Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

NCV : Summary

Code

NCV

One-letter code

X

Molecule name

N-Methyl-6-(1,3-dihydroxy-isobutyl)thymine

Systematic names

ProgramVersionName
ACDLabs 10.04 6-[3-hydroxy-2-(hydroxymethyl)propyl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.5.0 6-[3-hydroxy-2-(hydroxymethyl)propyl]-1,5-dimethyl-pyrimidine-2,4-dione

Formula

C10 H16 N2 O4

Formal charge

0

Molecular weight

228.245 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1C(=C(N(C(=O)N1)C)CC(CO)CO)C
SMILES CACTVS 3.341 CN1C(=O)NC(=O)C(=C1CC(CO)CO)C
SMILES OpenEye OEToolkits 1.5.0 CC1=C(N(C(=O)NC1=O)C)CC(CO)CO
Canonical SMILES CACTVS 3.341 CN1C(=O)NC(=O)C(=C1CC(CO)CO)C
Canonical SMILES OpenEye OEToolkits 1.5.0 CC1=C(N(C(=O)NC1=O)C)CC(CO)CO

IUPAC InChI

InChI=1S/C10H16N2O4/c1-6-8(3-7(4-13)5-14)12(2)10(16)11-9(6)15/h7,13-14H,3-5H2,1-2H3,(H,11,15,16)

IUPAC InChI key

FMPCUJIPAJPVKR-UHFFFAOYSA-N
NCV

wwPDB Information

Atom count

32 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-10-29

Last modified at

2020-05-27

Status

Released

Obsoleted

Not Assigned



NCV : Atoms of Molecule

Total Number of Atoms: 32
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -1.037 1.227 -0.232
2 C6 C C6 N N N 0 -0.328 2.499 -0.39
3 C5 C C5 N N N 0 -0.446 0.065 -0.65
4 C11 C C11 N N N 0 0.924 0.095 -1.276
5 C12 C C12 N N N 0 1.983 0.224 -0.178
6 C14 C C14 N N N 0 1.972 -1.035 0.691
7 O4 O O4 N N N 0 2.876 -0.867 1.785
8 C13 C C13 N N N 0 3.363 0.39 -0.817
9 O3 O O3 N N N 0 4.335 0.626 0.203
10 C3 C C3 N N N 0 -1.098 -1.108 -0.5
11 C4 C C4 N N N 0 -0.463 -2.397 -0.954
12 C2 C C2 N N N 0 -2.384 -1.11 0.091
13 O2 O O2 N N N 0 -2.991 -2.156 0.237
14 N2 N N2 N N N 0 -2.932 0.056 0.49
15 C1 C C1 N N N 0 -2.26 1.211 0.327
16 O1 O O1 N N N 0 -2.764 2.254 0.697
17 H6 H H6 N N N 0 -0.982 3.319 -0.094
18 H6A H H6A N N N 0 0.562 2.499 0.239
19 H6B H H6B N N N 0 -0.036 2.626 -1.433
20 H11 H H11 N N N 0 1.09 -0.826 -1.834
21 H11A H H11A N N N 0 0.997 0.947 -1.952
22 H12 H H12 N N N 0 1.762 1.094 0.44
23 H14 H H14 N N N 0 0.965 -1.204 1.074
24 H14A H H14A N N N 0 2.28 -1.893 0.092
25 HO4 H HO4 N N N 0 2.92 -1.629 2.379
26 H13 H H13 N N N 0 3.622 -0.517 -1.363
27 H13A H H13A N N N 0 3.345 1.236 -1.505
28 HO3 H HO3 N N N 0 5.235 0.742 -0.131
29 H4 H H4 N N N 0 0.192 -2.776 -0.169
30 H4A H H4A N N N 0 -1.241 -3.131 -1.163
31 H4B H H4B N N N 0 0.119 -2.217 -1.858
32 HN2 H HN2 N N N 0 -3.813 0.062 0.895



NCV : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 N1 C N sing 1.37 N N
2 N1 C1 N C sing 1.34 N N
3 N1 C6 N C sing 1.46 N N
4 C6 H6 C H sing 1.09 N N
5 C6 H6A C H sing 1.09 N N
6 C6 H6B C H sing 1.09 N N
7 C3 C5 C C doub 1.35 N N
8 C5 C11 C C sing 1.51 N N
9 C12 C11 C C sing 1.53 N N
10 C11 H11 C H sing 1.09 N N
11 C11 H11A C H sing 1.09 N N
12 C13 C12 C C sing 1.53 N N
13 C12 C14 C C sing 1.53 N N
14 C12 H12 C H sing 1.09 N N
15 C14 O4 C O sing 1.43 N N
16 C14 H14 C H sing 1.09 N N
17 C14 H14A C H sing 1.09 N N
18 O4 HO4 O H sing 0.97 N N
19 C13 O3 C O sing 1.43 N N
20 C13 H13 C H sing 1.09 N N
21 C13 H13A C H sing 1.09 N N
22 O3 HO3 O H sing 0.97 N N
23 C4 C3 C C sing 1.51 N N
24 C3 C2 C C sing 1.42 N N
25 C4 H4 C H sing 1.09 N N
26 C4 H4A C H sing 1.09 N N
27 C4 H4B C H sing 1.09 N N
28 O2 C2 O C doub 1.22 N N
29 C2 N2 C N sing 1.35 N N
30 N2 C1 N C sing 1.35 N N
31 N2 HN2 N H sing 0.97 N N
32 C1 O1 C O doub 1.22 N N



NCV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NCV 3f0t Open in New Window Bound ligand 2 1