Chemical Components in the PDB

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CSL : Summary

Code

CSL

One-letter code

C

Molecule name

(D)-2'-METHYLSELENYL-2'-DEOXYCYTIDINE-5'-PHOSPHATE

Synonyms

(D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-Se-methyl-2'-selenocytidine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-4-methylselanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H16 N3 O7 P Se

Formal charge

0

Molecular weight

400.184 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1N=C(N)C=CN1C2OC(C(O)C2[Se]C)COP(=O)(O)O
SMILES CACTVS 3.341 C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=NC2=O)N
SMILES OpenEye OEToolkits 1.5.0 C[Se]C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 C[Se][C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=NC2=O)N
Canonical SMILES OpenEye OEToolkits 1.5.0 C[Se][C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H16N3O7PSe/c1-22-8-7(14)5(4-19-21(16,17)18)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1

IUPAC InChI key

INVVCVIDTHAWAJ-ZOQUXTDFSA-N
CSL

wwPDB Information

Atom count

38 (22 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DC

Defined at

2005-02-15

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CSL : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -1.071 0.086 0.712
2 C2 C C2 N N N 0 -1.689 1.979 -0.687
3 C2' C C2' R N N 0 -1.363 -0.994 -0.347
4 C3' C C3' R N N 0 0.014 -1.268 -1.0
5 C4 C C4 N N N 0 -3.345 3.483 -0.109
6 C4' C C4' R N N 0 0.995 -0.749 0.083
7 C5 C C5 N N N 0 -3.572 2.77 1.086
8 C5' C C5' N N N 0 2.334 -0.359 -0.547
9 C6 C C6 N N N 0 -2.832 1.665 1.341
10 CA' C CA' N N N 0 -2.321 -3.774 -1.057
11 H1' H H1' N N N 0 -1.293 -0.297 1.707
12 H2' H H2' N N N 0 -2.071 -0.622 -1.087
13 H3' H H3' N N N 0 0.124 -0.705 -1.926
14 H3T H H3T N N Y 0 1.082 -2.897 -1.553
15 H4' H H4' N N N 0 1.141 -1.497 0.862
16 H5 H H5 N N N 0 -4.327 3.098 1.785
17 H5'1 H H5'1 N N N 0 2.174 0.434 -1.277
18 H5'2 H H5'2 N N N 0 2.769 -1.227 -1.042
19 H6 H H6 N N N 0 -2.991 1.099 2.247
20 HA'1 H HA'1 N N N 0 -1.37 -3.921 -1.567
21 HA'2 H HA'2 N N N 0 -2.713 -4.739 -0.733
22 HA'3 H HA'3 N N N 0 -3.031 -3.305 -1.739
23 HN41 H HN41 N N N 0 -3.927 5.094 -1.22
24 HN42 H HN42 N N N 0 -4.767 4.909 0.223
25 HOP2 H HOP2 N N N 0 6.385 1.226 1.449
26 HOP3 H HOP3 N N N 0 4.211 2.668 -0.329
27 N1 N N1 N N N 0 -1.882 1.277 0.445
28 N3 N N3 N N N 0 -2.412 3.064 -0.955
29 N4 N N4 N N N 0 -4.086 4.606 -0.397
30 O1P O O1P N N N 0 5.457 -0.467 -0.552
31 O2 O O2 N N N 0 -0.837 1.614 -1.481
32 O2P O O2P N N N 0 5.473 0.922 1.556
33 O3' O O3' N N N 0 0.201 -2.666 -1.229
34 O3P O O3P N N Y 0 4.678 1.927 -0.739
35 O4' O O4' N N N 0 0.325 0.414 0.614
36 O5' O O5' N N N 0 3.222 0.104 0.472
37 P P P N N N 0 4.724 0.598 0.168
38 SE2' SE SE2' N N N 0 -2.054 -2.619 0.504



CSL : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O2P P O sing 1.61 N N
2 P O1P P O doub 1.48 N N
3 P O5' P O sing 1.61 N N
4 P O3P P O sing 1.61 N N
5 O2P HOP2 O H sing 0.97 N N
6 O5' C5' O C sing 1.43 N N
7 C5' C4' C C sing 1.53 N N
8 C5' H5'1 C H sing 1.09 N N
9 C5' H5'2 C H sing 1.09 N N
10 C4' O4' C O sing 1.44 N N
11 C4' C3' C C sing 1.55 N N
12 C4' H4' C H sing 1.09 N N
13 O4' C1' O C sing 1.44 N N
14 C1' N1 C N sing 1.47 N N
15 C1' C2' C C sing 1.54 N N
16 C1' H1' C H sing 1.09 N N
17 N1 C2 N C sing 1.35 N N
18 N1 C6 N C sing 1.36 N N
19 C2 O2 C O doub 1.22 N N
20 C2 N3 C N sing 1.33 N N
21 N3 C4 N C doub 1.33 N N
22 C4 N4 C N sing 1.38 N N
23 C4 C5 C C sing 1.41 N N
24 N4 HN41 N H sing 0.97 N N
25 N4 HN42 N H sing 0.97 N N
26 C5 C6 C C doub 1.35 N N
27 C5 H5 C H sing 1.08 N N
28 C6 H6 C H sing 1.08 N N
29 C2' SE2' C SE sing 1.96 N N
30 C2' C3' C C sing 1.55 N N
31 C2' H2' C H sing 1.09 N N
32 SE2' CA' SE C sing 1.96 N N
33 CA' HA'1 C H sing 1.09 N N
34 CA' HA'2 C H sing 1.09 N N
35 CA' HA'3 C H sing 1.09 N N
36 C3' O3' C O sing 1.43 N N
37 C3' H3' C H sing 1.09 N N
38 O3' H3T O H sing 0.97 N N
39 O3P HOP3 O H sing 0.97 N N



CSL : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
CSL 1yls Open in New Window Polymer component 6 3
CSL 4ys5 Open in New Window Polymer component 1 1
CSL 6d4l Open in New Window Polymer component 1 1
CSL 6d54 Open in New Window Polymer component 1 1
CSL 6qiq Open in New Window Polymer component 2 1