Chemical Components in the PDB

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RUS : Summary

Code

RUS

One-letter code

U

Molecule name

1-(5-O-phosphono-beta-D-ribofuranosyl)-2-selanylpyrimidin-4(1H)-one

Systematic names

ProgramVersionName
ACDLabs 12.01 1-(5-O-phosphono-beta-D-ribofuranosyl)-2-selanylpyrimidin-4(1H)-one
OpenEye OEToolkits 1.7.2 [(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4-oxidanylidene-2-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C9 H13 N2 O8 P Se

Formal charge

0

Molecular weight

387.142 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=NC(=O)C=C1)[SeH])C(O)C2O
SMILES CACTVS 3.370 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)N=C2[SeH]
SMILES OpenEye OEToolkits 1.7.2 C1=CN(C(=NC1=O)[SeH])C2C(C(C(O2)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.370 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)N=C2[SeH]
Canonical SMILES OpenEye OEToolkits 1.7.2 C1=CN(C(=NC1=O)[SeH])[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C9H13N2O8PSe/c12-5-1-2-11(9(21)10-5)8-7(14)6(13)4(19-8)3-18-20(15,16)17/h1-2,4,6-8,13-14H,3H2,(H,10,12,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1

IUPAC InChI key

OOOIYMZGLXSVKX-XVFCMESISA-N
RUS

wwPDB Information

Atom count

34 (21 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

U

Defined at

2011-06-02

Last modified at

2011-06-24

Status

Released

Obsoleted

Not Assigned



RUS : 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 4.33 0.936 0.358
2 N1 N N1 N N N 0 -2.284 -0.162 0.904
3 C2 C C2 N N N 0 -2.408 0.634 -0.174
4 O4 O O4 N N N 0 -5.313 2.291 0.506
5 SE2 SE SE2 N N N 0 -1.041 0.564 -1.577
6 N3 N N3 N N N 0 -3.417 1.452 -0.307
7 C4 C C4 N N N 0 -4.372 1.524 0.637
8 C5 C C5 N N N 0 -4.275 0.701 1.786
9 C6 C C6 N N N 0 -3.218 -0.136 1.896
10 C1' C C1* R N N 0 -1.139 -1.069 1.009
11 O1P O O1P N N N 0 4.026 1.863 -0.754
12 C2' C C2* R N N 0 -1.152 -2.089 -0.152
13 O2' O O2* N N N 0 -1.714 -3.33 0.28
14 O2P O O2P N N N 0 5.495 -0.079 -0.093
15 C3' C C3* S N N 0 0.339 -2.265 -0.513
16 O3' O O3* N N N 0 0.745 -3.621 -0.317
17 O3P O O3P N N Y 0 4.818 1.778 1.641
18 C4' C C4* R N N 0 1.078 -1.331 0.471
19 O4' O O4* N N N 0 0.097 -0.339 0.844
20 C5' C C5* N N N 0 2.271 -0.667 -0.219
21 O5' O O5* N N N 0 3.007 0.1 0.737
22 H5 H H5 N N N 0 -5.029 0.741 2.559
23 H6 H H6 N N N 0 -3.115 -0.777 2.759
24 H1' H H1* N N N 0 -1.15 -1.584 1.969
25 H2' H H2* N N N 0 -1.709 -1.693 -1.001
26 HO2' H HO2* N N N 0 -1.746 -4.007 -0.41
27 HO2P H HO2P N N N 0 5.747 -0.717 0.589
28 H3' H H3* N N N 0 0.522 -1.956 -1.543
29 HO3' H HO3* N N N 0 0.269 -4.258 -0.868
30 HO3P H HO3P N N Y 0 5.612 2.307 1.485
31 H4' H H4* N N N 0 1.407 -1.888 1.348
32 H5' H H5* N N N 0 2.918 -1.434 -0.645
33 H5'A H H5*A N N N 0 1.913 -0.012 -1.013
34 HSE2 H HSE2 N N N 0 -1.592 1.622 -2.583



RUS : 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 O1P P O P doub 1.48 N N
2 O2P P O P sing 1.61 N N
3 P O5' 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 C1' N1 C N sing 1.46 N N
7 N1 C2 N C sing 1.35 N N
8 C2 N3 C N doub 1.31 N N
9 C2 SE2 C SE sing 1.96 N N
10 C4 N3 C N sing 1.34 N N
11 C5 C4 C C sing 1.42 N N
12 C4 O4 C O doub 1.22 N N
13 C6 C5 C C doub 1.35 N N
14 C5 H5 C H sing 1.08 N N
15 C6 H6 C H sing 1.08 N N
16 C2' C1' C C sing 1.55 N N
17 C1' O4' C O sing 1.44 N N
18 C1' H1' C H sing 1.09 N N
19 C3' C2' C C sing 1.54 N N
20 C2' O2' C O sing 1.43 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 O2P HO2P O H sing 0.97 N N
24 O3' C3' O C sing 1.43 N N
25 C3' C4' C C sing 1.54 N N
26 C3' H3' C H sing 1.09 N N
27 O3' HO3' O H sing 0.97 N N
28 O3P HO3P O H sing 0.97 N N
29 C5' C4' C C sing 1.53 N N
30 C4' O4' C O sing 1.44 N N
31 C4' H4' C H sing 1.09 N N
32 C5' O5' C O sing 1.43 N N
33 C5' H5' C H sing 1.09 N N
34 C5' H5'A C H sing 1.09 N N
35 SE2 HSE2 SE H sing 1.56 N N



RUS : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
RUS 3s49 Open in New Window Polymer component 7 1
RUS 4jah Open in New Window Polymer component 6 1