Chemical Components in the PDB

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DUT : Summary

Code

DUT

One-letter code

X

Molecule name

DEOXYURIDINE-5'-TRIPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxyuridine 5'-(tetrahydrogen triphosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl (hydroxy-phosphonooxy-phosphoryl) hydrogen phosphate

Formula

C9 H15 N2 O14 P3

Formal charge

0

Molecular weight

468.142 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O

IUPAC InChI

InChI=1S/C9H15N2O14P3/c12-5-3-8(11-2-1-7(13)10-9(11)14)23-6(5)4-22-27(18,19)25-28(20,21)24-26(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,20,21)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1

IUPAC InChI key

AHCYMLUZIRLXAA-SHYZEUOFSA-N
DUT

wwPDB Information

Atom count

43 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-05-11

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DUT : Atoms of Molecule

Total Number of Atoms: 43
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 -0.317 0.514 5.166
2 C2 C C2 N N N 0 -0.972 -0.648 4.995
3 N3 N N3 N N N 0 -2.078 -0.93 5.708
4 C4 C C4 N N N 0 -2.554 -0.042 6.604
5 C5 C C5 N N N 0 -1.877 1.187 6.79
6 C6 C C6 N N N 0 -0.767 1.442 6.065
7 O2 O O2 N N N 0 -0.554 -1.459 4.191
8 O4 O O4 N N N 0 -3.558 -0.294 7.246
9 C1' C C1* R N N 0 0.886 0.791 4.379
10 C2' C C2* N N N 0 1.969 -0.274 4.659
11 C3' C C3* S N N 0 2.645 -0.492 3.287
12 C4' C C4* R N N 0 1.891 0.464 2.337
13 O4' O O4* N N N 0 0.606 0.669 2.967
14 O3' O O3* N N N 0 4.03 -0.147 3.35
15 C5' C C5* N N N 0 1.713 -0.173 0.958
16 O5' O O5* N N N 0 0.951 0.701 0.123
17 PA P PA R N N 0 0.802 -0.028 -1.303
18 O1A O O1A N N N 0 2.145 -0.265 -1.878
19 O2A O O2A N N N 0 0.046 -1.436 -1.109
20 O3A O O3A N N N 0 -0.049 0.906 -2.298
21 PB P PB R N N 0 -0.158 0.118 -3.698
22 O1B O O1B N N N 0 -0.839 -1.177 -3.483
23 O2B O O2B N N N 0 1.318 -0.141 -4.283
24 O3B O O3B N N N 0 -1.003 1.001 -4.746
25 PG P PG N N N 0 -1.071 0.157 -6.116
26 O1G O O1G N N N 0 -1.738 -1.139 -5.864
27 O2G O O2G N N N 0 -1.907 0.985 -7.215
28 O3G O O3G N N N 0 0.42 -0.103 -6.661
29 HN3 H HN3 N N N 0 -2.536 -1.775 5.575
30 H5 H H5 N N N 0 -2.243 1.91 7.503
31 H6 H H6 N N N 0 -0.237 2.374 6.194
32 H1' H H1* N N N 0 1.266 1.787 4.606
33 H2'1 H 1H2* N N N 0 1.513 -1.199 5.011
34 H2'2 H 2H2* N N N 0 2.692 0.097 5.386
35 H3' H H3* N N N 0 2.525 -1.526 2.962
36 H4' H H4* N N N 0 2.427 1.41 2.25
37 HO3' H *HO3 N N N 0 4.442 -0.756 3.978
38 H5'1 H 1H5* N N N 0 2.69 -0.345 0.507
39 H5'2 H 2H5* N N N 0 1.189 -1.123 1.062
40 HOA2 H 2HOA N N N 0 -0.822 -1.237 -0.733
41 HOB2 H 2HOB N N N 0 1.726 0.726 -4.409
42 HOG2 H 2HOG N N N 0 -1.924 0.446 -8.018
43 HOG3 H 3HOG N N N 0 0.818 0.764 -6.812



DUT : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C sing 1.34 N N
2 N1 C6 N C sing 1.37 N N
3 N1 C1' N C sing 1.46 N N
4 C2 N3 C N sing 1.35 N N
5 C2 O2 C O doub 1.22 N N
6 N3 C4 N C sing 1.35 N N
7 N3 HN3 N H sing 0.97 N N
8 C4 C5 C C sing 1.42 N N
9 C4 O4 C O doub 1.22 N N
10 C5 C6 C C doub 1.35 N N
11 C5 H5 C H sing 1.08 N N
12 C6 H6 C H sing 1.08 N N
13 C1' C2' C C sing 1.54 N N
14 C1' O4' C O sing 1.44 N N
15 C1' H1' C H sing 1.09 N N
16 C2' C3' C C sing 1.54 N N
17 C2' H2'1 C H sing 1.09 N N
18 C2' H2'2 C H sing 1.09 N N
19 C3' C4' C C sing 1.54 N N
20 C3' O3' C O sing 1.43 N N
21 C3' H3' C H sing 1.09 N N
22 C4' O4' C O sing 1.45 N N
23 C4' C5' C C sing 1.53 N N
24 C4' H4' C H sing 1.09 N N
25 O3' HO3' O H sing 0.97 N N
26 C5' O5' C O sing 1.43 N N
27 C5' H5'1 C H sing 1.09 N N
28 C5' H5'2 C H sing 1.09 N N
29 O5' PA O P sing 1.61 N N
30 PA O1A P O doub 1.48 N N
31 PA O2A P O sing 1.61 N N
32 PA O3A P O sing 1.61 N N
33 O2A HOA2 O H sing 0.97 N N
34 O3A PB O P sing 1.61 N N
35 PB O1B P O doub 1.48 N N
36 PB O2B P O sing 1.61 N N
37 PB O3B P O sing 1.61 N N
38 O2B HOB2 O H sing 0.97 N N
39 O3B PG O P sing 1.61 N N
40 PG O1G P O doub 1.48 N N
41 PG O2G P O sing 1.61 N N
42 PG O3G P O sing 1.61 N N
43 O2G HOG2 O H sing 0.97 N N
44 O3G HOG3 O H sing 0.97 N N



DUT : Used in PDB Entries

Total Number of PDB Entries: 18
Ligand Code PDB Entry ID Type Total Distinct
DUT 1exc Open in New Window Bound ligand 4 1
DUT 1f7q Open in New Window Bound ligand 2 1
DUT 1pkj Open in New Window Bound ligand 1 1
DUT 1sm8 Open in New Window Bound ligand 3 1
DUT 1smc Open in New Window Bound ligand 3 1
DUT 1syl Open in New Window Bound ligand 1 1
DUT 1xs1 Open in New Window Bound ligand 6 1
DUT 1xs6 Open in New Window Bound ligand 6 1
DUT 2nom Open in New Window Bound ligand 2 1
DUT 2nvq Open in New Window Bound ligand 1 1
DUT 2nvx Open in New Window Bound ligand 1 1
DUT 2v9x Open in New Window Bound ligand 12 1
DUT 2we3 Open in New Window Bound ligand 1 1
DUT 4qg0 Open in New Window Bound ligand 8 1
DUT 4rxq Open in New Window Bound ligand 4 1
DUT 5tfa Open in New Window Bound ligand 1 1
DUT 5y5q Open in New Window Bound ligand 3 1
DUT 7eev Open in New Window Bound ligand 2 1