom count

22 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-09-04

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NFM : Atoms of Molecule

Total Number of Atoms: 22
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 0.665 0.949 0.162
2 N1 N N1 N Y N 0 1.977 0.939 -0.058
3 O1 O O1 N N N 0 -4.168 -0.285 0.335
4 C2 C C2 N Y N 0 2.641 -0.198 -0.107
5 N2 N N2 N Y N 0 2.043 -1.361 0.056
6 C3 C C3 N Y N 0 0.738 -1.432 0.279
7 N3 N N3 N N N 0 -0.031 2.145 0.207
8 C4 C C4 N Y N 0 0.0 -0.266 0.34
9 N4 N N4 N N N 0 -2.199 -0.15 -0.679
10 C5 C C5 N N N 0 4.127 -0.168 -0.357
11 C6 C C6 N N N 0 -1.485 -0.305 0.591
12 C7 C C7 N N N 0 -3.547 -0.154 -0.699
13 H3 H H3 N N N 0 0.258 -2.39 0.412
14 HN3 H HN3 N N N 0 -0.989 2.144 0.364
15 HN3A H HN3A N N N 0 0.438 2.985 0.083
16 HN4 H HN4 N N N 0 -1.702 -0.046 -1.505
17 H5 H H5 N N N 0 4.655 -0.105 0.594
18 H5A H H5A N N N 0 4.426 -1.076 -0.88
19 H5B H H5B N N N 0 4.375 0.701 -0.968
20 H6 H H6 N N N 0 -1.752 -1.259 1.045
21 H6A H H6A N N N 0 -1.761 0.507 1.264
22 H7 H H7 N N N 0 -4.074 -0.041 -1.635



NFM : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C1 N C doub 1.33 N Y
2 N3 C1 N C sing 1.38 N N
3 C1 C4 C C sing 1.4 N Y
4 N1 C2 N C sing 1.32 N Y
5 C7 O1 C O doub 1.21 N N
6 C5 C2 C C sing 1.51 N N
7 C2 N2 C N doub 1.32 N Y
8 N2 C3 N C sing 1.33 N Y
9 C4 C3 C C doub 1.38 N Y
10 C3 H3 C H sing 1.08 N N
11 N3 HN3 N H sing 0.97 N N
12 N3 HN3A N H sing 0.97 N N
13 C4 C6 C C sing 1.51 N N
14 N4 C6 N C sing 1.47 N N
15 N4 C7 N C sing 1.35 N N
16 N4 HN4 N H sing 0.97 N N
17 C5 H5 C H sing 1.09 N N
18 C5 H5A C H sing 1.09 N N
19 C5 H5B C H sing 1.09 N N
20 C6 H6 C H sing 1.09 N N
21 C6 H6A C H sing 1.09 N N
22 C7 H7 C H sing 1.08 N N



NFM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NFM 3ix1 Open in New Window Bound ligand 2 1