Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

CFZ : Summary

Code

CFZ

One-letter code

C

Molecule name

2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.0 [(2R,3R,4R,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H13 F N3 O7 P

Formal charge

0

Molecular weight

325.188 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(F)C2O
SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2F
SMILES OpenEye OEToolkits 1.7.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)F
Canonical SMILES CACTVS 3.370 NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2F
Canonical SMILES OpenEye OEToolkits 1.7.0 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F

IUPAC InChI

InChI=1S/C9H13FN3O7P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)13-2-1-5(11)12-9(13)15/h1-2,4,6-8,14H,3H2,(H2,11,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

KTAATIGPZHTGOP-XVFCMESISA-N
CFZ

wwPDB Information

Atom count

34 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2010-04-13

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CFZ : Atoms of Molecule

Total Number of Atoms: 34
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 4.176 1.031 0.067
2 N1 N N1 N N N 0 -2.467 0.031 0.464
3 C2 C C2 N N N 0 -2.544 0.708 -0.696
4 O2 O O2 N N N 0 -1.667 0.569 -1.532
5 N3 N N3 N N N 0 -3.563 1.528 -0.946
6 C4 C C4 N N N 0 -4.53 1.699 -0.054
7 N4 N N4 N N N 0 -5.578 2.548 -0.324
8 C5 C C5 N N N 0 -4.478 1.004 1.171
9 C6 C C6 N N N 0 -3.439 0.169 1.408
10 C1' C C1' R N N 0 -1.334 -0.865 0.71
11 O1P O O1P N N N 0 4.62 2.004 1.27
12 C2' C C2' R N N 0 -1.311 -2.003 -0.334
13 F2' F F2' N N N 0 -1.886 -3.164 0.194
14 O2P O O2P N N N 0 3.925 1.834 -1.15
15 C3' C C3' R N N 0 0.192 -2.224 -0.616
16 O3' O O3' N N N 0 0.579 -3.553 -0.259
17 O3P O O3P N N Y 0 5.349 -0.033 -0.224
18 C4' C C4' R N N 0 0.9 -1.193 0.291
19 O4' O O4' N N N 0 -0.086 -0.162 0.517
20 C5' C C5' N N N 0 2.126 -0.614 -0.417
21 O5' O O5' N N N 0 2.831 0.248 0.479
22 HN4 H HN4 N N N 0 -5.612 3.025 -1.168
23 HN4A H HN4A N N N 0 -6.284 2.671 0.33
24 H5 H H5 N N N 0 -5.258 1.132 1.908
25 H6 H H6 N N N 0 -3.377 -0.375 2.339
26 H1' H H1' N N N 0 -1.387 -1.274 1.719
27 HO1P H HO1P N N N 0 5.425 2.509 1.091
28 H2' H H2' N N N 0 -1.831 -1.699 -1.242
29 H3' H H3' N N N 0 0.417 -2.03 -1.665
30 HO3' H HO3' N N Y 0 0.119 -4.243 -0.757
31 HO3P H HO3P N N Y 0 5.566 -0.595 0.533
32 H4' H H4' N N N 0 1.19 -1.654 1.235
33 H5' H H5' N N N 0 2.782 -1.426 -0.731
34 H5'A H H5'A N N N 0 1.807 -0.046 -1.291



CFZ : Chemical Bonds

Total Number of Bonds: 35
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2P P O P doub 1.48 N N
2 P O5' P O sing 1.61 N N
3 P O1P P O sing 1.61 N N
4 P O3P P O sing 1.61 N N
5 C6 N1 C N sing 1.36 N N
6 C2 N1 C N sing 1.35 N N
7 N1 C1' N C sing 1.47 N N
8 N3 C2 N C sing 1.33 N N
9 C2 O2 C O doub 1.22 N N
10 C4 N3 C N doub 1.33 N N
11 N4 C4 N C sing 1.38 N N
12 C4 C5 C C sing 1.41 N N
13 N4 HN4 N H sing 0.97 N N
14 N4 HN4A N H sing 0.97 N N
15 C5 C6 C C doub 1.35 N N
16 C5 H5 C H sing 1.08 N N
17 C6 H6 C H sing 1.08 N N
18 C2' C1' C C sing 1.54 N N
19 C1' O4' C O sing 1.45 N N
20 C1' H1' C H sing 1.09 N N
21 O1P HO1P O H sing 0.97 N N
22 C3' C2' C C sing 1.55 N N
23 C2' F2' C F sing 1.4 N N
24 C2' H2' C H sing 1.09 N N
25 C3' O3' C O sing 1.43 N N
26 C3' C4' C C sing 1.54 N N
27 C3' H3' C H sing 1.09 N N
28 O3' HO3' O H sing 0.97 N N
29 O3P HO3P O H sing 0.97 N N
30 O4' C4' O C sing 1.44 N N
31 C5' C4' C C sing 1.53 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



CFZ : Used in PDB Entries

Total Number of PDB Entries: 16
Ligand Code PDB Entry ID Type Total Distinct
CFZ 2kwg Open in New Window Polymer component 2 2
CFZ 2m84 Open in New Window Polymer component 4 2
CFZ 2m8a Open in New Window Polymer component 4 2
CFZ 3agv Open in New Window Polymer component 12 6
CFZ 3p4a Open in New Window Polymer component 12 2
CFZ 3p4b Open in New Window Polymer component 12 2
CFZ 3p4c Open in New Window Polymer component 4 2
CFZ 3p4d Open in New Window Polymer component 4 2
CFZ 5do4 Open in New Window Polymer component 6 6
CFZ 5swm Open in New Window Polymer component 4 4
CFZ 6rti Open in New Window Polymer component 12 12
CFZ 7yq4 Open in New Window Polymer component 3 3
CFZ 7yq5 Open in New Window Polymer component 3 3
CFZ 7yq6 Open in New Window Polymer component 6 3
CFZ 7z6a Open in New Window Polymer component 4 4
CFZ 8epk Open in New Window Polymer component 12 6