Chemical Components in the PDB

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C46 : Summary

Code

C46

One-letter code

C

Molecule name

6H,8H-3,4-DIHYDROPYRIMIDO[4,5-C][1,2]OXAZIN-7-0NE(CYTIDINE)-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4,6-dihydro-1H-pyrimido[4,5-c][1,2]oxazin-7(3H)-one
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(7-oxo-3,4-dihydro-1H-pyrimido[4,5-c][1,2]oxazin-6-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C11 H16 N3 O8 P

Formal charge

0

Molecular weight

349.234 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(N1C=C2C(=NC1=O)NOCC2)CC3O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C3CCONC3=NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1CONC2=NC(=O)N(C=C21)C3CC(C(O3)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C3CCONC3=NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1CONC2=NC(=O)N(C=C21)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C11H16N3O8P/c15-7-3-9(22-8(7)5-21-23(17,18)19)14-4-6-1-2-20-13-10(6)12-11(14)16/h4,7-9,15H,1-3,5H2,(H,12,13,16)(H2,17,18,19)/t7-,8+,9+/m0/s1

IUPAC InChI key

XJTHSWZLLXTCDX-DJLDLDEBSA-N
C46

wwPDB Information

Atom count

39 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

1999-04-22

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



C46 : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -1.267 0.106 -4.584
2 O1P O O1P N N N 0 -2.508 1.035 -5.017
3 O2P O O2P N N N 0 -1.763 -1.239 -4.217
4 O3P O O3P N N Y 0 -0.236 -0.019 -5.814
5 O5' O O5* N N N 0 -0.518 0.765 -3.321
6 C5' C C5* N N N 0 0.567 -0.101 -2.986
7 C4' C C4* R N N 0 1.325 0.469 -1.786
8 O4' O O4* N N N 0 0.454 0.554 -0.634
9 C3' C C3* S N N 0 2.458 -0.486 -1.351
10 O3' O O3* N N N 0 3.71 -0.053 -1.886
11 C2' C C2* N N N 0 2.464 -0.389 0.19
12 C1' C C1* R N N 0 1.335 0.616 0.507
13 N1 N N1 N N N 0 0.624 0.217 1.725
14 C2 C C2 N N N 0 0.002 -0.974 1.775
15 O2 O O2 N N N 0 0.038 -1.711 0.803
16 N3 N N3 N N N 0 -0.644 -1.37 2.872
17 C4 C C4 N N N 0 -0.698 -0.587 3.938
18 N4 N N4 N N N 0 -1.364 -0.984 5.076
19 C5 C C5 N N N 0 -0.064 0.671 3.913
20 C6 C C6 N N N 0 0.593 1.058 2.798
21 CM5 C CM5 N N N 0 -0.131 1.565 5.123
22 O4 O O4 N N N 0 -1.111 -0.308 6.297
23 C7 C C7 N N N 0 -1.265 1.088 6.036
24 H1P H H1P N N N 0 -2.928 0.606 -5.775
25 H3P H H3P N N N 0 0.062 0.876 -6.021
26 H5'1 H 1H5* N N N 0 1.243 -0.183 -3.837
27 H5'2 H 2H5* N N N 0 0.179 -1.089 -2.734
28 H4' H H4* N N N 0 1.731 1.452 -2.028
29 H3' H H3* N N N 0 2.24 -1.505 -1.669
30 HA H HA N N N 0 4.381 -0.667 -1.558
31 H2'1 H 1H2* N N N 0 2.247 -1.36 0.635
32 H2'2 H 2H2* N N N 0 3.423 -0.01 0.545
33 H1' H H1* N N N 0 1.742 1.621 0.619
34 H4 H H4 N N N 0 -1.999 -1.717 5.042
35 H6 H H6 N N N 0 1.087 2.017 2.758
36 HM51 H 1HM5 N N N 0 0.814 1.519 5.663
37 HM52 H 2HM5 N N N 0 -0.323 2.591 4.809
38 H7C1 H 1H7C N N N 0 -1.231 1.639 6.975
39 H7C2 H 2H7C N N N 0 -2.223 1.263 5.546



C46 : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O sing 1.61 N N
2 P O2P P O doub 1.48 N N
3 P O3P P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 O1P H1P O H sing 0.97 N N
6 O3P H3P O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'1 C H sing 1.09 N N
10 C5' H5'2 C H sing 1.09 N N
11 C4' O4' C O sing 1.45 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.54 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HA O H sing 0.97 N N
19 C2' C1' C C sing 1.54 N N
20 C2' H2'1 C H sing 1.09 N N
21 C2' H2'2 C H sing 1.09 N N
22 C1' N1 C N sing 1.47 N N
23 C1' H1' C H sing 1.09 N N
24 N1 C2 N C sing 1.34 N N
25 N1 C6 N C sing 1.36 N N
26 C2 O2 C O doub 1.22 N N
27 C2 N3 C N sing 1.33 N N
28 N3 C4 N C doub 1.32 N N
29 C4 N4 C N sing 1.38 N N
30 C4 C5 C C sing 1.41 N N
31 N4 O4 N O sing 1.42 N N
32 N4 H4 N H sing 0.97 N N
33 C5 C6 C C doub 1.35 N N
34 C5 CM5 C C sing 1.51 N N
35 C6 H6 C H sing 1.08 N N
36 CM5 C7 C C sing 1.53 N N
37 CM5 HM51 C H sing 1.09 N N
38 CM5 HM52 C H sing 1.09 N N
39 O4 C7 O C sing 1.43 N N
40 C7 H7C1 C H sing 1.09 N N
41 C7 H7C2 C H sing 1.09 N N



C46 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
C46 223d Open in New Window Polymer component 2 1
C46 417d Open in New Window Polymer component 2 1