Chemical Components in the PDB

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5CF : Summary

Code

5CF

One-letter code

X

Molecule name

5-fluorocytidine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 11.02 5-fluorocytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.6.1 [(2R,3S,4R,5R)-5-(4-azanyl-5-fluoro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H13 F N3 O8 P

Formal charge

0

Molecular weight

341.187 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 11.02 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(F)=C1)C(O)C2O
SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1F)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.7.0 C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)F
Canonical SMILES CACTVS 3.352 NC1=NC(=O)N(C=C1F)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.7.0 C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)F

IUPAC InChI

InChI=1S/C9H13FN3O8P/c10-3-1-13(9(16)12-7(3)11)8-6(15)5(14)4(21-8)2-20-22(17,18)19/h1,4-6,8,14-15H,2H2,(H2,11,12,16)(H2,17,18,19)/t4-,5-,6-,8-/m1/s1

IUPAC InChI key

VLZKLBLFWAHHJM-UAKXSSHOSA-N
5CF

wwPDB Information

Atom count

35 (22 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-10-05

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



5CF : Atoms of Molecule

Total Number of Atoms: 35
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O OP3 N N Y 0 -4.85 1.915 -1.416
2 P P P N N N 0 -4.335 1.068 -0.148
3 N1 N N1 N N N 0 2.135 -0.149 -0.239
4 C2 C C2 N N N 0 2.005 0.724 0.776
5 O2 O O2 N N N 0 0.985 0.717 1.446
6 N3 N N3 N N N 0 2.97 1.596 1.062
7 C4 C C4 N N N 0 4.089 1.626 0.351
8 N4 N N4 N N N 0 5.08 2.531 0.658
9 C5 C C5 N N N 0 4.259 0.724 -0.721
10 F5 F F5 N N N 0 5.392 0.738 -1.457
11 C6 C C6 N N N 0 3.268 -0.157 -1.0
12 C1' C C1' R N N 0 1.059 -1.1 -0.525
13 C2' C C2' R N N 0 0.844 -2.059 0.674
14 O2' O O2' N N N 0 1.724 -3.182 0.593
15 C3' C C3' S N N 0 -0.629 -2.495 0.48
16 O3' O O3' N N N 0 -0.693 -3.762 -0.178
17 C4' C C4' R N N 0 -1.236 -1.393 -0.409
18 O4' O O4' N N N 0 -0.207 -0.415 -0.644
19 C5' C C5' N N N 0 -2.422 -0.742 0.305
20 O5' O O5' N N N 0 -3.049 0.196 -0.572
21 OP1 O OP1 N N N 0 -3.932 2.075 1.042
22 OP2 O OP2 N N N 0 -5.413 0.165 0.314
23 HOP3 H HOP3 N N Y 0 -5.625 2.465 -1.234
24 HN4 H HN4 N N N 0 4.96 3.15 1.395
25 HN4A H HN4A N N N 0 5.897 2.551 0.136
26 H6 H H6 N N N 0 3.374 -0.858 -1.814
27 H1' H H1' N N N 0 1.277 -1.664 -1.433
28 H2' H H2' N N N 0 0.973 -1.533 1.62
29 HO2' H HO2' N N N 0 1.627 -3.811 1.321
30 H3' H H3' N N N 0 -1.143 -2.537 1.44
31 HO3' H HO3' N N N 0 -0.273 -4.482 0.312
32 H4' H H4' N N N 0 -1.561 -1.82 -1.358
33 H5' H H5' N N N 0 -3.141 -1.51 0.59
34 H5'A H H5'A N N N 0 -2.069 -0.225 1.198
35 HOP1 H HOP1 N N N 0 -3.229 2.697 0.809



5CF : Chemical Bonds

Total Number of Bonds: 36
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP3 P O sing 1.61 N N
2 OP3 HOP3 O H sing 0.97 N N
3 OP2 P O P doub 1.48 N N
4 OP1 P O P sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 C6 N1 C N sing 1.36 N N
7 C1' N1 C N sing 1.46 N N
8 N1 C2 N C sing 1.35 N N
9 C2 N3 C N sing 1.33 N N
10 C2 O2 C O doub 1.22 N N
11 C4 N3 C N doub 1.33 N N
12 C5 C4 C C sing 1.41 N N
13 C4 N4 C N sing 1.38 N N
14 N4 HN4 N H sing 0.97 N N
15 N4 HN4A N H sing 0.97 N N
16 F5 C5 F C sing 1.35 N N
17 C6 C5 C C doub 1.36 N N
18 C6 H6 C H sing 1.08 N N
19 C2' C1' C C sing 1.55 N N
20 O4' C1' O C sing 1.44 N N
21 C1' H1' C H sing 1.09 N N
22 C3' C2' C C sing 1.55 N N
23 C2' O2' C O sing 1.43 N N
24 C2' H2' C H sing 1.09 N N
25 O2' HO2' O H sing 0.97 N N
26 O3' C3' O C sing 1.43 N N
27 C3' C4' C C sing 1.54 N N
28 C3' H3' C H sing 1.09 N N
29 O3' HO3' O H sing 0.97 N N
30 C5' C4' C C sing 1.53 N N
31 C4' O4' C O sing 1.44 N N
32 C4' H4' C H sing 1.09 N N
33 O5' C5' O C sing 1.43 N N
34 C5' H5' C H sing 1.09 N N
35 C5' H5'A C H sing 1.09 N N
36 OP1 HOP1 O H sing 0.97 N N



5CF : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5CF 3jxq Open in New Window Polymer component 4 1
5CF 3jxr Open in New Window Polymer component 3 1