Chemical Components in the PDB

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T5S : Summary

Code

T5S

One-letter code

T

Molecule name

2'-deoxy-5-(methylselanyl)uridine 5'-phosphate

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-5-(methylselanyl)uridine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(5-methylselanyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H15 N2 O8 P Se

Formal charge

0

Molecular weight

401.168 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C([Se]C)=C1)CC2O
SMILES CACTVS 3.341 C[Se]C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.5.0 C[Se]C1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 C[Se]C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[Se]C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H15N2O8PSe/c1-22-7-3-12(10(15)11-9(7)14)8-2-5(13)6(20-8)4-19-21(16,17)18/h3,5-6,8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,8+/m0/s1

IUPAC InChI key

KJNLUXBKSKRISX-SHYZEUOFSA-N
T5S

wwPDB Information

Atom count

37 (22 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DT

Defined at

2007-12-27

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



T5S : Atoms of Molecule

Total Number of Atoms: 37
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 -5.438 2.545 -1.291
2 P P P N N N 0 -5.374 1.298 -0.274
3 OP1 O OP1 N N N 0 -5.276 1.799 1.115
4 OP2 O OP2 N N N 0 -6.707 0.409 -0.431
5 O5' O O5' N N N 0 -4.085 0.395 -0.612
6 N1 N N1 N N N 0 1.025 -0.597 0.16
7 C6 C C6 N N N 0 2.181 -0.499 -0.566
8 C2 C C2 N N N 0 0.944 -0.067 1.394
9 O2 O O2 N N N 0 -0.093 -0.166 2.022
10 N3 N N3 N N N 0 1.994 0.57 1.944
11 C4 C C4 N N N 0 3.151 0.688 1.261
12 O4 O O4 N N N 0 4.102 1.265 1.757
13 C5 C C5 N N N 0 3.25 0.134 -0.039
14 SE SE SE N N N 0 4.917 0.287 -1.059
15 CH3 C CH3 N N N 0 6.041 1.276 0.207
16 C2' C C2' N N N 0 -0.471 -2.55 0.398
17 C5' C C5' N N N 0 -3.692 -0.728 0.179
18 C4' C C4' R N N 0 -2.432 -1.357 -0.417
19 O4' O O4' N N N 0 -1.314 -0.45 -0.302
20 C1' C C1' R N N 0 -0.137 -1.28 -0.415
21 C3' C C3' S N N 0 -2.015 -2.602 0.396
22 O3' O O3' N N N 0 -2.475 -3.795 -0.243
23 HOP3 H HOP3 N N N 0 -6.191 3.133 -1.146
24 HOP2 H HOP2 N N N 0 -6.837 0.047 -1.318
25 H6 H H6 N N N 0 2.238 -0.928 -1.556
26 HN3 H HN3 N N N 0 1.919 0.946 2.834
27 HH3 H HH3 N N N 0 7.025 1.44 -0.232
28 HH3A H HH3A N N N 0 5.577 2.237 0.43
29 HH3B H HH3B N N N 0 6.144 0.701 1.127
30 H2' H H2' N N N 0 -0.058 -3.434 -0.088
31 H2'A H H2'A N N N 0 -0.091 -2.463 1.416
32 H5' H H5' N N N 0 -3.487 -0.401 1.199
33 H5'A H H5'A N N N 0 -4.496 -1.464 0.189
34 H4' H H4' N N N 0 -2.599 -1.622 -1.461
35 H1' H H1' N N N 0 0.049 -1.534 -1.458
36 H3' H H3' N N N 0 -2.4 -2.54 1.414
37 HO3' H HO3' N N Y 0 -2.19 -4.61 0.194



T5S : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP3 P O sing 1.61 N N
2 OP3 HOP3 O H sing 0.97 N N
3 OP1 P O P doub 1.48 N N
4 P OP2 P O sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 OP2 HOP2 O H sing 0.97 N N
7 C5' O5' C O sing 1.43 N N
8 C1' N1 C N sing 1.47 N N
9 C6 N1 C N sing 1.37 N N
10 N1 C2 N C sing 1.35 N N
11 C6 C5 C C doub 1.35 N N
12 C6 H6 C H sing 1.08 N N
13 C2 O2 C O doub 1.22 N N
14 C2 N3 C N sing 1.35 N N
15 C4 N3 C N sing 1.35 N N
16 N3 HN3 N H sing 0.97 N N
17 C5 C4 C C sing 1.42 N N
18 C4 O4 C O doub 1.22 N N
19 SE C5 SE C sing 1.96 N N
20 CH3 SE C SE sing 1.96 N N
21 CH3 HH3 C H sing 1.09 N N
22 CH3 HH3A C H sing 1.09 N N
23 CH3 HH3B C H sing 1.09 N N
24 C3' C2' C C sing 1.54 N N
25 C2' C1' C C sing 1.54 N N
26 C2' H2' C H sing 1.09 N N
27 C2' H2'A C H sing 1.09 N N
28 C5' C4' C C sing 1.53 N N
29 C5' H5' C H sing 1.09 N N
30 C5' H5'A C H sing 1.09 N N
31 C3' C4' C C sing 1.54 N N
32 C4' O4' C O sing 1.44 N N
33 C4' H4' C H sing 1.09 N N
34 O4' C1' O C sing 1.44 N N
35 C1' H1' C H sing 1.09 N N
36 O3' C3' O C sing 1.43 N N
37 C3' H3' C H sing 1.09 N N
38 O3' HO3' O H sing 0.97 N N



T5S : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
T5S 3bm0 Open in New Window Polymer component 1 1
T5S 3ltu Open in New Window Polymer component 1 1
T5S 4rhd Open in New Window Polymer component 8 2
T5S 5usa Open in New Window Polymer component 1 1
T5S 5use Open in New Window Polymer component 1 1
T5S 5usg Open in New Window Polymer component 2 2