Chemical Components in the PDB

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UFT : Summary

Code

UFT

One-letter code

U

Molecule name

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

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H12 F N2 O8 P

Formal charge

0

Molecular weight

326.172 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(F)C2O
SMILES CACTVS 3.341 O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)F
Canonical SMILES CACTVS 3.341 O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F

IUPAC InChI

InChI=1S/C9H12FN2O8P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

RTGGYPQTXNSBPD-XVFCMESISA-N
UFT

wwPDB Information

Atom count

33 (21 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DU

Defined at

2008-07-07

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



UFT : Atoms of Molecule

Total Number of Atoms: 33
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 4.622 -2.05 -1.261
2 P P P N N N 0 4.266 -1.014 -0.082
3 OP1 O OP1 N N N 0 4.116 -1.75 1.194
4 OP2 O OP2 N N N 0 5.45 0.068 0.058
5 O5' O O5' N N N 0 2.888 -0.258 -0.43
6 N1 N N1 N N N 0 -2.364 -0.139 -0.132
7 C6 C C6 N N N 0 -2.32 -0.86 1.031
8 C2 C C2 N N N 0 -3.401 -0.269 -0.979
9 O2 O O2 N N N 0 -3.422 0.385 -2.004
10 N3 N N3 N N N 0 -4.415 -1.112 -0.709
11 C4 C C4 N N N 0 -4.406 -1.843 0.424
12 O4 O O4 N N N 0 -5.323 -2.606 0.67
13 C5 C C5 N N N 0 -3.326 -1.709 1.33
14 F2' F F2' N N N 0 -1.867 3.074 0.073
15 C2' C C2' R N N 0 -1.226 1.937 0.577
16 C5' C C5' N N N 0 2.249 0.65 0.47
17 C4' C C4' R N N 0 0.967 1.186 -0.17
18 O4' O O4' N N N 0 0.001 0.124 -0.328
19 C1' C C1' R N N 0 -1.276 0.787 -0.453
20 C3' C C3' R N N 0 0.283 2.206 0.767
21 O3' O O3' N N N 0 0.607 3.542 0.376
22 HOP3 H HOP3 N N Y 0 5.442 -2.543 -1.118
23 HOP2 H HOP2 N N N 0 5.605 0.588 -0.742
24 H6 H H6 N N N 0 -1.484 -0.75 1.706
25 H5 H H5 N N N 0 -3.304 -2.284 2.243
26 H2' H H2' N N N 0 -1.683 1.628 1.517
27 H5' H H5' N N N 0 2.002 0.13 1.396
28 H5'A H H5'A N N N 0 2.922 1.48 0.688
29 H4' H H4' N N N 0 1.189 1.644 -1.134
30 H1' H H1' N N N 0 -1.402 1.185 -1.46
31 H3' H H3' N N N 0 0.575 2.029 1.802
32 HO3' H HO3' N N Y 0 0.157 4.223 0.894
33 HN3 H HN3 N N N 0 -5.155 -1.193 -1.331



UFT : Chemical Bonds

Total Number of Bonds: 34
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.61 N N
2 OP1 P O P doub 1.48 N N
3 P OP2 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 OP3 HOP3 O H sing 0.97 N N
6 OP2 HOP2 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C6 N1 C N sing 1.37 N N
9 N1 C2 N C sing 1.35 N N
10 N1 C1' N C sing 1.46 N N
11 C5 C6 C C doub 1.35 N N
12 C6 H6 C H sing 1.08 N N
13 N3 C2 N C sing 1.35 N N
14 C2 O2 C O doub 1.22 N N
15 C4 N3 C N sing 1.35 N N
16 O4 C4 O C doub 1.22 N N
17 C5 C4 C C sing 1.42 N N
18 C5 H5 C H sing 1.08 N N
19 C2' F2' C F sing 1.4 N N
20 C3' C2' C C sing 1.54 N N
21 C2' C1' C C sing 1.54 N N
22 C2' H2' C H sing 1.09 N N
23 C5' C4' C C sing 1.53 N N
24 C5' H5' C H sing 1.09 N N
25 C5' H5'A C H sing 1.09 N N
26 C3' C4' C C sing 1.54 N N
27 C4' O4' C O sing 1.44 N N
28 C4' H4' C H sing 1.09 N N
29 O4' C1' O C sing 1.44 N N
30 C1' H1' C H sing 1.09 N N
31 C3' O3' C O sing 1.43 N N
32 C3' H3' C H sing 1.09 N N
33 O3' HO3' O H sing 0.97 N N
34 N3 HN3 N H sing 0.97 N N



UFT : Used in PDB Entries

Total Number of PDB Entries: 17
Ligand Code PDB Entry ID Type Total Distinct
UFT 2kwg Open in New Window Polymer component 7 7
UFT 2m8a Open in New Window Polymer component 2 1
UFT 3agv Open in New Window Polymer component 6 3
UFT 3dd2 Open in New Window Polymer component 4 4
UFT 3mo7 Open in New Window Bound ligand 1 1
UFT 3mwa Open in New Window Bound ligand 2 1
UFT 3p4a Open in New Window Polymer component 12 2
UFT 3p4b Open in New Window Polymer component 6 1
UFT 3p4c Open in New Window Polymer component 2 1
UFT 5do4 Open in New Window Polymer component 2 2
UFT 5js2 Open in New Window Polymer component 2 2
UFT 5swm Open in New Window Polymer component 3 3
UFT 5voe Open in New Window Polymer component 7 7
UFT 5vof Open in New Window Polymer component 7 7
UFT 6rti Open in New Window Polymer component 10 10
UFT 7n33 Open in New Window Polymer component 6 1
UFT 8epk Open in New Window Polymer component 10 5